This structure has broken O3'[i] to P[i+1] linkages **************************************************************************** 3DNA v2.4.5-2021may19, created and maintained by xiangjun@x3dna.org **************************************************************************** 1. The list of the parameters given below correspond to the 5' to 3' direction of strand I and 3' to 5' direction of strand II. 2. All angular parameters, except for the phase angle of sugar pseudo- rotation, are measured in degrees in the range of [-180, +180], and all displacements are measured in Angstrom units. **************************************************************************** File name: 1f7u.pdb Date and time: Sun Dec 21 22:01:03 2025 Number of base-pairs: 27 Number of atoms: 7126 **************************************************************************** HEADER LIGASE/RNA 28-JUN-00 1F7U TITLE CRYSTAL STRUCTURE OF THE ARGINYL-TRNA SYNTHETASE COMPLEXED WITH THE TITLE 2 TRNA(ARG) AND L-ARG COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRNA(ARG); COMPND 3 CHAIN: B; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: ARGINYL-TRNA SYNTHETASE; COMPND 7 CHAIN: A; COMPND 8 SYNONYM: CYTOPLASMIC ARGININE-TRNA LIGASE, ARGRS; COMPND 9 EC: 6.1.1.19; COMPND 10 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: THIS SEQUENCE OCCURS NATURALLY IN YEAST SACCHAROMYCES SOURCE 4 CEREVISAE; SOURCE 5 MOL_ID: 2; SOURCE 6 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 7 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 8 ORGANISM_TAXID: 4932; SOURCE 9 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 10 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 11 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 12 EXPRESSION_SYSTEM_PLASMID: PTRC99 KEYWDS RNA-PROTEIN COMPLEX, AMINOACYLATION, ARGINYL-TRNA SYNTHETASE, LIGASE, KEYWDS 2 LIGASE-RNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR B.DELAGOUTTE,D.MORAS,J.CAVARELLI REVDAT 3 13-JUL-11 1F7U 1 VERSN REVDAT 2 24-FEB-09 1F7U 1 VERSN REVDAT 1 27-JUN-01 1F7U 0 JRNL AUTH B.DELAGOUTTE,D.MORAS,J.CAVARELLI JRNL TITL TRNA AMINOACYLATION BY ARGINYL-TRNA SYNTHETASE: INDUCED JRNL TITL 2 CONFORMATIONS DURING SUBSTRATES BINDING JRNL REF EMBO J. V. 19 5599 2000 JRNL REFN ISSN 0261-4189 JRNL PMID 11060012 JRNL DOI 10.1093/EMBOJ/19.21.5599 HELIX 1 1 ALA A 2 LEU A 14 1 13 HELIX 2 2 GLU A 18 LYS A 23 1 6 HELIX 3 3 ASN A 30 GLY A 48 1 19 HELIX 4 4 ASP A 50 PHE A 55 1 6 HELIX 5 5 PRO A 56 LEU A 58 5 3 HELIX 6 6 THR A 63 GLY A 67 5 5 HELIX 7 7 PRO A 74 ARG A 77 5 4 HELIX 8 8 ASN A 82 LYS A 93 1 12 HELIX 9 9 ASN A 115 LYS A 131 1 17 HELIX 10 10 GLU A 132 TYR A 134 5 3 HELIX 11 11 HIS A 162 LEU A 179 1 18 HELIX 12 12 GLY A 193 GLY A 207 1 15 HELIX 13 13 ASN A 208 ASP A 215 1 8 HELIX 14 14 ASP A 215 GLU A 234 1 20 HELIX 15 15 ASN A 245 GLY A 258 1 14 HELIX 16 16 ASP A 259 LEU A 284 1 26 HELIX 17 17 SER A 295 VAL A 297 5 3 HELIX 18 18 SER A 298 LYS A 312 1 15 HELIX 19 19 THR A 327 PHE A 329 5 3 HELIX 20 20 LEU A 346 HIS A 363 1 18 HELIX 21 21 ALA A 372 GLN A 374 5 3 HELIX 22 22 GLN A 375 MET A 389 1 15 HELIX 23 23 PHE A 391 LYS A 395 5 5 HELIX 24 24 PHE A 417 LYS A 435 1 19 HELIX 25 25 ASN A 436 ALA A 441 1 6 HELIX 26 26 HIS A 445 GLN A 464 1 20 HELIX 27 27 LYS A 474 SER A 480 1 7 HELIX 28 28 THR A 485 ALA A 503 1 19 HELIX 29 29 THR A 507 ILE A 512 1 6 HELIX 30 30 ASN A 513 ALA A 514 5 2 HELIX 31 31 ASP A 515 LEU A 519 5 5 HELIX 32 32 GLU A 521 GLY A 532 1 12 HELIX 33 33 GLN A 533 HIS A 545 1 13 HELIX 34 34 GLU A 546 LEU A 568 1 23 HELIX 35 35 THR A 574 GLY A 600 1 27 SHEET 1 A 4 GLU A 59 TRP A 60 0 SHEET 2 A 4 LEU A 69 PRO A 72 -1 O LEU A 70 N GLU A 59 SHEET 3 A 4 PHE A 109 PHE A 114 -1 O ILE A 110 N ILE A 71 SHEET 4 A 4 LEU A 100 ASN A 106 -1 N GLU A 101 O PHE A 113 SHEET 1 B 5 VAL A 290 GLY A 293 0 SHEET 2 B 5 GLU A 182 LEU A 189 1 O ARG A 185 N VAL A 290 SHEET 3 B 5 LYS A 144 GLU A 148 1 N VAL A 145 O GLU A 182 SHEET 4 B 5 LYS A 366 VAL A 370 1 O LYS A 366 N ILE A 146 SHEET 5 B 5 LEU A 397 VAL A 400 1 O GLN A 398 N TYR A 369 SHEET 1 C 3 THR A 315 ASP A 318 0 SHEET 2 C 3 ALA A 321 ASP A 325 -1 O ALA A 321 N ASP A 318 SHEET 3 C 3 LYS A 335 GLN A 339 -1 O ALA A 336 N ILE A 324 SHEET 1 D 2 VAL A 405 GLN A 406 0 SHEET 2 D 2 TYR A 471 GLU A 472 1 O TYR A 471 N GLN A 406 **************************************************************************** RMSD of the bases (----- for WC bp, + for isolated bp, x for helix change) Strand I Strand II Helix 1 (0.044) ....>B:.901_:[PSU]P-**--A[..A]:.972_:B<.... (0.003) | 2 (0.003) ....>B:.902_:[..U]U-----A[..A]:.971_:B<.... (0.003) | 3 (0.002) ....>B:.903_:[..C]C-----G[..G]:.970_:B<.... (0.003) | 4 (0.002) ....>B:.904_:[..C]C-----G[..G]:.969_:B<.... (0.004) | 5 (0.002) ....>B:.905_:[..U]U-*---G[..G]:.968_:B<.... (0.007) | 6 (0.006) ....>B:.906_:[..C]C-----G[..G]:.967_:B<.... (0.007) | 7 (0.004) ....>B:.907_:[..G]G-----C[..C]:.966_:B<.... (0.002) | 8 (0.016) ....>B:.949_:[5MC]c-----G[..G]:.965_:B<.... (0.004) | 9 (0.004) ....>B:.950_:[..C]C-----G[..G]:.964_:B<.... (0.008) | 10 (0.002) ....>B:.951_:[..A]A-----U[..U]:.963_:B<.... (0.004) | 11 (0.010) ....>B:.952_:[..G]G-----C[..C]:.962_:B<.... (0.006) | 12 (0.005) ....>B:.953_:[..G]G-----C[..C]:.961_:B<.... (0.004) | 13 (0.003) ....>B:.954_:[5MU]t-**--a[1MA]:.958_:B<.... (0.005) | 14 (0.044) ....>B:.955_:[PSU]P-**+-G[..G]:.917_:B<.... (0.006) x 15 (0.005) ....>B:.939_:[..C]C-----G[..G]:.931_:B<.... (0.005) | 16 (0.005) ....>B:.940_:[..C]C-----G[..G]:.930_:B<.... (0.005) | 17 (0.002) ....>B:.941_:[..A]A-----U[..U]:.929_:B<.... (0.002) | 18 (0.006) ....>B:.942_:[..G]G-----C[..C]:.928_:B<.... (0.003) | 19 (0.003) ....>B:.943_:[..A]A-**--P[PSU]:.927_:B<.... (0.045) | 20 (0.004) ....>B:.944_:[..A]A-**--g[M2G]:.926_:B<.... (0.005) | 21 (0.007) ....>B:.910_:[2MG]g-----C[..C]:.925_:B<.... (0.003) | 22 (0.005) ....>B:.911_:[..C]C-----G[..G]:.924_:B<.... (0.008) | 23 (0.004) ....>B:.912_:[..C]C-----G[..G]:.923_:B<.... (0.012) | 24 (0.005) ....>B:.913_:[..C]C-**--C[..C]:.922_:B<.... (0.002) | 25 (0.009) ....>B:.914_:[..A]A-**--U[..U]:.908_:B<.... (0.004) | 26 (0.012) ....>B:.915_:[..A]A-**+-U[..U]:.948_:B<.... (0.004) x 27 (0.015) ....>B:.918_:[..G]G-----C[..C]:.956_:B<.... (0.001) + Note: This structure contains 9[8] non-Watson-Crick base-pairs. **************************************************************************** Detailed H-bond information: atom-name pair and length [ O N] 1 P-**--A [2] N3 * N1 2.78 O2 * N6 2.83 2 U-----A [2] N3 - N1 2.82 O4 - N6 2.98 3 C-----G [3] O2 - N2 2.82 N3 - N1 2.93 N4 - O6 2.96 4 C-----G [3] O2 - N2 2.73 N3 - N1 2.90 N4 - O6 2.97 5 U-*---G [2] O2 - N1 2.72 N3 - O6 2.76 6 C-----G [3] O2 - N2 2.71 N3 - N1 2.87 N4 - O6 3.03 7 G-----C [3] O6 - N4 2.91 N1 - N3 2.92 N2 - O2 2.84 8 c-----G [3] O2 - N2 2.66 N3 - N1 2.75 N4 - O6 2.76 9 C-----G [3] O2 - N2 2.63 N3 - N1 2.85 N4 - O6 2.94 10 A-----U [2] N6 - O4 2.92 N1 - N3 2.95 11 G-----C [3] O6 - N4 2.89 N1 - N3 2.95 N2 - O2 2.91 12 G-----C [3] O6 - N4 2.98 N1 - N3 2.94 N2 - O2 2.81 13 t-**--a [2] N3 - N7 2.81 O2 - N6 3.06 14 P-**+-G [2] O4 * N1 2.89 O2'* O6 3.47 15 C-----G [3] O2 - N2 2.78 N3 - N1 2.93 N4 - O6 2.98 16 C-----G [3] O2 - N2 2.77 N3 - N1 2.88 N4 - O6 2.86 17 A-----U [2] N6 - O4 3.18 N1 - N3 2.89 18 G-----C [3] O6 - N4 2.95 N1 - N3 2.76 N2 - O2 2.61 19 A-**--P [2] N6 * O2 3.34 N1 * N3 2.91 20 A-**--g [1] N1 * O6 3.43 21 g-----C [3] O6 - N4 3.05 N1 - N3 2.91 N2 - O2 2.62 22 C-----G [3] O2 - N2 2.72 N3 - N1 2.93 N4 - O6 3.04 23 C-----G [3] O2 - N2 2.65 N3 - N1 2.84 N4 - O6 2.91 24 C-**--C [1] O2 - N4 2.85 25 A-**--U [3] OP2* O4 2.93 N7 - N3 2.93 N6 - O2 2.81 26 A-**+-U [2] N6 - O2 2.94 N1 - N3 2.99 27 G-----C [3] O6 - N4 2.97 N1 - N3 2.95 N2 - O2 2.88 **************************************************************************** Overlap area in Angstrom^2 between polygons defined by atoms on successive bases. Polygons projected in the mean plane of the designed base-pair step. Values in parentheses measure the overlap of base ring atoms only. Those outside parentheses include exocyclic atoms on the ring. Intra- and inter-strand overlap is designated according to the following diagram: i2 3' 5' j2 /|\ | | | Strand I | | II | | | | | \|/ i1 5' 3' j1 step i1-i2 i1-j2 j1-i2 j1-j2 sum 1 PU/AA 0.43( 0.00) 0.00( 0.00) 0.00( 0.00) 4.06( 3.11) 4.49( 3.11) 2 UC/GA 0.72( 0.00) 0.00( 0.00) 0.00( 0.00) 4.26( 2.98) 4.98( 2.98) 3 CC/GG 0.00( 0.00) 0.00( 0.00) 0.36( 0.00) 3.59( 2.20) 3.95( 2.20) 4 CU/GG 1.14( 0.29) 0.00( 0.00) 0.18( 0.00) 4.78( 3.02) 6.10( 3.31) 5 UC/GG 0.38( 0.00) 0.00( 0.00) 0.18( 0.00) 1.61( 0.35) 2.17( 0.35) 6 CG/CG 0.30( 0.00) 0.00( 0.00) 3.32( 0.73) 0.35( 0.00) 3.97( 0.73) 7 Gc/GC 6.21( 1.29) 0.00( 0.00) 0.00( 0.00) 7.14( 4.30) 13.35( 5.58) 8 cC/GG 0.00( 0.00) 0.00( 0.00) 0.96( 0.00) 3.02( 1.49) 3.97( 1.49) 9 CA/UG 0.03( 0.00) 0.00( 0.00) 2.75( 0.91) 0.47( 0.03) 3.25( 0.93) 10 AG/CU 5.04( 3.71) 0.00( 0.00) 0.00( 0.00) 0.21( 0.00) 5.25( 3.71) 11 GG/CC 3.63( 1.99) 0.00( 0.00) 0.85( 0.00) 0.00( 0.00) 4.48( 1.99) 12 Gt/aC 8.02( 2.73) 0.00( 0.00) 0.00( 0.00) 5.32( 1.87) 13.34( 4.60) 13 tP/Ga 6.43( 2.46) 0.00( 0.00) 0.00( 0.00) 7.33( 2.23) 13.77( 4.69) 14 PC/GG 0.00( 0.00) 0.00( 0.00) 0.00( 0.00) 0.00( 0.00) 0.00( 0.00) 15 CC/GG 0.00( 0.00) 0.00( 0.00) 0.71( 0.00) 3.53( 2.01) 4.24( 2.01) 16 CA/UG 0.00( 0.00) 0.00( 0.00) 4.37( 2.15) 0.00( 0.00) 4.37( 2.15) 17 AG/CU 2.67( 2.41) 0.00( 0.00) 0.62( 0.00) 0.00( 0.00) 3.29( 2.41) 18 GA/PC 3.43( 2.04) 0.00( 0.00) 0.00( 0.00) 0.00( 0.00) 3.43( 2.04) 19 AA/gP 6.10( 4.47) 0.00( 0.00) 0.00( 0.00) 4.42( 1.76) 10.53( 6.22) 20 Ag/Cg 0.00( 0.00) 0.00( 0.00) 1.54( 0.04) 0.32( 0.08) 1.87( 0.13) 21 gC/GC 2.65( 0.59) 0.00( 0.00) 0.00( 0.00) 5.05( 2.34) 7.71( 2.93) 22 CC/GG 0.00( 0.00) 0.00( 0.00) 0.69( 0.00) 3.66( 2.17) 4.34( 2.17) 23 CC/CG 2.99( 1.28) 0.00( 0.00) 0.00( 0.00) 2.34( 1.19) 5.32( 2.46) 24 CA/UC 0.00( 0.00) 2.63( 0.15) 4.30( 2.92) 0.00( 0.00) 6.93( 3.07) 25 AA/UU 6.29( 4.00) 0.00( 0.00) 0.00( 0.00) 0.00( 0.00) 6.29( 4.00) 26 AG/CU 0.00( 0.00) 0.00( 0.00) 0.00( 0.00) 0.00( 0.00) 0.00( 0.00) **************************************************************************** Origin (Ox, Oy, Oz) and mean normal vector (Nx, Ny, Nz) of each base-pair in the coordinate system of the given structure bp Ox Oy Oz Nx Ny Nz 1 P-A 6.194 37.038 15.985 0.550 -0.518 0.655 2 U-A 8.687 35.011 17.554 0.542 -0.431 0.721 3 C-G 11.435 33.923 19.151 0.539 -0.374 0.755 4 C-G 14.537 33.729 21.596 0.409 -0.377 0.831 5 U-G 16.536 33.900 24.671 0.361 -0.364 0.858 6 C-G 16.629 34.381 27.961 0.162 -0.352 0.922 7 G-C 16.029 33.680 31.396 -0.086 -0.559 0.824 8 c-G 14.498 32.625 34.271 -0.116 -0.640 0.759 9 C-G 12.349 29.792 36.124 -0.043 -0.715 0.697 10 A-U 11.020 26.736 37.473 0.079 -0.811 0.580 11 G-C 12.271 23.344 37.920 0.199 -0.814 0.545 12 G-C 14.953 19.883 38.225 0.325 -0.783 0.530 13 t-a 18.090 16.390 37.062 0.362 -0.791 0.494 14 P+G 18.742 15.045 41.200 0.398 -0.672 0.625 15 C-G 56.732 36.969 34.544 -0.780 -0.406 0.477 16 C-G 54.977 36.619 37.956 -0.782 -0.413 0.467 17 A-U 52.336 36.657 40.805 -0.862 -0.377 0.340 18 G-C 48.509 37.466 41.678 -0.943 -0.299 0.149 19 A-P 44.573 37.967 40.999 -0.938 -0.346 -0.034 20 A-g 41.245 37.056 39.815 -0.886 -0.441 -0.145 21 g-C 38.059 39.413 36.426 -0.704 -0.596 -0.387 22 C-G 37.290 36.421 33.733 -0.693 -0.636 -0.340 23 C-G 36.351 32.729 32.732 -0.739 -0.638 -0.217 24 C-C 34.429 29.842 32.961 -0.760 -0.632 -0.149 25 A-U 32.531 26.612 33.974 -0.719 -0.655 -0.232 26 A+U 29.364 24.796 36.070 -0.849 -0.505 -0.154 27 G-C 23.700 8.252 40.835 0.494 -0.817 0.296 **************************************************************************** Local base-pair parameters bp Shear Stretch Stagger Buckle Propeller Opening 1 P-A -0.78 -0.18 -0.22 9.95 -16.21 -6.85 2 U-A -0.09 -0.10 -0.03 5.99 -12.85 1.46 3 C-G 0.36 -0.11 -0.36 12.63 -13.23 1.18 4 C-G 0.16 -0.11 0.13 3.62 -6.88 1.31 5 U-G 2.32 -0.63 0.01 3.42 -10.44 -1.76 6 C-G 0.16 -0.11 -0.06 7.15 -17.49 3.36 7 G-C -0.22 -0.12 -0.09 -3.27 -11.65 -0.06 8 c-G 0.21 -0.28 -0.08 4.71 -12.53 0.33 9 C-G 0.11 -0.14 0.18 -4.03 -7.70 2.28 10 A-U -0.02 -0.03 -0.10 -0.47 -4.35 -2.44 11 G-C -0.03 -0.07 -0.05 5.27 -7.23 -1.36 12 G-C -0.20 -0.07 -0.13 -13.34 -11.91 0.80 13 t-a 4.17 -1.87 0.20 -8.14 9.05 -101.72 14 P+G 0.59 -5.66 0.45 11.48 19.52 -99.85 15 C-G 0.21 -0.08 -0.11 -4.34 7.94 0.86 16 C-G 0.30 -0.17 0.08 6.17 -7.24 -0.69 17 A-U -0.25 -0.05 0.18 1.64 -10.26 5.06 18 G-C 0.01 -0.19 -0.13 -7.23 -18.56 4.56 19 A-P 0.30 0.04 0.04 -19.23 -24.91 -0.24 20 A-g 4.42 0.93 0.76 -31.01 -16.85 5.50 21 g-C -0.19 -0.07 0.07 6.99 -4.63 3.44 22 C-G 0.17 -0.07 -0.29 0.71 -5.94 3.11 23 C-G 0.24 -0.18 -0.20 1.07 4.10 1.40 24 C-C 4.36 -1.86 -0.33 7.89 -4.78 5.52 25 A-U -4.22 -2.07 0.80 9.38 11.39 -94.34 26 A+U -0.06 1.22 0.07 -5.36 11.79 163.42 27 G-C -0.19 -0.03 0.04 -22.14 -17.22 -1.21 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ave. 0.44 -0.45 0.03 -0.76 -6.63 -3.96 s.d. 1.70 1.26 0.28 10.69 10.81 46.29 **************************************************************************** Local base-pair step parameters step Shift Slide Rise Tilt Roll Twist 1 PU/AA -0.19 -1.07 3.41 -4.11 4.76 40.42 2 UC/GA -0.29 -1.25 3.10 0.06 3.82 33.57 3 CC/GG -0.33 -1.83 3.49 -5.63 6.56 30.70 4 CU/GG -0.37 -1.56 3.31 0.42 3.18 39.19 5 UC/GG 0.16 -1.80 2.80 5.33 10.81 25.45 6 CG/CG -0.17 -1.20 3.34 0.72 19.41 31.68 7 Gc/GC -0.67 -1.36 3.07 0.64 6.14 37.86 8 cC/GG -0.11 -2.05 3.45 -1.26 6.86 33.67 9 CA/UG -0.68 -1.52 3.19 3.62 10.54 28.89 10 AG/CU 0.94 -1.49 3.19 1.18 7.08 26.51 11 GG/CC 0.92 -2.28 3.64 2.89 6.88 32.99 12 Gt/aC -2.71 -2.36 3.23 2.41 -1.81 89.43 13 tP/Ga 1.84 -1.81 3.56 9.96 2.82 39.20 14 PC/GG ---- ---- ---- ---- ---- ---- 15 CC/GG -0.21 -2.25 3.12 -0.71 -0.04 27.48 16 CA/UG -0.42 -1.98 3.32 -2.55 8.43 28.66 17 AG/CU 0.41 -2.06 3.41 3.24 12.32 28.82 18 GA/PC 0.21 -1.95 3.51 1.23 10.73 36.15 19 AA/gP -0.01 -1.00 3.51 2.76 8.45 46.06 20 Ag/Cg -4.47 -1.46 2.25 18.12 7.49 46.21 21 gC/GC -0.68 -2.24 3.36 0.69 3.58 37.60 22 CC/GG -0.39 -2.10 3.31 -0.60 7.52 29.94 23 CC/CG -0.03 -1.27 3.23 1.93 3.62 38.68 24 CA/UC -1.23 -1.64 3.29 -4.95 -2.40 59.08 25 AA/UU 0.96 -2.62 3.15 2.25 12.03 -82.69 26 AG/CU ---- ---- ---- ---- ---- ---- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ave. -0.31 -1.76 3.26 1.57 6.62 32.73 s.d. 1.23 0.44 0.29 4.83 4.83 27.98 **************************************************************************** Local base-pair helical parameters step X-disp Y-disp h-Rise Incl. Tip h-Twist 1 PU/AA -2.06 -0.19 3.27 6.84 5.90 40.88 2 UC/GA -2.73 0.50 2.95 6.58 -0.10 33.78 3 CC/GG -4.55 -0.45 3.06 12.10 10.38 31.87 4 CU/GG -2.69 0.59 3.17 4.73 -0.62 39.32 5 UC/GG -5.61 0.62 1.89 22.97 -11.32 28.12 6 CG/CG -4.31 0.35 2.26 32.07 -1.18 37.03 7 Gc/GC -2.77 1.09 2.81 9.39 -0.98 38.34 8 cC/GG -4.53 -0.01 2.99 11.69 2.15 34.36 9 CA/UG -4.66 1.89 2.40 20.19 -6.94 30.92 10 AG/CU -4.75 -1.72 2.74 15.10 -2.51 27.45 11 GG/CC -5.09 -1.08 3.18 11.93 -5.01 33.80 12 Gt/aC -1.64 1.98 3.21 -1.28 -1.71 89.47 13 tP/Ga -2.98 -1.39 3.76 4.12 -14.54 40.49 14 PC/GG ---- ---- ---- ---- ---- ---- 15 CC/GG -4.72 0.28 3.13 -0.08 1.50 27.49 16 CA/UG -5.47 0.31 2.66 16.54 5.00 29.95 17 AG/CU -5.94 -0.20 2.39 23.37 -6.15 31.46 18 GA/PC -4.40 -0.16 2.85 16.84 -1.93 37.68 19 AA/gP -1.99 0.26 3.28 10.69 -3.49 46.87 20 Ag/Cg -1.95 5.84 0.35 9.08 -21.96 49.98 21 gC/GC -3.93 1.14 3.13 5.53 -1.07 37.77 22 CC/GG -5.32 0.63 2.72 14.27 1.14 30.86 23 CC/CG -2.34 0.28 3.10 5.44 -2.90 38.89 24 CA/UC -1.53 0.99 3.44 -2.43 5.01 59.31 25 AA/UU 1.68 0.77 3.42 -9.06 1.69 -83.43 26 AG/CU ---- ---- ---- ---- ---- ---- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ave. -3.51 0.51 2.84 10.28 -2.07 33.86 s.d. 1.78 1.44 0.68 9.22 6.82 28.20 **************************************************************************** The 'simple' parameters are intuitive for non-Watson-Crick base pairs and associated base-pair steps (where the above corresponding 3DNA parameters often appear cryptic). Note that they are for structural *description* only, not to be fed into the 'rebuild' program. See URL http://x3dna.org/highlights/details-on-the-simple-base-pair-parameters and related blogposts on the 3DNA home page for details. This structure contains 9 non-Watson-Crick (with leading *) base pair(s) ---------------------------------------------------------------------------- Simple base-pair parameters based on RC8--YC6 vectors bp Shear Stretch Stagger Buckle Propeller Opening * 1 P-A -0.80 -0.11 -0.22 8.49 -17.02 -6.81 2 U-A -0.09 -0.10 -0.03 5.79 -12.95 1.45 3 C-G 0.36 -0.10 -0.36 12.96 -12.91 1.18 4 C-G 0.16 -0.10 0.13 3.70 -6.85 1.31 * 5 U-G 2.40 -0.07 0.01 5.78 -9.35 -1.75 6 C-G 0.16 -0.11 -0.06 7.29 -17.43 3.33 7 G-C -0.22 -0.11 -0.09 -3.46 -11.60 -0.06 8 c-G 0.21 -0.27 -0.08 4.89 -12.46 0.33 9 C-G 0.11 -0.14 0.18 -3.97 -7.73 2.27 10 A-U -0.02 -0.03 -0.10 -0.46 -4.35 -2.44 11 G-C -0.03 -0.07 -0.05 5.28 -7.23 -1.36 12 G-C -0.20 -0.06 -0.13 -13.45 -11.79 0.80 * 13 t-a 4.30 1.55 0.20 -12.14 0.87 -101.69 * 14 P+G 4.32 3.71 0.45 -22.58 -1.69 -99.31 15 C-G 0.21 -0.08 -0.11 -4.46 7.87 0.86 16 C-G 0.31 -0.17 0.08 6.34 -7.09 -0.69 17 A-U -0.25 -0.04 0.18 1.43 -10.30 5.04 18 G-C 0.01 -0.19 -0.13 -7.07 -18.62 4.51 * 19 A-P 0.30 0.06 0.04 -18.01 -25.81 -0.24 * 20 A-g 3.66 2.64 0.76 -21.64 -27.88 5.64 21 g-C -0.19 -0.07 0.07 6.92 -4.73 3.45 22 C-G 0.17 -0.07 -0.29 0.78 -5.93 3.11 23 C-G 0.24 -0.17 -0.20 0.99 4.12 1.40 * 24 C-C 4.72 0.39 -0.33 9.21 -0.56 5.52 * 25 A-U -4.51 1.32 0.80 14.61 2.08 -94.25 * 26 A+U 1.21 0.21 0.07 11.03 6.79 163.35 27 G-C -0.19 -0.03 0.04 -22.11 -17.25 -1.22 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ave. 0.61 0.29 0.03 -0.88 -8.51 -3.94 s.d. 1.88 0.94 0.28 10.98 8.99 46.23 ---------------------------------------------------------------------------- Simple base-pair step parameters based on consecutive C1'-C1' vectors step Shift Slide Rise Tilt Roll Twist * 1 PU/AA -0.23 -1.06 3.41 -3.90 4.93 36.72 2 UC/GA -0.27 -1.26 3.10 0.03 3.82 31.24 3 CC/GG -0.29 -1.83 3.49 -5.78 6.43 31.45 * 4 CU/GG -0.18 -1.59 3.31 0.04 3.20 27.33 * 5 UC/GG 0.37 -1.76 2.80 4.02 11.36 37.54 6 CG/CG -0.17 -1.20 3.34 0.77 19.41 33.42 7 Gc/GC -0.67 -1.36 3.07 0.65 6.14 35.88 8 cC/GG -0.08 -2.05 3.45 -1.36 6.84 33.80 9 CA/UG -0.67 -1.53 3.19 3.55 10.56 29.72 10 AG/CU 0.94 -1.49 3.19 1.20 7.08 26.82 11 GG/CC 0.89 -2.29 3.64 2.96 6.85 33.51 * 12 Gt/aC -2.14 -2.89 3.23 2.74 -1.25 62.86 * 13 tP/Ga 2.44 0.85 3.56 1.87 10.18 -36.96 * 14 PC/GG ---- ---- ---- ---- ---- ---- 15 CC/GG -0.16 -2.25 3.12 -0.71 -0.05 27.10 16 CA/UG -0.41 -1.98 3.32 -2.55 8.43 31.61 17 AG/CU 0.39 -2.06 3.41 3.37 12.29 27.23 * 18 GA/PC 0.26 -1.94 3.51 0.96 10.76 33.67 * 19 AA/gP 0.21 -0.98 3.51 0.83 8.85 25.91 * 20 Ag/Cg -4.12 -2.28 2.25 16.37 10.78 70.02 21 gC/GC -0.68 -2.24 3.36 0.69 3.58 35.61 22 CC/GG -0.35 -2.11 3.31 -0.74 7.51 29.80 * 23 CC/CG 0.27 -1.24 3.23 1.01 3.97 13.21 * 24 CA/UC -1.21 -1.65 3.29 -4.92 -2.45 111.09 * 25 AA/UU -2.05 -1.90 3.15 11.96 2.57 1.06 * 26 AG/CU ---- ---- ---- ---- ---- ---- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ave. -0.33 -1.67 3.26 1.38 6.74 32.90 s.d. 1.23 0.71 0.29 4.72 4.82 25.48 **************************************************************************** Structure classification: This structure contains more than one helical regions This is a right-handed nucleic acid structure **************************************************************************** lambda: virtual angle between C1'-YN1 or C1'-RN9 glycosidic bonds and the base-pair C1'-C1' line C1'-C1': distance between C1' atoms for each base-pair RN9-YN1: distance between RN9-YN1 atoms for each base-pair RC8-YC6: distance between RC8-YC6 atoms for each base-pair bp lambda(I) lambda(II) C1'-C1' RN9-YN1 RC8-YC6 1 P-A 45.8 55.5 10.8 9.0 9.7 2 U-A 54.7 56.1 10.5 8.9 9.8 3 C-G 55.8 53.7 10.6 8.9 9.9 4 C-G 55.0 55.2 10.6 8.9 9.9 5 U-G 66.5 41.3 10.4 8.8 9.6 6 C-G 55.6 55.4 10.6 8.9 9.9 7 G-C 53.3 54.9 10.7 9.0 9.9 8 c-G 54.9 53.2 10.5 8.8 9.8 9 C-G 55.8 56.2 10.5 8.9 9.9 10 A-U 53.4 54.3 10.8 9.0 9.9 11 G-C 54.1 53.4 10.8 9.0 9.9 12 G-C 55.3 54.7 10.6 9.0 9.9 13 t-a 29.4 21.2 9.7 7.1 6.1 14 P+G 99.5 27.7 9.2 8.4 9.9 15 C-G 54.7 54.8 10.7 9.0 9.9 16 C-G 55.0 52.4 10.7 8.9 9.9 17 A-U 56.0 59.0 10.4 8.8 9.9 18 G-C 58.3 55.7 10.4 8.8 9.8 19 A-P 57.5 52.7 10.6 8.9 9.8 20 A-g 80.7 36.1 12.0 10.6 11.4 21 g-C 54.1 56.5 10.6 8.9 9.9 22 C-G 55.9 55.4 10.6 9.0 10.0 23 C-G 55.9 53.0 10.6 8.9 9.9 24 C-C 84.0 30.2 9.7 8.3 9.3 25 A-U 17.5 34.2 9.7 7.2 6.3 26 A+U 28.4 45.7 11.2 9.0 9.9 27 G-C 56.7 53.2 10.6 8.9 9.8 **************************************************************************** Classification of each dinucleotide step in a right-handed nucleic acid structure: A-like; B-like; TA-like, or other cases. step Xp Yp Zp XpH YpH ZpH Form 1 PU/AA -1.69 8.54 2.08 -3.56 8.25 3.08 2 UC/GA -1.54 8.46 2.17 -4.15 8.17 3.08 A 3 CC/GG -1.47 8.24 2.59 -5.75 7.55 4.13 A 4 CU/GG -1.37 8.20 2.76 -3.90 7.96 3.40 A 5 UC/GG -1.50 8.10 2.56 -6.92 6.50 5.49 A 6 CG/CG -1.85 8.45 2.23 -5.94 6.13 6.23 A 7 Gc/GC -1.62 8.04 2.92 -4.25 7.50 4.12 A 8 cC/GG -1.66 8.00 2.85 -5.99 7.30 4.34 A 9 CA/UG -1.31 8.54 2.41 -5.75 7.24 5.10 A 10 AG/CU -1.36 8.86 2.14 -5.98 8.03 4.32 A 11 GG/CC -1.63 7.75 2.98 -6.49 7.00 4.47 A 12 Gt/aC -0.64 7.07 3.20 -1.78 7.12 3.16 13 tP/Ga 4.13 4.59 -0.14 0.78 4.56 0.96 14 PC/GG --- --- --- --- --- --- --- 15 CC/GG -1.22 8.10 2.93 -5.80 8.10 2.91 A 16 CA/UG -1.98 8.48 2.49 -7.21 7.47 4.70 A 17 AG/CU -2.18 8.54 2.41 -7.87 6.96 5.48 A 18 GA/PC -2.12 8.27 2.37 -6.27 7.29 4.56 19 AA/gP -1.90 8.64 2.39 -3.61 8.10 3.90 20 Ag/Cg -3.34 6.65 4.73 -5.08 5.93 5.08 21 gC/GC -1.77 7.67 3.03 -5.48 7.36 3.71 A 22 CC/GG -1.09 7.83 2.94 -6.21 6.90 4.72 A 23 CC/CG -1.48 8.54 2.26 -3.71 8.30 3.08 24 CA/UC -1.60 5.82 2.36 -2.86 5.89 1.88 25 AA/UU 2.67 0.97 1.92 3.94 1.20 1.94 26 AG/CU --- --- --- --- --- --- --- **************************************************************************** Minor and major groove widths: direct P-P distances and refined P-P distances which take into account the directions of the sugar-phosphate backbones (Subtract 5.8 Angstrom from the values to take account of the vdw radii of the phosphate groups, and for comparison with FreeHelix and Curves.) Ref: M. A. El Hassan and C. R. Calladine (1998). ``Two Distinct Modes of Protein-induced Bending in DNA.'' J. Mol. Biol., v282, pp331-343. Minor Groove Major Groove P-P Refined P-P Refined 1 PU/AA --- --- --- --- 2 UC/GA --- --- --- --- 3 CC/GG 16.4 --- 16.1 --- 4 CU/GG 16.6 15.3 15.8 12.3 5 UC/GG 17.7 15.8 14.9 9.6 6 CG/CG 18.1 16.1 14.5 9.0 7 Gc/GC 17.1 15.4 15.3 11.3 8 cC/GG 17.0 15.4 16.5 13.8 9 CA/UG 17.8 16.5 15.4 9.9 10 AG/CU 17.4 16.2 15.9 12.4 11 GG/CC 16.2 --- 15.3 --- 12 Gt/aC --- --- --- --- 13 tP/Ga --- --- --- --- 14 PC/GG --- --- --- --- 15 CC/GG --- --- --- --- 16 CA/UG --- --- --- --- 17 AG/CU 16.7 --- 16.9 --- 18 GA/PC 18.4 14.8 16.2 8.1 19 AA/gP 19.6 14.8 14.7 10.8 20 Ag/Cg 17.6 14.5 12.5 11.0 21 gC/GC 16.8 14.6 14.4 14.4 22 CC/GG 16.9 15.3 16.0 12.0 23 CC/CG 16.8 --- 8.2 --- 24 CA/UC --- --- --- --- 25 AA/UU --- --- --- --- 26 AG/CU --- --- --- --- **************************************************************************** Global linear helical axis defined by equivalent C1' and RN9/YN1 atom pairs Deviation from regular linear helix: 0.90(3.35) **************************************************************************** Main chain and chi torsion angles: Note: alpha: O3'(i-1)-P-O5'-C5' beta: P-O5'-C5'-C4' gamma: O5'-C5'-C4'-C3' delta: C5'-C4'-C3'-O3' epsilon: C4'-C3'-O3'-P(i+1) zeta: C3'-O3'-P(i+1)-O5'(i+1) chi for pyrimidines(Y): O4'-C1'-N1-C2 chi for purines(R): O4'-C1'-N9-C4 Strand I base alpha beta gamma delta epsilon zeta chi 1 P --- 179.9 63.4 89.2 -146.0 -79.6 -157.5 2 U -74.5 175.6 54.9 84.5 -155.9 -71.9 -156.8 3 C -70.4 173.6 55.4 83.6 -161.1 -71.3 -153.8 4 C -64.8 -179.6 50.5 83.0 -155.0 -67.1 -163.6 5 U -62.4 174.5 52.2 84.5 -148.7 -82.1 -160.2 6 C -65.5 166.0 57.0 83.8 -156.1 -74.4 -154.9 7 G -54.3 175.3 62.1 146.4 -89.6 -60.4 -133.1 8 c 64.2 152.3 40.1 81.9 -152.7 -69.6 -168.3 9 C -64.7 -174.6 49.0 82.3 -151.9 -76.1 -161.8 10 A -57.3 -177.1 42.1 82.6 -160.2 -77.6 -146.9 11 G 141.5 -159.5 177.7 83.3 -143.5 -71.7 -173.1 12 G -55.8 167.9 60.1 83.6 -151.3 -68.2 -178.0 13 t -72.1 -170.4 51.2 81.4 -138.3 -68.2 -155.9 14 P -59.0 172.3 47.6 85.6 -140.6 -71.1 -144.9 15 C -51.9 177.7 57.5 85.9 -153.7 -74.5 -173.9 16 C -58.3 169.5 59.2 82.9 -156.0 -73.7 -166.9 17 A -70.8 -175.4 50.9 82.4 -144.2 -66.8 -163.2 18 G -60.7 170.9 53.3 76.6 -161.0 -68.5 -164.7 19 A -57.1 179.5 53.3 81.6 -149.9 -71.4 -160.6 20 A -53.6 168.8 45.3 82.9 -146.5 -78.7 -152.0 21 g 176.5 152.6 53.2 89.6 -129.3 -84.7 171.4 22 C -66.4 176.3 47.5 81.7 -148.0 -77.4 -167.7 23 C -58.5 -179.8 46.3 81.1 -143.7 -70.0 -162.3 24 C -62.0 160.9 63.0 82.2 -170.8 -81.2 -167.7 25 A -61.3 -171.2 55.7 83.2 -147.0 -72.5 -168.0 26 A -54.2 173.2 58.2 147.9 -95.7 -63.1 -128.5 27 G -71.4 -156.1 40.2 143.7 -81.7 148.2 -74.2 Strand II base alpha beta gamma delta epsilon zeta chi 1 A -64.7 170.4 55.4 82.4 -152.1 -173.6 -157.2 2 A -59.2 170.9 57.1 83.4 -154.6 -69.4 -160.2 3 G -57.2 173.0 53.3 80.0 -154.2 -73.4 -165.1 4 G -54.9 171.7 48.3 80.8 -154.3 -72.0 -166.4 5 G -62.4 -179.1 47.9 79.5 -147.9 -71.9 -169.1 6 G -66.9 170.7 50.1 79.3 -154.8 -74.8 -166.4 7 C -56.1 168.8 48.5 79.7 -146.0 -76.7 -156.8 8 G -60.0 179.9 51.1 80.5 -146.5 -72.8 -165.0 9 G -63.2 167.0 55.6 79.6 -159.2 -69.7 -166.0 10 U -60.1 177.6 44.0 80.1 -148.1 -72.3 -155.5 11 C -67.1 -171.1 50.6 82.8 -149.3 -77.1 -164.4 12 C -83.2 -179.0 39.0 82.2 -153.6 -73.0 -170.6 13 a -63.6 -132.4 59.9 151.9 -95.8 -178.9 -71.4 14 G -86.5 156.7 -84.1 142.9 -146.5 -101.8 -110.2 15 G -49.0 172.2 46.0 80.9 -142.0 -75.8 -159.8 16 G 146.9 -173.7 179.9 82.8 -137.9 -76.7 -173.9 17 U -57.9 -174.0 40.9 81.2 -164.5 -71.2 -154.3 18 C -64.2 -179.0 48.8 81.7 -154.7 -67.5 -156.9 19 P -65.1 178.7 49.0 85.6 -148.3 -78.1 -154.3 20 g -59.0 176.2 44.8 80.8 -143.2 -64.5 -162.6 21 C -58.6 -178.2 49.2 81.3 -144.6 -64.7 -168.9 22 G -57.1 168.2 53.4 81.9 -151.1 -67.9 -174.4 23 G 127.3 -163.5 -165.8 84.8 -142.2 -74.9 -174.2 24 C -52.4 175.6 42.6 80.4 -152.8 -73.5 -151.9 25 U -58.7 -175.3 57.8 82.5 -119.7 -133.6 -162.7 26 U -78.7 -178.4 168.9 144.9 -144.7 76.7 -140.3 27 C 165.6 167.5 50.2 86.4 -139.9 -65.2 -170.3 **************************************************************************** Sugar conformational parameters: Note: v0: C4'-O4'-C1'-C2' v1: O4'-C1'-C2'-C3' v2: C1'-C2'-C3'-C4' v3: C2'-C3'-C4'-O4' v4: C3'-C4'-O4'-C1' tm: the amplitude of pucker P: the phase angle of pseudorotation Strand I base v0 v1 v2 v3 v4 tm P Puckering 1 P 10.7 -29.4 35.8 -30.8 12.7 35.8 1.8 C3'-endo 2 U 1.6 -23.2 34.6 -34.7 20.9 36.1 16.2 C3'-endo 3 C 0.9 -23.8 36.2 -36.6 22.5 37.9 17.2 C3'-endo 4 C 2.7 -25.2 36.7 -36.1 21.1 37.9 14.6 C3'-endo 5 U 2.6 -24.5 35.8 -35.3 20.7 37.0 14.7 C3'-endo 6 C 0.8 -23.6 36.0 -36.5 22.6 37.7 17.4 C3'-endo 7 G -21.8 34.5 -33.5 22.0 -0.4 35.3 161.8 C2'-endo 8 c 2.9 -25.3 36.8 -36.1 21.0 38.0 14.3 C3'-endo 9 C 2.6 -25.4 37.4 -36.8 21.6 38.6 14.8 C3'-endo 10 A 1.4 -23.3 35.0 -35.2 21.3 36.5 16.5 C3'-endo 11 G 9.0 -30.3 39.0 -34.9 16.4 39.2 5.7 C3'-endo 12 G 1.4 -23.9 35.8 -36.1 21.9 37.4 16.5 C3'-endo 13 t 1.0 -24.5 37.2 -37.6 23.0 38.9 17.0 C3'-endo 14 P 15.0 -33.5 38.4 -30.8 10.0 38.5 356.3 C2'-exo 15 C 4.9 -26.9 37.4 -35.5 19.3 38.2 11.4 C3'-endo 16 C 0.1 -23.1 36.1 -36.9 23.2 38.0 18.4 C3'-endo 17 A 2.9 -25.6 37.2 -36.6 21.3 38.5 14.4 C3'-endo 18 G -5.7 -20.4 37.1 -41.2 29.6 41.3 26.2 C3'-endo 19 A -1.6 -21.2 34.6 -36.6 24.1 37.1 21.1 C3'-endo 20 A 4.1 -25.6 36.3 -34.8 19.4 37.2 12.4 C3'-endo 21 g 8.6 -28.6 36.5 -32.6 15.3 36.7 5.4 C3'-endo 22 C 3.6 -26.7 38.3 -37.1 21.2 39.4 13.4 C3'-endo 23 C 4.0 -27.0 38.3 -36.9 20.8 39.3 12.8 C3'-endo 24 C 0.3 -23.8 36.5 -37.3 23.5 38.4 18.1 C3'-endo 25 A 1.3 -24.4 36.8 -37.1 22.6 38.4 16.7 C3'-endo 26 A -19.9 33.1 -32.9 22.3 -1.6 34.3 164.0 C2'-endo 27 G -22.6 35.5 -34.4 22.4 -0.1 36.3 161.4 C2'-endo Strand II base v0 v1 v2 v3 v4 tm P Puckering 1 A 0.9 -23.2 35.4 -35.8 22.0 37.1 17.2 C3'-endo 2 A 0.5 -23.3 35.8 -36.6 22.8 37.7 17.9 C3'-endo 3 G 0.3 -24.2 37.4 -38.1 23.9 39.3 18.0 C3'-endo 4 G 0.9 -24.6 37.8 -38.1 23.4 39.5 17.2 C3'-endo 5 G -0.4 -23.7 37.3 -38.4 24.5 39.4 19.1 C3'-endo 6 G 2.2 -26.0 38.5 -38.1 22.7 39.9 15.4 C3'-endo 7 C 0.4 -23.6 36.6 -37.3 23.3 38.5 18.0 C3'-endo 8 G 1.5 -24.5 36.8 -37.0 22.5 38.4 16.5 C3'-endo 9 G -1.9 -22.4 36.7 -38.7 25.7 39.4 21.3 C3'-endo 10 U 1.6 -25.4 38.0 -38.0 23.0 39.5 16.2 C3'-endo 11 C 2.1 -23.9 35.5 -35.2 20.9 36.8 15.4 C3'-endo 12 C 2.2 -24.0 35.4 -35.1 20.8 36.7 15.2 C3'-endo 13 a -19.4 33.8 -34.6 24.4 -3.3 35.5 166.5 C2'-endo 14 G -24.1 37.0 -34.8 22.1 1.0 37.2 159.5 C2'-endo 15 G -2.5 -20.7 34.6 -37.1 25.0 37.4 22.4 C3'-endo 16 G 6.3 -27.4 37.2 -34.6 17.8 37.7 9.3 C3'-endo 17 U -0.5 -21.8 34.5 -35.9 22.9 36.6 19.4 C3'-endo 18 C 0.1 -22.8 35.5 -36.5 22.9 37.5 18.5 C3'-endo 19 P 17.0 -35.8 40.0 -31.4 9.2 40.2 354.3 C2'-exo 20 g 3.4 -26.2 37.7 -36.7 21.1 38.8 13.6 C3'-endo 21 C 3.2 -26.3 38.1 -37.3 21.5 39.3 13.9 C3'-endo 22 G 4.7 -27.9 39.1 -37.3 20.6 39.9 11.9 C3'-endo 23 G 13.3 -32.7 39.0 -32.2 12.0 39.0 359.1 C2'-exo 24 C -0.2 -22.6 35.5 -36.7 23.3 37.5 19.0 C3'-endo 25 U 3.0 -26.2 38.1 -37.3 21.6 39.3 14.2 C3'-endo 26 U -23.0 36.6 -35.7 23.4 -0.4 37.6 161.9 C2'-endo 27 C 2.8 -23.7 34.3 -33.7 19.5 35.4 14.2 C3'-endo **************************************************************************** Same strand P--P and C1'--C1' virtual bond distances Strand I Strand II step P--P C1'--C1' step P--P C1'--C1' 1 P/U 5.92 5.83 1 A/A 6.02 5.19 2 U/C 5.96 5.33 2 A/G 5.92 5.31 3 C/C 6.07 5.49 3 G/G 5.77 5.38 4 C/U 5.75 5.24 4 G/G 5.60 5.41 5 U/C 5.82 5.46 5 G/G 5.84 5.78 6 C/G 6.16 5.62 6 G/C 5.63 5.44 7 G/c 7.63 6.28 7 C/G 5.61 5.32 8 c/C 5.74 5.84 8 G/G 6.11 5.54 9 C/A 5.53 5.85 9 G/U 5.47 5.16 10 A/G 5.56 4.99 10 U/C 5.42 5.70 11 G/G 6.85 5.37 11 C/C 5.43 6.07 12 G/t 6.08 6.06 12 C/a 13.52 7.55 13 t/P 5.27 5.38 13 a/G 14.75 6.70 14 P/C --- --- 14 G/G --- --- 15 C/C 5.86 5.39 15 G/G 6.58 5.74 16 C/A 6.08 5.85 16 G/U 5.60 5.41 17 A/G 5.46 5.39 17 U/C 5.69 5.73 18 G/A 6.14 5.49 18 C/P 5.63 5.99 19 A/A 5.76 5.15 19 P/g 5.45 5.41 20 A/g 15.89 12.50 20 g/C 5.49 5.39 21 g/C 5.82 6.36 21 C/G 5.88 5.74 22 C/C 5.57 5.93 22 G/G 6.61 5.45 23 C/C 5.48 5.01 23 G/C 5.52 5.06 24 C/A 6.59 6.23 24 C/U 16.31 11.62 25 A/A 5.58 5.47 25 U/U 11.78 4.12 26 A/G --- --- 26 U/C --- --- **************************************************************************** Helix radius (radial displacement of P, O4', and C1' atoms in local helix frame of each dimer) Strand I Strand II step P O4' C1' P O4' C1' 1 PU/AA 8.79 7.79 6.85 9.22 7.76 6.92 2 UC/GA 9.57 8.58 7.76 8.76 7.87 7.16 3 CC/GG 8.55 8.84 8.26 10.43 9.82 9.19 4 CU/GG 9.19 8.22 7.36 8.61 8.05 7.39 5 UC/GG 10.20 9.94 9.42 8.80 9.89 9.53 6 CG/CG 9.19 9.13 8.53 7.88 8.57 8.07 7 Gc/GC 9.21 9.04 8.25 8.02 7.35 6.70 8 cC/GG 9.32 9.25 8.68 9.57 9.43 8.84 9 CA/UG 11.12 10.76 10.04 7.47 8.03 7.66 10 AG/CU 8.99 8.32 7.99 11.12 10.70 9.96 11 GG/CC 8.80 9.10 8.70 10.37 10.40 9.78 12 Gt/aC 10.31 8.67 7.67 6.72 4.64 3.97 13 tP/Ga 5.02 3.31 2.21 6.62 8.02 7.57 14 PC/GG ---- ---- ---- ---- ---- ---- 15 CC/GG 9.88 9.63 9.03 10.05 9.42 8.88 16 CA/UG 9.75 10.11 9.57 11.01 9.87 9.42 17 AG/CU 10.89 10.42 9.96 10.13 10.34 9.83 18 GA/PC 9.81 9.13 8.53 9.42 9.48 8.71 19 AA/gP 9.59 7.59 6.67 8.44 8.44 7.57 20 Ag/Cg 12.91 12.92 11.86 2.96 4.85 5.14 21 gC/GC 10.14 9.89 9.18 8.23 8.27 7.75 22 CC/GG 10.00 10.30 9.69 8.61 9.60 9.19 23 CC/CG 8.39 7.33 6.37 9.92 8.29 7.68 24 CA/UC 6.73 6.47 5.65 8.22 6.54 5.77 25 AA/UU 7.83 5.76 4.72 11.75 8.33 7.19 26 AG/CU ---- ---- ---- ---- ---- ---- **************************************************************************** Position (Px, Py, Pz) and local helical axis vector (Hx, Hy, Hz) for each dinucleotide step step Px Py Pz Hx Hy Hz 1 PU/AA 8.35 37.62 17.39 0.42 -0.53 0.74 2 UC/GA 10.32 36.84 19.52 0.45 -0.43 0.78 3 CC/GG 10.61 35.74 23.54 0.41 -0.61 0.68 4 CU/GG 13.44 34.60 24.45 0.35 -0.44 0.82 5 UC/GG 11.21 33.14 26.61 0.17 -0.72 0.67 6 CG/CG 13.22 31.57 28.63 0.38 -0.72 0.58 7 Gc/GC 13.80 31.26 31.36 0.05 -0.64 0.77 8 cC/GG 15.35 28.17 32.79 0.08 -0.59 0.80 9 CA/UG 14.53 25.71 33.82 0.29 -0.57 0.77 10 AG/CU 16.23 26.77 37.96 0.20 -0.64 0.74 11 GG/CC 17.30 24.60 39.59 0.25 -0.66 0.71 12 Gt/aC 17.90 19.18 38.23 0.36 -0.77 0.53 13 tP/Ga 15.37 15.46 39.53 0.15 -0.75 0.64 14 PC/GG ---- ---- ---- ---- ---- ---- 15 CC/GG 53.21 40.41 35.26 -0.77 -0.43 0.48 16 CA/UG 50.26 39.14 36.20 -0.72 -0.63 0.27 17 AG/CU 49.33 37.88 35.69 -0.75 -0.66 0.05 18 GA/PC 47.01 36.19 37.49 -0.82 -0.56 0.12 19 AA/gP 43.65 36.20 39.35 -0.86 -0.51 0.04 20 Ag/Cg 42.42 35.89 33.88 -0.66 -0.75 -0.01 21 gC/GC 38.56 35.27 37.76 -0.76 -0.57 -0.31 22 CC/GG 35.45 33.60 38.11 -0.84 -0.44 -0.32 23 CC/CG 34.37 32.11 34.63 -0.81 -0.55 -0.21 24 CA/UC 32.42 29.10 34.26 -0.69 -0.70 -0.15 25 AA/UU 31.77 24.65 35.35 -0.77 -0.63 -0.08 26 AG/CU ---- ---- ---- ---- ---- ----