**************************************************************************** This structure has broken O3'[i] to P[i+1] linkages **************************************************************************** 3DNA (v1.5, Nov. 2002) by Xiang-Jun Lu at Wilma K. Olson's Lab. **************************************************************************** 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: 1QTQ_old.PDB Date and time: Mon Sep 26 20:38:22 2011 Number of base-pairs: 28 Number of atoms: 1570 **************************************************************************** HEADER LIGASE/RNA 28-JAN-98 1QTQ COMPND RNA (TRNA GLN II ); EXPDTA X-RAY DIFFRACTION **************************************************************************** RMSD of the bases (----- for WC bp, + for isolated bp, x for helix change) Strand I Strand II Helix 1 (0.005) B:.902_:[..G]G-----C[..C]:.971_:B (0.004) | 2 (0.007) B:.903_:[..G]G-----C[..C]:.970_:B (0.005) | 3 (0.009) B:.904_:[..G]G-----C[..C]:.969_:B (0.003) | 4 (0.003) B:.905_:[..G]G-----C[..C]:.968_:B (0.005) | 5 (0.006) B:.906_:[..U]U-----A[..A]:.967_:B (0.004) | 6 (0.004) B:.907_:[..A]Ax----U[..U]:.966_:B (0.002) | 7 (0.002) B:.949_:[..C]C-----G[..G]:.965_:B (0.003) | 8 (0.003) B:.950_:[..G]G-----C[..C]:.964_:B (0.003) | 9 (0.003) B:.951_:[..A]A-----U[..U]:.963_:B (0.002) | 10 (0.008) B:.952_:[..G]G-----C[..C]:.962_:B (0.003) | 11 (0.004) B:.953_:[..G]G----xC[..C]:.961_:B (0.004) | 12 (0.002) B:.954_:[..U]U-**-xA[..A]:.958_:B (0.004) | 13 (0.004) B:.955_:[..U]Ux**+xG[..G]:.918_:B (0.013) x 14 (0.002) B:.937_:[..A]A-*---U[..U]:.933_:B (0.004) | 15 (0.006) B:.938_:[..U]U-*---U[..U]:.932_:B (0.004) | 16 (0.003) B:.939_:[..U]U-----A[..A]:.931_:B (0.004) | 17 (0.006) B:.940_:[..C]C-*---G[..G]:.930_:B (0.010) | 18 (0.006) B:.941_:[..C]C-----G[..G]:.929_:B (0.003) | 19 (0.007) B:.942_:[..G]G-----C[..C]:.928_:B (0.003) | 20 (0.006) B:.943_:[..G]G-----C[..C]:.927_:B (0.004) | 21 (0.005) B:.944_:[..C]Cx*---A[..A]:.926_:B (0.009) | 22 (0.005) B:.910_:[..G]G-----C[..C]:.925_:B (0.003) | 23 (0.006) B:.911_:[..C]C-----G[..G]:.924_:B (0.008) | 24 (0.008) B:.912_:[..C]C----xG[..G]:.923_:B (0.005) | 25 (0.003) B:.913_:[..A]A-**+xA[..A]:.945_:B (0.005) | 26 (0.004) B:.914_:[..A]A-**-xU[..U]:.908_:B (0.009) | 27 (0.020) B:.915_:[..G]Gx**+xC[..C]:.948_:B (0.003) x 28 (0.008) B:.919_:[..G]G-----C[..C]:.956_:B (0.003) + Note: This structure contains 9[5] non-Watson-Crick base-pairs. **************************************************************************** Detailed H-bond information: atom-name pair and length [ON] 1 G-----C [3] O6 - N4 2.64 N1 - N3 2.98 N2 - O2 3.19 2 G-----C [3] O6 - N4 2.93 N1 - N3 2.81 N2 - O2 2.56 3 G-----C [3] O6 - N4 2.96 N1 - N3 2.84 N2 - O2 2.71 4 G-----C [3] O6 - N4 2.95 N1 - N3 2.92 N2 - O2 2.85 5 U-----A [2] N3 - N1 2.92 O4 - N6 3.23 6 A-----U [2] N6 - O4 3.01 N1 - N3 2.86 7 C-----G [3] O2 - N2 2.65 N3 - N1 2.73 N4 - O6 2.71 8 G-----C [3] O6 - N4 2.97 N1 - N3 2.83 N2 - O2 2.64 9 A-----U [2] N6 - O4 3.07 N1 - N3 2.73 10 G-----C [2] O6 * N3 3.09 N2 - O2 3.00 11 G-----C [3] O6 - N4 3.20 N1 - N3 2.98 N2 - O2 2.62 12 U-**--A [2] O2 - N6 3.17 N3 - N7 3.05 13 U-**+-G [2] O4'* O6 3.64 O2 - N2 2.96 14 A-*---U [1] N6 - O2 2.76 15 U-*---U [1] O4 - N3 2.96 16 U-----A [2] N3 - N1 3.34 O4 - N6 3.21 17 C-*---G [3] O2'- N2 3.99 O2 - N1 2.87 N3 * O6 3.98 18 C-----G [3] O2 - N2 2.89 N3 - N1 2.89 N4 - O6 2.74 19 G-----C [3] O6 - N4 3.55 N1 - N3 3.21 N2 - O2 2.77 20 G-----C [3] O6 - N4 3.02 N1 - N3 2.90 N2 - O2 2.69 21 C-*---A [2] O2 * N1 3.27 N3 - N6 3.13 22 G-----C [3] O6 - N4 3.10 N1 - N3 2.94 N2 - O2 2.67 23 C-----G [3] O2 - N2 2.56 N3 - N1 2.82 N4 - O6 2.94 24 C-----G [3] O2 - N2 2.98 N3 - N1 3.00 N4 - O6 2.91 25 A-**+-A [1] N6 - N1 3.85 26 A-**--U [3] O2P* O4 3.62 N7 - N3 2.82 N6 - O2 2.75 27 G-**+-C [2] N1 - O2 3.02 N2 - N3 2.74 28 G-----C [3] O6 - N4 2.92 N1 - N3 2.90 N2 - O2 2.83 **************************************************************************** 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 GG/CC 3.64( 2.15) 0.00( 0.00) 0.23( 0.00) 0.22( 0.00) 4.10( 2.15) 2 GG/CC 3.81( 2.47) 0.00( 0.00) 0.39( 0.00) 0.00( 0.00) 4.21( 2.47) 3 GG/CC 4.01( 2.71) 0.00( 0.00) 0.44( 0.00) 0.00( 0.00) 4.45( 2.71) 4 GU/AC 5.53( 2.66) 0.00( 0.00) 0.00( 0.00) 4.34( 2.81) 9.87( 5.46) 5 UA/UA 0.67( 0.04) 0.00( 0.00) 1.10( 0.85) 0.00( 0.00) 1.77( 0.89) 6 AC/GU 2.22( 1.10) 0.00( 0.00) 0.00( 0.00) 5.96( 3.01) 8.18( 4.11) 7 CG/CG 0.00( 0.00) 0.00( 0.00) 4.53( 1.86) 0.01( 0.00) 4.55( 1.86) 8 GA/UC 3.98( 2.27) 0.00( 0.00) 0.00( 0.00) 1.27( 0.04) 5.25( 2.31) 9 AG/CU 2.32( 2.22) 0.00( 0.00) 0.59( 0.00) 0.02( 0.00) 2.92( 2.22) 10 GG/CC 4.15( 2.32) 0.00( 0.00) 0.76( 0.00) 0.00( 0.00) 4.91( 2.32) 11 GU/AC 7.14( 4.20) 0.00( 0.00) 0.00( 0.00) 3.94( 1.36) 11.08( 5.57) 12 UU/GA 5.40( 2.87) 0.00( 0.00) 0.00( 0.00) 4.81( 2.37) 10.21( 5.24) 13 UA/UG 0.00( 0.00) 0.00( 0.00) 0.00( 0.00) 0.00( 0.00) 0.00( 0.00) 14 AU/UU 4.20( 0.79) 0.00( 0.00) 0.00( 0.00) 3.56( 1.72) 7.77( 2.50) 15 UU/AU 3.26( 1.58) 0.00( 0.00) 0.00( 0.00) 5.98( 3.96) 9.24( 5.54) 16 UC/GA 3.01( 1.36) 0.00( 0.00) 0.00( 0.00) 1.24( 0.16) 4.25( 1.52) 17 CC/GG 0.00( 0.00) 0.00( 0.00) 0.37( 0.00) 3.03( 1.48) 3.40( 1.48) 18 CG/CG 0.00( 0.00) 0.00( 0.00) 4.33( 1.75) 0.00( 0.00) 4.33( 1.75) 19 GG/CC 2.42( 0.93) 0.00( 0.00) 0.89( 0.00) 0.00( 0.00) 3.31( 0.93) 20 GC/AC 6.90( 4.22) 0.00( 0.00) 0.00( 0.00) 5.38( 3.66) 12.28( 7.87) 21 CG/CA 0.00( 0.00) 0.00( 0.00) 0.00( 0.00) 0.94( 0.28) 0.95( 0.28) 22 GC/GC 4.63( 1.75) 0.00( 0.00) 0.00( 0.00) 6.67( 3.56) 11.30( 5.31) 23 CC/GG 0.24( 0.04) 0.00( 0.00) 0.52( 0.00) 2.81( 1.28) 3.58( 1.32) 24 CA/AG 1.67( 0.83) 0.00( 0.00) 0.00( 0.00) 0.00( 0.00) 1.67( 0.83) 25 AA/UA 0.00( 0.00) 1.97( 0.00) 0.00( 0.00) 0.00( 0.00) 1.97( 0.00) 26 AG/CU 2.31( 0.84) 0.00( 0.00) 0.22( 0.00) 0.00( 0.00) 2.53( 0.84) 27 GG/CC 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 G-C 43.32 41.11 33.84 -0.95 0.01 -0.30 2 G-C 40.49 39.41 32.64 -0.98 -0.03 -0.20 3 G-C 37.11 37.53 32.50 -0.99 -0.08 -0.14 4 G-C 33.66 35.93 34.32 -0.98 -0.09 0.16 5 U-A 30.69 35.32 35.94 -0.99 0.03 0.14 6 A-U 28.31 36.11 37.75 -0.97 0.10 0.21 7 C-G 25.54 37.26 40.04 -0.97 0.14 0.22 8 G-C 22.60 39.53 41.50 -0.97 0.20 0.13 9 A-U 19.71 41.04 41.26 -0.98 0.17 0.06 10 G-C 16.51 42.39 39.71 -0.99 0.11 -0.07 11 G-C 13.28 42.02 37.16 -0.99 -0.01 -0.15 12 U-A 10.85 41.64 33.42 -0.98 0.03 -0.17 13 U+G 7.33 40.88 35.20 -1.00 -0.08 -0.03 14 A-U 19.24 -6.49 19.59 -0.52 0.86 0.03 15 U-U 15.90 -4.58 19.12 -0.37 0.92 0.13 16 U-A 13.78 -2.43 21.59 -0.42 0.86 0.30 17 C-G 13.64 1.06 24.77 -0.33 0.93 0.14 18 C-G 11.62 2.76 26.99 -0.09 0.97 0.23 19 G-C 13.09 6.14 28.91 0.04 1.00 0.09 20 G-C 15.54 9.01 29.74 0.15 0.99 -0.03 21 C-A 17.50 11.90 29.30 0.20 0.97 -0.12 22 G-C 22.36 14.61 29.39 0.08 0.96 -0.26 23 C-G 22.49 17.31 27.04 0.08 0.97 -0.22 24 C-G 20.71 20.08 25.36 -0.00 0.98 -0.22 25 A+A 18.15 23.56 29.36 -0.16 0.98 0.09 26 A-U 16.83 26.36 26.27 -0.24 0.96 -0.12 27 G+C 15.91 29.49 29.72 -0.05 0.98 0.20 28 G-C 1.33 40.30 28.92 -0.92 -0.05 -0.39 **************************************************************************** Local base-pair parameters bp Shear Stretch Stagger Buckle Propeller Opening 1 G-C -0.33 -0.17 -0.03 -11.68 0.51 -8.71 2 G-C -0.20 -0.19 0.16 -1.08 -5.75 3.23 3 G-C 0.01 -0.12 0.05 -9.05 -18.00 2.57 4 G-C -0.04 -0.04 -0.74 -22.89 -17.03 2.67 5 U-A -0.12 0.07 0.25 -17.26 -10.82 6.02 6 A-U 0.04 -0.06 0.23 8.83 -6.34 1.55 7 C-G -0.12 -0.26 0.02 5.91 -10.18 -0.94 8 G-C 0.14 -0.12 -0.05 -3.26 -15.09 3.46 9 A-U -0.17 -0.17 -0.08 4.49 -4.08 7.38 10 G-C -1.32 -0.31 -0.32 0.42 -8.20 2.10 11 G-C 0.03 0.07 -0.21 -14.97 -4.84 6.03 12 U-A 4.70 -2.72 0.77 0.91 14.42 -93.47 13 U+G 0.52 -5.90 0.50 25.12 7.36 -89.11 14 A-U -6.07 -4.60 -0.34 -7.31 22.55 -30.54 15 U-U -3.24 -1.18 0.23 7.93 17.36 -30.25 16 U-A 0.49 0.05 -1.49 17.30 -12.42 -1.48 17 C-G 2.73 0.45 0.39 -1.93 -12.44 29.13 18 C-G 0.03 -0.19 -0.54 6.77 -3.53 -3.45 19 G-C 0.84 0.26 -0.44 -12.65 -6.73 9.70 20 G-C 0.15 -0.05 -0.18 -9.62 -12.13 3.17 21 C-A 2.28 -0.10 -0.25 -4.12 -3.89 -3.27 22 G-C -0.83 -0.22 -0.50 -8.05 -6.16 4.91 23 C-G -0.24 -0.14 -0.02 -5.31 -2.77 3.73 24 C-G 0.30 -0.09 -0.22 2.30 5.12 -2.45 25 A+A -2.58 -0.56 -0.04 20.91 -15.85 169.87 26 A-U -4.18 -2.39 0.98 -0.08 8.16 -92.74 27 G+C 0.14 4.13 -0.37 -7.27 2.46 164.38 28 G-C 0.34 -0.05 -0.03 -18.87 -16.88 -0.79 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ave. -0.24 -0.52 -0.08 -1.95 -4.11 2.24 s.d. 2.01 1.73 0.47 11.57 10.63 55.82 **************************************************************************** Local base-pair step parameters step Shift Slide Rise Tilt Roll Twist 1 GG/CC 0.54 -1.65 3.06 -1.53 6.52 34.75 2 GG/CC 0.38 -1.71 3.45 2.93 3.46 34.71 3 GG/CC 0.74 -2.06 3.60 10.36 13.39 28.83 4 GU/AC 0.04 -1.27 3.19 -3.92 6.32 29.90 5 UA/UA 0.48 -1.40 2.71 4.14 3.65 31.35 6 AC/GU -0.45 -1.74 3.32 1.79 0.89 37.66 7 CG/CG -0.42 -1.89 3.49 2.29 6.39 31.68 8 GA/UC 0.23 -1.06 3.09 -1.00 4.06 30.14 9 AG/CU 0.45 -1.73 3.35 2.86 7.58 26.31 10 GG/CC 0.98 -2.03 3.47 3.24 7.67 38.36 11 GU/AC -2.31 -2.40 2.99 -0.93 -2.56 87.14 12 UU/GA 1.62 -1.55 3.33 9.05 4.45 42.60 13 UA/UG ---- ---- ---- ---- ---- ---- 14 AU/UU 0.21 -2.25 3.14 -10.95 1.45 51.24 15 UU/AU 1.24 -1.69 3.30 7.87 7.28 42.77 16 UC/GA 2.14 -1.62 3.89 -11.38 1.54 39.86 17 CC/GG -1.85 -1.55 2.47 7.59 13.31 24.81 18 CG/CG 0.32 -2.03 3.62 -1.55 10.91 33.40 19 GG/CC -0.05 -2.29 3.11 3.78 8.65 29.86 20 GC/AC -0.20 -1.42 3.22 4.21 4.10 37.39 21 CG/CA -4.23 -1.47 3.29 4.07 9.73 53.42 22 GC/GC -0.40 -1.57 3.19 -2.16 0.51 38.11 23 CC/GG 0.34 -2.13 3.00 3.76 3.41 29.00 24 CA/AG 4.70 0.91 3.41 -4.41 19.39 -34.01 25 AA/UA -3.12 -0.12 3.07 2.36 -13.05 135.23 26 AG/CU 2.17 -2.55 3.37 4.31 21.46 -73.96 27 GG/CC ---- ---- ---- ---- ---- ---- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ave. 0.14 -1.61 3.24 1.47 6.02 34.42 s.d. 1.77 0.72 0.29 5.36 6.89 35.66 **************************************************************************** Local base-pair helical parameters step X-disp Y-disp h-Rise Incl. Tip h-Twist 1 GG/CC -3.57 -1.08 2.69 10.79 2.54 35.37 2 GG/CC -3.39 -0.18 3.29 5.76 -4.89 35.00 3 GG/CC -5.85 0.45 2.53 24.41 -18.88 33.34 4 GU/AC -3.54 -0.79 2.84 12.02 7.46 30.79 5 UA/UA -3.09 -0.26 2.57 6.68 -7.59 31.82 6 AC/GU -2.81 0.93 3.26 1.38 -2.78 37.71 7 CG/CG -4.52 1.15 3.02 11.55 -4.13 32.38 8 GA/UC -2.77 -0.63 2.92 7.75 1.91 30.42 9 AG/CU -5.42 -0.27 2.79 16.18 -6.09 27.51 10 GG/CC -3.96 -1.07 3.09 11.51 -4.86 39.22 11 GU/AC -1.69 1.66 3.07 -1.86 0.68 87.17 12 UU/GA -2.53 -1.27 3.42 6.03 -12.26 43.72 13 UA/UG ---- ---- ---- ---- ---- ---- 14 AU/UU -2.64 -0.93 2.98 1.65 12.49 52.34 15 UU/AU -2.94 -0.91 3.16 9.80 -10.59 44.03 16 UC/GA -2.47 -4.35 3.13 2.20 16.29 41.42 17 CC/GG -4.72 4.61 0.94 27.84 -15.89 29.10 18 CG/CG -5.01 -0.77 2.82 18.37 2.62 35.12 19 GG/CC -5.64 0.69 2.35 16.28 -7.11 31.28 20 GC/AC -2.70 0.82 3.01 6.34 -6.51 37.84 21 CG/CA -2.16 4.86 2.70 10.71 -4.47 54.38 22 GC/GC -2.47 0.35 3.19 0.77 3.31 38.17 23 CC/GG -4.84 0.04 2.76 6.75 -7.45 29.43 24 CA/AG -3.82 6.45 3.04 -30.17 -6.85 -39.25 25 AA/UA 0.01 1.70 3.04 -7.05 -1.28 135.54 26 AG/CU 1.36 1.89 3.77 -17.47 3.51 -76.68 27 GG/CC ---- ---- ---- ---- ---- ---- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ave. -3.25 0.52 2.89 6.33 -2.83 35.09 s.d. 1.66 2.23 0.51 12.09 8.10 36.47 **************************************************************************** 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 G-C 48.8 51.2 10.9 9.1 9.8 2 G-C 56.5 56.8 10.4 8.8 9.8 3 G-C 57.0 54.9 10.5 8.9 9.9 4 G-C 56.1 54.7 10.6 8.9 9.8 5 U-A 58.4 56.7 10.4 8.8 9.9 6 A-U 55.5 55.8 10.5 8.9 9.9 7 C-G 52.1 54.8 10.6 8.8 9.8 8 G-C 56.6 54.0 10.6 8.9 9.9 9 A-U 57.7 59.5 10.2 8.6 9.8 10 G-C 48.8 61.7 10.5 8.8 9.8 11 G-C 59.5 56.8 10.5 8.9 10.0 12 U-A 38.3 20.8 9.5 7.1 6.3 13 U+G 111.4 30.9 8.8 8.3 9.7 14 A-U 4.3 80.4 9.3 7.8 7.9 15 U-U 23.8 55.9 10.9 8.8 9.1 16 U-A 56.9 51.8 10.9 9.2 10.0 17 C-G 83.4 53.7 10.1 9.0 10.5 18 C-G 51.8 52.4 10.8 9.0 9.8 19 G-C 65.1 54.3 10.6 9.1 10.2 20 G-C 57.4 54.0 10.6 9.0 10.0 21 C-A 64.1 41.9 11.0 9.3 10.1 22 G-C 52.5 61.3 10.4 8.8 9.8 23 C-G 54.9 58.3 10.5 8.8 9.9 24 C-G 54.3 51.9 10.8 9.1 9.9 25 A+A 30.4 41.7 14.1 11.8 12.3 26 A-U 17.9 35.1 9.6 7.1 6.2 27 G+C 45.2 57.8 10.5 9.0 10.6 28 G-C 57.4 50.5 10.7 9.0 9.9 **************************************************************************** Classification of each dinucleotide step in a right-handed nucleic acid structure: A-like; B-like; TA-like; intermediate of A and B, or other cases step Xp Yp Zp XpH YpH ZpH Form 1 GG/CC -1.28 8.21 2.64 -4.69 7.61 4.08 A 2 GG/CC -1.76 8.01 2.71 -4.98 7.71 3.46 A 3 GG/CC -2.27 8.58 1.95 -7.37 7.13 4.97 A 4 GU/AC -1.75 8.51 1.98 -5.29 7.93 3.66 A 5 UA/UA -1.90 8.49 2.05 -4.77 8.21 2.93 A 6 AC/GU -1.85 7.63 3.33 -4.55 7.55 3.50 A 7 CG/CG -2.11 8.55 2.41 -6.46 7.92 4.02 A 8 GA/UC -1.65 8.42 2.18 -4.32 8.06 3.26 A 9 AG/CU -1.96 8.35 2.32 -7.21 7.42 4.45 A 10 GG/CC -2.02 7.85 2.89 -5.71 7.17 4.29 A 11 GU/AC -0.85 6.92 3.44 -2.08 7.00 3.25 12 UU/GA 3.53 4.49 0.36 0.65 4.40 1.47 13 UA/UG --- --- --- --- --- --- --- 14 AU/UU 0.97 6.99 2.84 -1.35 6.91 3.42 15 UU/AU -0.22 8.37 2.28 -3.12 7.92 3.41 16 UC/GA -2.39 7.96 2.43 -4.44 7.87 2.42 17 CC/GG -2.63 7.93 2.56 -7.02 5.87 5.93 18 CG/CG -2.08 8.34 2.67 -6.84 7.14 5.05 A 19 GG/CC -2.07 8.10 2.48 -7.40 7.12 4.58 A 20 GC/AC -1.50 8.63 2.23 -3.93 8.35 3.15 A 21 CG/CA -3.66 7.08 3.61 -5.59 6.40 4.59 22 GC/GC -1.91 7.97 2.58 -4.26 7.94 2.70 A 23 CC/GG -1.65 8.39 2.65 -6.24 8.04 3.54 A 24 CA/AG -2.79 6.69 2.74 -6.40 7.06 -1.30 25 AA/UA 0.15 7.84 4.18 0.18 8.02 3.76 26 AG/CU 2.26 1.85 1.75 3.31 2.26 1.60 27 GG/CC --- --- --- --- --- --- --- **************************************************************************** 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 GG/CC --- --- --- --- 2 GG/CC --- --- --- --- 3 GG/CC 16.4 --- 16.8 --- 4 GU/AC 17.3 15.6 17.2 14.7 5 UA/UA 17.3 15.8 19.6 18.8 6 AC/GU 16.0 14.7 17.9 17.2 7 CG/CG 16.1 14.8 17.8 17.2 8 GA/UC 16.8 15.7 14.9 11.2 9 AG/CU 16.7 15.4 15.9 12.6 10 GG/CC 16.0 --- 15.1 --- 11 GU/AC --- --- --- --- 12 UU/GA --- --- --- --- 13 UA/UG --- --- --- --- 14 AU/UU --- --- --- --- 15 UU/AU --- --- --- --- 16 UC/GA 16.5 --- 15.6 --- 17 CC/GG 16.6 14.7 16.6 11.2 18 CG/CG 16.5 15.2 16.8 9.6 19 GG/CC 17.7 14.4 17.1 13.5 20 GC/AC 17.9 13.5 15.8 13.3 21 CG/CA 16.8 14.2 13.3 12.2 22 GC/GC 16.8 15.0 11.2 10.0 23 CC/GG 16.8 15.4 11.0 3.6 24 CA/AG 16.5 --- 8.9 --- 25 AA/UA --- --- --- --- 26 AG/CU --- --- --- --- 27 GG/CC --- --- --- --- **************************************************************************** Global linear helical axis defined by equivalent C1' and RN9/YN1 atom pairs Deviation from regular linear helix: 0.27(3.50) **************************************************************************** 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 G --- --- -176.7 86.5 -135.0 -75.5 176.3 2 G -80.2 177.0 60.7 82.4 -159.9 -71.4 -167.4 3 G -47.6 172.5 47.1 82.9 -157.8 -61.2 -162.7 4 G 163.0 177.5 174.7 83.7 -143.5 -72.1 -171.5 5 U -59.2 179.0 48.6 82.3 -175.7 -62.0 -158.1 6 A -172.2 -178.4 172.6 145.4 --- --- -143.3 7 C --- 171.9 49.0 86.8 -147.8 -70.9 -169.6 8 G -60.2 -179.7 46.1 81.7 -158.2 -68.3 -156.6 9 A -63.9 -178.5 46.4 83.4 -169.2 -77.6 -150.6 10 G 158.1 -165.5 167.8 82.7 -135.7 -69.0 -176.0 11 G -53.8 174.4 50.0 81.6 -157.8 -66.7 -170.0 12 U -61.8 -175.8 51.6 84.5 -144.5 -66.7 -159.3 13 U -72.5 178.4 51.4 85.5 --- --- -148.9 14 A --- -164.8 48.3 83.3 -148.3 -57.1 -173.6 15 U -62.6 -179.0 52.5 83.7 -140.3 -65.6 -174.8 16 U -60.7 168.5 52.5 86.6 -153.0 -57.4 -155.8 17 C -62.1 171.2 55.1 86.8 -110.9 -147.9 -175.0 18 C 116.1 -118.6 167.3 83.8 -137.2 -72.2 -174.8 19 G -62.4 172.1 44.6 79.5 -148.6 -76.9 -175.6 20 G -54.8 179.5 51.9 82.4 -157.3 -62.5 -156.4 21 C -64.7 -178.5 48.7 83.5 --- --- -143.8 22 G --- 177.5 55.3 89.4 -149.1 -70.1 179.9 23 C -68.8 -172.2 48.7 84.5 -160.2 -68.1 -158.6 24 C 149.6 -173.8 179.0 84.8 -136.7 -59.2 -171.1 25 A -52.3 172.5 49.6 82.9 179.8 -79.0 -155.8 26 A 172.2 -178.1 171.9 88.4 -125.5 -52.4 -174.9 27 G -45.7 169.2 46.0 146.2 --- --- -114.2 28 G --- 159.6 58.3 145.9 --- --- -94.0 Strand II base alpha beta gamma delta epsilon zeta chi 1 C -61.2 177.3 50.1 84.3 --- --- -151.8 2 C -70.3 -176.9 51.7 84.2 -151.7 -77.8 -161.7 3 C -69.2 -179.2 51.8 83.0 -153.5 -75.4 -164.0 4 C -60.7 165.7 56.1 84.1 -159.0 -71.7 -149.0 5 A -60.8 178.4 48.3 84.9 -151.4 -75.2 -150.3 6 U -56.5 167.5 50.2 82.9 -153.1 -80.2 -169.0 7 G 150.7 -162.9 175.3 84.0 -136.3 -78.3 177.8 8 C -48.3 159.5 51.8 84.5 -165.1 -70.1 -155.8 9 U -64.2 -178.5 45.7 83.0 -154.1 -83.7 -159.4 10 C -62.5 -178.1 48.4 85.9 -151.6 -76.6 -166.3 11 C --- -175.3 42.9 81.5 -152.2 -75.0 -171.7 12 A --- -130.5 58.6 149.4 --- --- -76.8 13 G --- -145.1 -53.6 145.9 --- --- -104.0 14 U -63.7 172.2 48.4 83.2 --- --- -156.2 15 U 158.2 -155.3 172.9 84.7 -123.6 -70.2 174.2 16 A -58.3 -169.9 45.8 81.8 -158.3 -82.8 -156.5 17 G -66.9 166.0 50.1 82.1 -164.0 -72.3 -172.9 18 G 164.1 -169.6 167.5 85.2 -124.8 -82.7 176.6 19 C -69.0 -166.8 46.1 82.9 -165.3 -73.1 -155.5 20 C -57.1 169.9 50.3 81.3 -154.5 -69.0 -166.7 21 A -61.6 176.0 51.7 80.3 -150.7 -71.1 -166.5 22 C -59.3 167.9 50.1 81.4 -137.7 -60.7 -163.4 23 G -59.8 175.2 53.2 83.1 -146.1 -77.1 -170.4 24 G --- 161.8 50.5 81.9 -151.6 -75.8 -176.4 25 A --- -160.0 62.0 86.6 --- --- -102.8 26 U --- -152.4 53.6 80.7 --- --- -160.0 27 C --- 142.1 36.4 141.0 --- --- -151.3 28 C --- 150.6 49.7 83.7 --- --- -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: amplitude of pseudorotation of the sugar ring P: phase angle of pseudorotation of the sugar ring Strand I base v0 v1 v2 v3 v4 tm P Puckering 1 G 4.2 -24.7 34.8 -33.4 18.3 35.6 12.0 C3'-endo 2 G 2.2 -25.4 37.6 -37.3 22.1 39.0 15.3 C3'-endo 3 G 1.3 -23.9 36.4 -36.7 22.2 38.0 16.7 C3'-endo 4 G 5.3 -26.3 36.3 -34.4 18.3 36.9 10.7 C3'-endo 5 U 1.0 -23.8 36.1 -36.5 22.5 37.8 17.1 C3'-endo 6 A -19.2 32.4 -32.4 22.3 -2.3 33.5 164.8 C2'-endo 7 C 3.5 -24.0 34.1 -33.2 18.8 35.1 13.2 C3'-endo 8 G 1.1 -22.9 34.9 -35.3 21.6 36.5 17.1 C3'-endo 9 A 1.5 -23.1 34.8 -35.0 21.1 36.3 16.4 C3'-endo 10 G 6.3 -27.0 36.5 -34.0 17.3 37.0 9.1 C3'-endo 11 G 0.5 -23.2 35.7 -36.4 22.6 37.5 17.8 C3'-endo 12 U 1.7 -22.6 33.9 -34.0 20.3 35.3 16.0 C3'-endo 13 U 1.6 -23.0 34.3 -34.4 20.7 35.7 16.2 C3'-endo 14 A 3.4 -25.4 36.5 -35.6 20.3 37.6 13.5 C3'-endo 15 U 2.5 -24.4 35.7 -35.4 20.8 37.0 14.9 C3'-endo 16 U 4.0 -24.9 35.1 -33.8 18.7 35.9 12.4 C3'-endo 17 C 4.4 -24.3 33.9 -32.4 17.7 34.6 11.6 C3'-endo 18 C 1.6 -22.3 33.5 -33.6 20.1 34.9 16.1 C3'-endo 19 G 1.2 -23.7 35.9 -36.4 22.2 37.6 17.0 C3'-endo 20 G -1.1 -21.4 34.5 -36.2 23.5 36.8 20.4 C3'-endo 21 C -2.9 -19.5 33.0 -35.8 24.4 35.9 23.2 C3'-endo 22 G 3.3 -23.4 33.5 -32.7 18.5 34.5 13.4 C3'-endo 23 C 2.4 -23.9 35.2 -34.9 20.5 36.4 15.1 C3'-endo 24 C 5.5 -26.8 36.8 -34.7 18.4 37.4 10.4 C3'-endo 25 A -0.3 -21.9 34.4 -35.6 22.6 36.4 19.1 C3'-endo 26 A 3.0 -23.0 33.0 -32.6 18.7 34.0 14.0 C3'-endo 27 G -29.3 41.6 -36.8 21.2 4.9 40.9 154.3 C2'-endo 28 G -17.3 31.2 -32.6 23.6 -4.2 33.3 168.3 C2'-endo Strand II base v0 v1 v2 v3 v4 tm P Puckering 1 C 1.2 -23.0 34.8 -35.2 21.5 36.3 16.9 C3'-endo 2 C 1.5 -23.9 36.0 -36.2 21.9 37.5 16.4 C3'-endo 3 C -0.9 -22.3 35.7 -37.2 23.9 37.9 19.9 C3'-endo 4 C 0.4 -22.9 35.3 -36.1 22.5 37.1 18.1 C3'-endo 5 A 4.6 -25.9 36.2 -34.6 18.9 36.9 11.7 C3'-endo 6 U 1.0 -23.3 35.7 -36.1 22.0 37.3 17.2 C3'-endo 7 G 2.8 -24.1 35.1 -34.5 20.0 36.2 14.3 C3'-endo 8 C 1.0 -22.1 33.6 -34.2 20.9 35.2 17.2 C3'-endo 9 U 2.5 -24.0 35.2 -34.9 20.5 36.4 14.9 C3'-endo 10 C 1.6 -22.0 32.9 -33.0 19.8 34.2 16.1 C3'-endo 11 C 0.8 -22.9 35.2 -35.9 22.1 37.0 17.6 C3'-endo 12 A -20.0 34.4 -34.9 24.4 -3.0 36.0 165.9 C2'-endo 13 G -21.0 34.1 -33.4 22.3 -1.0 34.9 162.8 C2'-endo 14 U 1.6 -23.6 35.3 -35.4 21.3 36.7 16.2 C3'-endo 15 U 5.0 -25.5 35.4 -33.6 18.1 36.1 11.0 C3'-endo 16 A 2.5 -24.5 36.0 -35.7 20.8 37.3 14.9 C3'-endo 17 G 2.3 -24.5 36.2 -35.9 21.2 37.5 15.2 C3'-endo 18 G 4.7 -24.8 34.4 -32.9 17.8 35.1 11.3 C3'-endo 19 C 1.4 -22.9 34.3 -34.7 21.0 35.8 16.5 C3'-endo 20 C 2.2 -24.8 36.8 -36.6 21.7 38.2 15.4 C3'-endo 21 A -0.2 -22.5 35.4 -36.6 23.3 37.4 19.0 C3'-endo 22 C 2.4 -25.4 37.6 -37.2 21.9 38.9 15.1 C3'-endo 23 G 2.4 -24.8 36.4 -36.2 21.3 37.7 15.1 C3'-endo 24 G 2.7 -24.6 36.0 -35.5 20.7 37.2 14.6 C3'-endo 25 A -8.5 -12.5 27.3 -33.2 26.3 32.8 33.4 C3'-endo 26 U -0.6 -22.7 36.1 -37.3 23.9 38.3 19.4 C3'-endo 27 C -24.2 36.2 -33.6 20.5 2.2 36.2 157.9 C2'-endo 28 C 1.7 -23.2 34.8 -34.8 20.9 36.2 16.1 C3'-endo **************************************************************************** Same strand P--P and C1'--C1' virtual bond distances Strand I Strand II base P--P C1'--C1' base P--P C1'--C1' 1 G/G --- 6.0 1 C/C 5.6 5.7 2 G/G 6.1 5.2 2 C/C 5.7 5.8 3 G/G 5.7 5.6 3 C/C 6.2 5.5 4 G/U 6.7 5.7 4 C/A 5.6 5.1 5 U/A 6.1 5.7 5 A/U 5.8 5.7 6 A/C 8.9 6.0 6 U/G 6.6 5.6 7 C/G 5.7 5.8 7 G/C 6.2 5.2 8 G/A 5.7 5.4 8 C/U 5.5 5.1 9 A/G 5.9 5.3 9 U/C 5.6 5.8 10 G/G 6.6 5.6 10 C/C 5.4 5.8 11 G/U 5.9 5.6 11 C/A 13.6 7.8 12 U/U 5.5 5.5 12 A/G 14.5 6.8 13 U/A --- --- 13 G/U --- --- 14 A/U 5.3 5.4 14 U/U 6.4 5.8 15 U/U 5.5 5.2 15 U/A 5.4 5.5 16 U/C 5.9 4.9 16 A/G 6.1 5.9 17 C/C 5.3 6.0 17 G/G 6.4 5.8 18 C/G 6.7 5.6 18 G/C 5.6 5.5 19 G/G 5.6 5.9 19 C/C 5.9 6.1 20 G/C 5.9 5.4 20 C/A 5.8 5.2 21 C/G 15.5 11.9 21 A/C 5.5 5.5 22 G/C 5.7 6.0 22 C/G 5.7 5.3 23 C/C 5.6 5.4 23 G/G 5.9 5.6 24 C/A 6.6 5.4 24 G/A 11.3 14.5 25 A/A 6.3 5.8 25 A/U 17.4 8.9 26 A/G 6.4 5.4 26 U/C 11.5 4.4 27 G/G --- --- 27 C/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 GG/CC 8.1 7.9 7.4 9.8 9.4 8.6 2 GG/CC 9.1 8.5 7.9 9.3 8.8 8.0 3 GG/CC 12.3 10.6 10.1 8.2 9.3 8.9 4 GU/AC 9.1 8.4 7.7 10.0 9.3 8.6 5 UA/UA 10.0 8.2 7.6 9.0 8.6 7.8 6 AC/GU 9.3 9.0 8.2 8.3 7.5 6.8 7 CG/CG 10.9 10.2 9.5 9.6 8.5 8.1 8 GA/UC 8.7 7.8 7.1 9.6 8.8 8.0 9 AG/CU 10.8 10.2 9.8 9.9 9.9 9.3 10 GG/CC 8.9 8.6 8.1 9.5 9.6 8.8 11 GU/AC 10.1 8.3 7.3 7.4 5.1 4.4 12 UU/GA 4.8 3.3 2.2 6.6 7.9 7.4 13 UA/UG ---- ---- ---- ---- ---- ---- 14 AU/UU 6.5 7.1 6.8 8.0 6.5 5.5 15 UU/AU 7.6 7.4 6.9 9.8 8.4 7.6 16 UC/GA 4.6 5.0 4.8 13.6 12.3 11.3 17 CC/GG 13.3 12.7 11.9 6.5 7.8 8.1 18 CG/CG 8.9 9.0 8.6 10.9 10.4 9.8 19 GG/CC 11.2 10.7 10.1 9.4 10.0 9.6 20 GC/AC 10.5 8.5 7.7 8.0 7.9 7.3 21 CG/CA 12.8 12.2 11.1 4.3 4.9 5.0 22 GC/GC 9.6 8.5 7.8 8.5 7.7 6.9 23 CC/GG 11.2 9.6 9.1 9.2 9.5 9.0 24 CA/AG 15.9 12.7 11.9 3.2 7.4 7.9 25 AA/UA 9.3 7.3 6.4 9.8 7.1 6.4 26 AG/CU 9.5 6.2 5.5 11.3 7.7 6.5 27 GG/CC ---- ---- ---- ---- ---- ---- **************************************************************************** Position (Px, Py, Pz) and local helical axis vector (Hx, Hy, Hz) for each dinucleotide step bp Px Py Pz Hx Hy Hz 1 GG/CC 41.10 39.26 36.55 -0.97 0.17 -0.19 2 GG/CC 38.52 38.73 35.79 -0.99 0.05 -0.09 3 GG/CC 36.76 39.24 38.24 -0.91 0.42 0.04 4 GU/AC 31.92 39.02 35.93 -0.99 -0.05 -0.08 5 UA/UA 30.02 38.60 36.26 -0.98 0.18 0.05 6 AC/GU 27.11 39.27 37.83 -0.98 0.14 0.17 7 CG/CG 23.84 40.59 36.88 -1.00 0.00 0.06 8 GA/UC 20.67 38.98 39.01 -0.98 0.07 0.16 9 AG/CU 18.18 37.83 36.93 -0.98 -0.13 0.12 10 GG/CC 15.17 38.36 38.65 -1.00 -0.07 0.06 11 GU/AC 12.03 40.13 35.48 -0.98 -0.00 -0.18 12 UU/GA 9.46 43.31 35.91 -0.99 0.15 0.03 13 UA/UG ---- ---- ---- ---- ---- ---- 14 AU/UU 17.30 -5.42 21.85 -0.35 0.93 -0.08 15 UU/AU 16.88 -3.75 22.33 -0.18 0.93 0.31 16 UC/GA 16.79 1.75 20.64 -0.58 0.81 0.07 17 CC/GG 17.74 3.21 29.50 -0.02 0.95 -0.32 18 CG/CG 15.54 5.09 24.38 -0.25 0.97 -0.05 19 GG/CC 16.63 7.03 24.39 -0.13 0.98 -0.17 20 GC/AC 16.52 10.05 26.88 0.04 0.99 -0.15 21 CG/CA 20.21 12.88 24.64 0.00 1.00 -0.08 22 GC/GC 20.13 16.38 28.57 0.14 0.96 -0.25 23 CC/GG 18.71 19.05 29.86 0.05 1.00 -0.05 24 CA/AG 13.52 17.98 26.92 -0.51 0.82 -0.27 25 AA/UA 16.88 24.81 27.94 -0.24 0.97 0.00 26 AG/CU 14.68 27.26 28.15 -0.35 0.92 0.16 27 GG/CC ---- ---- ---- ---- ---- ----