Warning: Coordinating ligands by symmetry operation are labeled with prefix 'sym-'
Warning: Partial occupancy of the metal is not adjusted upon symmetry operation
ID Res. Metal Occupancy B factor (env.)1 Ligands Valence2 nVECSUM3 Geometry1,4 gRMSD(°)1 Vacancy1 Bidentate Alt. metal
A:3001MGMg110.7 (10.2)O5N120.029Octahedral4.7°00
A:3002MGMg114.4 (13.6)O510.09Octahedral10.5°16%0Ca
A:3005MGMg125.5 (31.3)O62.30.045Octahedral6.6°00
A:3101NANa111.7 (13.3)O51.20.11Trigonal Bipyramidal12.5°00
A:3102NANa112.2 (14.3)O51.10.19Octahedral12.3°16%0Ca, Na
A:3103NANa125.9 (18.9)O30.60.57Octahedral11.5°50%0
A:3104NANa123 (24.7)O61.30.093Octahedral9.7°00
A:3105MGMg0.519.5 (24.2)O61.60.097Octahedral4.4°00Co, Cu
B:3001MGMg110.4 (10)O5N11.90.03Octahedral4.7°00
B:3002MGMg113.3 (12.8)O510.088Octahedral10.3°16%0Ca
B:3101NANa111.4 (13.1)O51.20.12Trigonal Bipyramidal12.1°00
B:3102NANa111.5 (14.6)O51.20.18Octahedral10.3°16%0Ca, Na
B:3103NANa122.9 (19.6)O40.60.43Trigonal Bipyramidal10.6°20%0
B:3104NANa124.8 (23.8)O61.30.089Octahedral10°00
B:3105MGMg0.519.2 (25.1)O61.60.1Octahedral5.2°00Co, Cu
C:3001MGMg110.6 (9.9)O5N120.04Octahedral4.6°00
C:3002MGMg112.5 (12.5)O510.087Octahedral9.9°16%0Ca
C:3006MGMg121 (25.9)O62.10.053Octahedral3.5°00
C:3101NANa111.5 (13.1)O51.10.11Trigonal Bipyramidal12.2°00
C:3102NANa112.1 (15.1)O51.10.19Octahedral11.2°16%0Ca, Na
C:3103NANa124 (23.2)O50.90.14Octahedral16°16%0
C:3104NANa124.3 (24.7)O61.30.085Octahedral10.1°00
C:3105MGMg0.520 (23.3)O51.50.22Octahedral7.4°16%0Cu
D:3001MGMg110.7 (10.7)O5N120.029Octahedral4.6°00
D:3002MGMg114.7 (14.3)O510.078Octahedral9.9°16%0Ca
D:3005MGMg125.1 (29.2)O62.10.15Octahedral12°16%1
D:3101NANa112.3 (13.6)O51.10.12Trigonal Bipyramidal12.3°00
D:3102NANa112 (13.6)O51.10.19Octahedral13.2°16%0Ca, Na
D:3103NANa127.9 (21.9)O30.50.49Trigonal Bipyramidal6.2°40%0
D:3104NANa126.9 (24.3)O51.10.19Octahedral12.4°16%0Ca, Na
D:3105MGMg0.521.7 (25.3)O51.50.21Octahedral5.6°16%0Cu
Legend:
Not applicableOutlierBorderlineAcceptable

Column Description
Occupancy Occupancy of ion under consideration
B factor (env.)1 Metal ion B factor, with valence-weighted environmental average B factor in parenthesis
Ligands Elemental composition of the coordination sphere
Valence2 Summation of bond valence values for an ion binding site. Valence accounts for metal-ligand distances
nVECSUM3 Summation of ligand vectors, weighted by bond valence values and normalized by overall valence. Increase when the coordination sphere is not symmetrical due to incompleteness.
Geometry1,4 Arrangement of ligands around the ion, as defined by the NEIGHBORHOOD algorithm
gRMSD(°)1 R.M.S. Deviation of observed geometry angles (L-M-L angles) compared to ideal geometry, in degrees
Vacancy1 Percentage of unoccupied sites in the coordination sphere for the given geometry
Bidentate Number of residues that form a bidentate interaction instead of being considered as multiple ligands
Alt. metal A list of alternative metal(s) is proposed in descending order of confidency, assuming metal environment is accurately determined. This feature is still experimental. It requires user discrimination and cannot be blindly accepted

Metal-ligand distance distributions for 1jz7_final.pdb in comparison with CSD


(1) Zheng H, Chordia MD, Cooper DR, Chruszcz M, Müller P, Sheldrick GM, Minor W (2014) Nature Protocols, 9(1), 156-70.
(2) Brown ID (2009) Chem. Rev., 109, 6858-6919.
(3) Müller P, Köpke S, Sheldrick GM (2003) Acta Crystallogr. D Biol. Crystallogr., 59, 32-37.
(4) Kuppuraj G, Dudev M, Lim C (2009) J. Phys. Chem. B, 113, 2952-2960.
(5) CSD: Cambridge Structural Database
Maintained by: Heping Zheng <dust@iwonka.med.virginia.edu>
Citing CheckMyMetal (CMM):
Validation of metal-binding sites in macromolecular structures with the CheckMyMetal web server. Zheng,H., Chordia,M.D., Cooper,D.R., Chruszcz,M., Müller,P., Sheldrick,G.M., Minor,W. (2014) Nature Protocols, 9(1), 156-70.