Center for Structural Genomics of Infectious Diseases
CheckMyMetal (CMM): Metal Binding Site Validation Server
Upload your own coordinate file in PDB format Sample coordinates
The CMM server is developed in Wladek Minor's lab.
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.
The service is based on several well-established concepts reported previously: bond valence (1), VECSUM (2), metal binding sites (3), coordination geometries (4), assignment of sodium versus water (5), metal binding environment (6) in protein structures. We thankfully acknowledge their important contributions. The list presented here may not be complete and suggestion for any additional references are appreicated.
1 Brown,I.D. (2009) Chem. Rev., 109, 6858-6919.
Recent developments in the methods and applications of the bond valence model.
2 Müller,P. et al. (2003) Acta Crystallogr. D Biol. Crystallogr., 59, 32-37.
Is the bond-valence method able to identify metal atoms in protein structures?
3 Harding,M.M. et al. (2010) Cryst. Rev., 16, 247-302.
Metals in protein structures: a review of their principal features.
4 Kuppuraj,G. et al. (2009) J. Phys. Chem. B, 113, 2952-2960.
Factors governing metal-ligand distances and coordination geometries of metal complexes.
5 Nayal,M. and Di Cera,E. (1996) J. Mol. Biol., 256, 228-234.
Valence screening of water in protein crystals reveals potential Na+ binding sites.
6 Zheng,H. et al. (2008) J. Inorg. Biochem., 102, 1765-1776.
Data mining of metal ion environments present in protein structures.
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