Check My Metal
3D-viewer selection: (JSmol | Jmol)
Return format selection: (HTML | REFMAC | CSV | JSON | XML)

Input PDBID Test Data
 Low resolution adjustment

Upload your own coordinate file in PDB format Sample coordinates
PDB file:
Example files
(Download)

CMM has validated 40276 PDB structures and 84878 uploaded structures submitted by 5565 users from 52 countries since June, 2012

The CMM server is developed in Wladek Minor's lab.
Citing CheckMyMetal (CMM):
1. Characterizing metal-binding sites in proteins with X-ray crystallography. Handing KB, Niedzialkowska E, Shabalin IG, Kuhn ML, Zheng H, Minor W (2018) Nat Protocols, 13, 1062-1090

2. CheckMyMetal: a macromolecular metal-binding validation tool. Zheng,H., Cooper,D.R., Porebski,P.J., Shabalin,I.G., Handing,K.B., Minor,W. (2017) Acta crystallographica. Section D, Structural biology, 73, 223-233.

3. 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.
1Brown,I.D. (2009) Chem. Rev., 109, 6858-6919.
Recent developments in the methods and applications of the bond valence model.
2Müller,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?
3Harding,M.M. et al. (2010) Cryst. Rev., 16, 247-302.
Metals in protein structures: a review of their principal features.
4Kuppuraj,G. et al. (2009) J. Phys. Chem. B, 113, 2952-2960.
Factors governing metal-ligand distances and coordination geometries of metal complexes.
5Nayal,M. and Di Cera,E. (1996) J. Mol. Biol., 256, 228-234.
Valence screening of water in protein crystals reveals potential Na+ binding sites.
6Zheng,H. et al. (2008) J. Inorg. Biochem., 102, 1765-1776.
Data mining of metal ion environments present in protein structures.

Contact Us
Problem reportSee below ⇓
Bulletin boardUnder construction
Model requestEmails are usually answered within 3 business days


Question, feedback or bug report

Track previously submitted request by ticket #
CMM Home ⇑

  • Use the following form to ask a question, report bug or request new feature (question may go to server FAQ after answered):

    Firstname Lastname Affiliation
    Screenshot or attachment:

  • Maintained by: Heping Zheng <dust@iwonka.med.virginia.edu>