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Acta Crystallogr D Struct Biol. 2017 Mar 1;73(Pt 3):223-233. doi: 10.1107/S2059798317001061. Epub 2017 Feb 22.

CheckMyMetal: a macromolecular metal-binding validation tool.

Author information

1
Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908, USA.

Abstract

Metals are essential in many biological processes, and metal ions are modeled in roughly 40% of the macromolecular structures in the Protein Data Bank (PDB). However, a significant fraction of these structures contain poorly modeled metal-binding sites. CheckMyMetal (CMM) is an easy-to-use metal-binding site validation server for macromolecules that is freely available at http://csgid.org/csgid/metal_sites. The CMM server can detect incorrect metal assignments as well as geometrical and other irregularities in the metal-binding sites. Guidelines for metal-site modeling and validation in macromolecules are illustrated by several practical examples grouped by the type of metal. These examples show CMM users (and crystallographers in general) problems they may encounter during the modeling of a specific metal ion.

KEYWORDS:

CheckMyMetal; coordination geometry; metal-binding environment; validation

PMID:
28291757
PMCID:
PMC5349434
DOI:
10.1107/S2059798317001061
[Indexed for MEDLINE]
Free PMC Article

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