CheckMyMetal: A macromolecular metal-binding validation tool

Heping Zheng, David R. Cooper, Przemyslaw J. Porebski, Ivan G. Shabalin, Katarzyna B. Handing, Wladek Minor

Research output: Contribution to journalArticlepeer-review

221 Scopus citations

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.

Original languageEnglish
Pages (from-to)223-233
Number of pages11
JournalActa Crystallographica Section D: Structural Biology
Volume73
DOIs
StatePublished - 2017
Externally publishedYes

Keywords

  • CheckMyMetal
  • Coordination geometry
  • Metal-binding environment
  • Validation

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