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Nat Protoc. 2014 Jan;9(1):156-70. doi: 10.1038/nprot.2013.172. Epub 2013 Dec 19.

Validation of metal-binding sites in macromolecular structures with the CheckMyMetal web server.

Author information

1
1] Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia, USA. [2] Center for Structural Genomics of Infectious Diseases (CSGID) Consortium, USA.
2
1] Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia, USA. [2] Center for Structural Genomics of Infectious Diseases (CSGID) Consortium, USA. [3] Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina, USA.
3
Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.
4
Lehrstuhl für Strukturchemie, Universität Göttingen, Göttingen, Germany.

Abstract

Metals have vital roles in both the mechanism and architecture of biological macromolecules. Yet structures of metal-containing macromolecules in which metals are misidentified and/or suboptimally modeled are abundant in the Protein Data Bank (PDB). This shows the need for a diagnostic tool to identify and correct such modeling problems with metal-binding environments. The CheckMyMetal (CMM) web server (http://csgid.org/csgid/metal_sites/) is a sophisticated, user-friendly web-based method to evaluate metal-binding sites in macromolecular structures using parameters derived from 7,350 metal-binding sites observed in a benchmark data set of 2,304 high-resolution crystal structures. The protocol outlines how the CMM server can be used to detect geometric and other irregularities in the structures of metal-binding sites, as well as how it can alert researchers to potential errors in metal assignment. The protocol also gives practical guidelines for correcting problematic sites by modifying the metal-binding environment and/or redefining metal identity in the PDB file. Several examples where this has led to meaningful results are described in the ANTICIPATED RESULTS section. CMM was designed for a broad audience--biomedical researchers studying metal-containing proteins and nucleic acids--but it is equally well suited for structural biologists validating new structures during modeling or refinement. The CMM server takes the coordinates of a metal-containing macromolecule structure in the PDB format as input and responds within a few seconds for a typical protein structure with 2-5 metal sites and a few hundred amino acids.

PMID:
24356774
PMCID:
PMC4410975
DOI:
10.1038/nprot.2013.172
[Indexed for MEDLINE]
Free PMC Article

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