title: Validation of metal-binding sites in macromolecular structures with the CheckMyMetal web server.
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.
authors.affiliation: 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.
authors.forename: Heping
authors.initials: H
authors.lastname: Zheng
authors.affiliation: 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.
authors.forename: Mahendra D
authors.initials: MD
authors.lastname: Chordia
authors.affiliation: 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.
authors.forename: David R
authors.initials: DR
authors.lastname: Cooper
authors.affiliation: 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.
authors.forename: Maksymilian
authors.initials: M
authors.lastname: Chruszcz
authors.affiliation: Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.
authors.forename: Peter
authors.initials: P
authors.lastname: Müller
authors.affiliation: Lehrstuhl für Strukturchemie, Universität Göttingen, Göttingen, Germany.
authors.forename: George M
authors.initials: GM
authors.lastname: Sheldrick
authors.affiliation: 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.
authors.forename: Wladek
authors.initials: W
authors.lastname: Minor
mesh_terms: D001665:Binding Sites; D019295:Computational Biology / Q000379:methods*; D018360:Crystallography, X-Ray; D030562:Databases, Protein; D020407:Internet; D008670:Metals / Q000737:chemistry*; D019906:Nuclear Magnetic Resonance, Biomolecular; D020539:Sequence Analysis, Protein; D012984:Software
chemical_list: D008670:Metals