title: CheckMyMetal: a macromolecular metal-binding validation tool.
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.
authors.affiliation: Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908, USA.
authors.forename: Heping
authors.initials: H
authors.lastname: Zheng
authors.affiliation: Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908, USA.
authors.forename: David R
authors.initials: DR
authors.lastname: Cooper
authors.affiliation: Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908, USA.
authors.forename: Przemyslaw J
authors.initials: PJ
authors.lastname: Porebski
authors.affiliation: Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908, USA.
authors.forename: Ivan G
authors.initials: IG
authors.lastname: Shabalin
authors.affiliation: Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908, USA.
authors.forename: Katarzyna B
authors.initials: KB
authors.lastname: Handing
authors.affiliation: Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908, USA.
authors.forename: Wladek
authors.initials: W
authors.lastname: Minor
mesh_terms: D001665:Binding Sites; D018360:Crystallography, X-Ray; D030562:Databases, Protein; D008274:Magnesium / Q000378:metabolism; D008670:Metals / Q000378:metabolism*; D008958:Models, Molecular; D011506:Proteins / Q000737:chemistry / Q000378:metabolism*; D012964:Sodium / Q000378:metabolism; D012984:Software
chemical_list: D008670:Metals; D011506:Proteins; D012964:Sodium; D008274:Magnesium
keywords: CheckMyMetal; coordination geometry; metal-binding environment; validation