title: Data mining of iron(II) and iron(III) bond-valence parameters, and their relevance for macromolecular crystallography.
abstract: The bond-valence model is a reliable way to validate assumed oxidation states based on structural data. It has successfully been employed for analyzing metal-binding sites in macromolecule structures. However, inconsistent results for heme-based structures suggest that some widely used bond-valence R0parameters may need to be adjusted in certain cases. Given the large number of experimental crystal structures gathered since these initial parameters were determined and the similarity of binding sites in organic compounds and macromolecules, the Cambridge Structural Database (CSD) is a valuable resource for refining metal-organic bond-valence parameters. R0bond-valence parameters for iron(II), iron(III) and other metals have been optimized based on an automated processing of all CSD crystal structures. Almost all R0bond-valence parameters were reproduced, except for iron-nitrogen bonds, for which distinct R0parameters were defined for two observed subpopulations, corresponding to low-spin and high-spin states, of iron in both oxidation states. The significance of this data-driven method for parameter discovery, and how the spin state affects the interpretation of heme-containing proteins and iron-binding sites in macromolecular structures, are discussed.
authors.affiliation: Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22901, USA.
authors.forename: Heping
authors.initials: H
authors.lastname: Zheng
authors.affiliation: Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22901, USA.
authors.forename: Karol M
authors.initials: KM
authors.lastname: Langner
authors.affiliation: Cambridge Crystallographic Data Centre, 12 Union Road, Cambridge CB2 1EZ, England.
authors.forename: Gregory P
authors.initials: GP
authors.lastname: Shields
authors.affiliation: Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22901, USA.
authors.forename: Jing
authors.initials: J
authors.lastname: Hou
authors.affiliation: Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22901, USA.
authors.forename: Marcin
authors.initials: M
authors.lastname: Kowiel
authors.affiliation: Cambridge Crystallographic Data Centre, 12 Union Road, Cambridge CB2 1EZ, England.
authors.forename: Frank H
authors.initials: FH
authors.lastname: Allen
authors.affiliation: MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, England.
authors.forename: Garib
authors.initials: G
authors.lastname: Murshudov
authors.affiliation: Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22901, USA.
authors.forename: Wladek
authors.initials: W
authors.lastname: Minor
mesh_terms: D018360:Crystallography, X-Ray; D057225:Data Mining; D005290:Ferric Compounds / Q000737:chemistry*; D005296:Ferrous Compounds / Q000737:chemistry*; D006418:Heme / Q000737:chemistry*; D006454:Hemoglobins / Q000737:chemistry*; D006801:Humans; D008958:Models, Molecular; D010084:Oxidation-Reduction
chemical_list: D005290:Ferric Compounds; D005296:Ferrous Compounds; D006454:Hemoglobins; D006418:Heme
keywords: Cambridge Structural Database; bond-valence model; metal–organics; nonlinear conjugate gradients; oxidation state