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Acta Crystallogr D Struct Biol. 2017 Apr 1;73(Pt 4):316-325. doi: 10.1107/S2059798317000584. Epub 2017 Mar 31.

Data mining of iron(II) and iron(III) bond-valence parameters, and their relevance for macromolecular crystallography.

Author information

1
Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22901, USA.
2
Cambridge Crystallographic Data Centre, 12 Union Road, Cambridge CB2 1EZ, England.
3
MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, England.

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 R0 parameters 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. R0 bond-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 R0 bond-valence parameters were reproduced, except for iron-nitrogen bonds, for which distinct R0 parameters 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.

KEYWORDS:

Cambridge Structural Database; bond-valence model; metal–organics; nonlinear conjugate gradients; oxidation state

PMID:
28375143
PMCID:
PMC5503122
DOI:
10.1107/S2059798317000584
[Indexed for MEDLINE]
Free PMC Article

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