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Open AccessArticle

Finding High-Quality Metal Ion-Centric Regions Across the Worldwide Protein Data Bank

by Sen Yao 1,2,3 and Hunter N.B. Moseley 1,2,3,4,5,*
1
Department of Molecular & Cellular Biochemistry, University of Kentucky, Lexington, KY 40536, USA
2
Markey Cancer Center, University of Kentucky, Lexington, KY 40536, USA
3
Resource Center for Stable Isotope Resolved Metabolomics, University of Kentucky, Lexington, KY 40536, USA
4
Institute for Biomedical Informatics, University of Kentucky, Lexington, KY 40536, USA
5
Center for Clinical and Translational Science, University of Kentucky, Lexington, KY 40536, USA
*
Author to whom correspondence should be addressed.
Academic Editors: Eugene A. Permyakov and Sergey Permyakov
Molecules 2019, 24(17), 3179; https://doi.org/10.3390/molecules24173179
Received: 8 August 2019 / Revised: 27 August 2019 / Accepted: 30 August 2019 / Published: 1 September 2019
(This article belongs to the Special Issue Metalloproteins)
As the number of macromolecular structures in the worldwide Protein Data Bank (wwPDB) continues to grow rapidly, more attention is being paid to the quality of its data, especially for use in aggregated structural and dynamics analyses. In this study, we systematically analyzed 3.5 Å regions around all metal ions across all PDB entries with supporting electron density maps available from the PDB in Europe. All resulting metal ion-centric regions were evaluated with respect to four quality-control criteria involving electron density resolution, atom occupancy, symmetry atom exclusion, and regional electron density discrepancy. The resulting list of metal binding sites passing all four criteria possess high regional structural quality and should be beneficial to a wide variety of downstream analyses. This study demonstrates an approach for the pan-PDB evaluation of metal binding site structural quality with respect to underlying X-ray crystallographic experimental data represented in the available electron density maps of proteins. For non-crystallographers in particular, we hope to change the focus and discussion of structural quality from a global evaluation to a regional evaluation, since all structural entries in the wwPDB appear to have both regions of high and low structural quality. View Full-Text
Keywords: metalloprotein; electron density analysis; pdb-eda; metal binding site; regional protein structure analysis metalloprotein; electron density analysis; pdb-eda; metal binding site; regional protein structure analysis
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Yao, S.; Moseley, H.N. Finding High-Quality Metal Ion-Centric Regions Across the Worldwide Protein Data Bank. Molecules 2019, 24, 3179.

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