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research article

Investigation of non-corrin cobalt(II)-containing sites in protein structures of the Protein Data Bank

Abriata, Luciano Andres
2013
Acta Crystallographica Section B-Structural Science

Protein X-ray structures with non-corrin cobalt(II)-containing sites, either natural or substituting another native ion, were downloaded from the Protein Data Bank and explored to (i) describe which amino acids are involved in their first ligand shells and (ii) analyze cobalt(II)donor bond lengths in comparison with previously reported target distances, CSD data and EXAFS data. The set of amino acids involved in CoII binding is similar to that observed for catalytic ZnII sites, i.e. with a large fraction of carboxylate O atoms from aspartate and glutamate and aromatic N atoms from histidine. The computed CoIIdonor bond lengths were found to depend strongly on structure resolution, an artifact previously detected for other metaldonor distances. Small corrections are suggested for the target bond lengths to the aromatic N atoms of histidines and the O atoms of water and hydroxide. The available target distance for cysteine (Scys) is confirmed; those for backbone O and other donors remain uncertain and should be handled with caution in refinement and modeling protocols. Finally, a relationship between both CoIIO bond lengths in bidentate carboxylates is quantified.

  • Details
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Type
research article
DOI
10.1107/S0108768113002954
Web of Science ID

WOS:000316741500009

Author(s)
Abriata, Luciano Andres
Date Issued

2013

Publisher

Wiley-Blackwell

Published in
Acta Crystallographica Section B-Structural Science
Volume

69

Start page

176

End page

183

Subjects

non-corrin cobalt(II) sites

•

proteins

•

Protein Data Bank

•

amino acids

•

CoIIdonor bond lengths

Editorial or Peer reviewed

REVIEWED

Written at

EPFL

EPFL units
IBI  
Available on Infoscience
May 13, 2013
Use this identifier to reference this record
https://infoscience.epfl.ch/handle/20.500.14299/92125
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