MESPEUS: a database of the geometry of metal sites in proteins

K. Hsin, Y. Sheng, M. M. Harding, P. Taylor, M. D. Walkinshaw

Research output: Contribution to journalArticlepeer-review

Abstract

A database with details of the geometry of metal sites in proteins has been set up. The data are derived from metalloprotein structures that are in the Protein Data Bank [PDB; Berman, Henrick, Nakamura & Markley (2006). Nucleic Acids Res. 35, D301-D303] and have been determined at 2.5 angstrom resolution or better. The database contains all contacts within the crystal asymmetric unit considered to be chemical bonds to any of the metals Na, Mg, K, Ca, Mn, Fe, Co, Ni, Cu or Zn. The stored information includes PDB code, crystal data, resolution of structure determination, refinement program and R factor, protein class (from PDB header), contact distances, atom names of metal and interacting atoms as they appear in the PDB, site occupancies, B values, coordination numbers, information on coordination shapes, and metal-metal distances. This may be accessed by SQL queries, or by a user-friendly web interface which searches for contacts between specified types of atoms [for example Ca and carboxylate O of aspartate, Co and imidazole N delta of histidine] or which delivers details of all the metal sites in a specified protein. The web interface allows graphical display of the metal site, on its own or within the whole protein molecule, and may be accessed at http://eduliss.bch.ed.ac.uk/MESPEUS/. Some applications are briefly described, including a study of the characteristics of Mg sites that bind adenosine triphosphate, the derivation of an average Mg-O-phosphate distance and some problems that arise when average bond distances with high precision are required. (c) 2008 International Union of Crystallography Printed in Singapore - all rights reserved.

Original languageEnglish
Pages (from-to)963-968
Number of pages6
JournalJournal of Applied Crystallography
Volume41
Issue numberPart 5
DOIs
Publication statusPublished - Oct 2008

Keywords

  • metal-site geometry
  • metal-protein bonds
  • metal-protein interaction distances
  • metalloproteins
  • metal coordination

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