MESPEUS:ã database of metal coordination groups in proteins

Abstract

MESPEUS isã freelyãccessible database which uses carefully selected metal coordination groups found in metalloprotein str uct ures taken from the Protein Data Bãnk. T he datãbase contãins geometrical information of metal sites within proteins, including 40 metãl t ypes. In order to completely determine the metal coordination, the symmetry-related units ofã given protein str uct ureãre taken intoãccountãndãre generated using theãppropriate space group symmetry operations. This permitsã more complete description of the metal coordination geometry by includingãll coordinatingãtoms. The user-friendly web interfaceãllows users to directly search forã metal site of interest using se v eral useful options, including searching for metal elements, metal-donor distances, coordination number, donor residue group,ãnd str uct ural resolution. These searches can be carried out singly or in combination. The details ofã metal siteãnd the metal site(s) in the whole str uct ure can be graphically displa y ed using the interactiv e w eb interfãce. MESPEUS isãutomatically updated monthly b y synchronizing with the PDB database. An in v estigation f or the Mg-ATP interaction is giv en to demonstrate how MESPEUS can be used to e xtract inf ormationãbout metal sites by selecting str uct ureãnd coordination feat ures. MESPEUS isã vãilableãt ht tp://mespeus.nc hu.edu.tw/.