3o4p

DFPase at 0.85 Angstrom resolution (H atoms included)

spinqualitylabelsall models 3o4p, resolution 0.85Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 3o4p is a 1 chain structure with sequence from Loligo vulgaris. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Ligands: CA, DXE, EDO, GOL, ME2, MES, MXE, PEG, PGE Related: 1pjx Activity: Diisopropyl-fluorophosphatase, with EC number 3.1.8.2 Resources: FirstGlance, OCA, RCSB, PDBsum Function [DFPA_LOLVU] Biological function and substrate unknown. However, it is capable of acting on phosphorus anhydride bonds (such as phosphorus-halide and phosphorus-cyanide) in organophosphorus compounds (including nerve gases). Publication Abstract from PubMed BACKGROUND: Hydrogen atoms represent about half of the total number of atoms in proteins and are often involved in substrate recognition and catalysis. Unfortunately, X-ray protein crystallography at usual resolution fails to access directly their positioning, mainly because light atoms display weak contributions to diffraction. However, sub-Angstrom diffraction data, careful modeling and a proper refinement strategy can allow the positioning of a significant part of hydrogen atoms. RESULTS: A comprehensive study on the X-ray structure of the diisopropyl-fluorophosphatase (DFPase) was performed, and the hydrogen atoms were modeled, including those of solvent molecules. This model was compared to the available neutron structure of DFPase, and differences in the protein and the active site solvation were noticed. CONCLUSIONS: A further examination of the DFPase X-ray structure provides substantial evidence about the presence of an activated water molecule that may constitute an interesting piece of information as regard to the enzymatic hydrolysis mechanism. Hydrogen atoms in protein structures: high-resolution X-ray diffraction structure of the DFPase.,Elias M, Liebschner D, Koepke J, Lecomte C, Guillot B, Jelsch C, Chabriere E BMC Res Notes. 2013 Aug 2;6:308. doi: 10.1186/1756-0500-6-308. PMID:23915572 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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