Cobalt in the structure of Crystal Structure Analysis of Oxidoreductase (pdb 2ehd)

The binding sites of Cobalt atom in the structure of Crystal Structure Analysis of Oxidoreductase (pdb code 2ehd). This binding sites where shown with 5.0 Angstroms radius around Cobalt atom. The 2ehd structure was solved by N.KAMIYA, T.HIKIMA, A.EBIHARA, Y.INOUE, RIKEN STRUCTURALGENOMICS/PROTEOMICS INITIATIVE (RSGI), with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 50.0-2.4 Space group P41212 a (A) 104.020 b (A) 104.020 c (A) 105.930 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 22.6 Rfree (%) 25.5 Cobalt Binding Sites: Cobalt binding site 1 out of 2 in 2ehd Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Cobalt in the PDB 2ehd. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Cobalt atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: Gly12, A: Ala13, A: Ser14, A: Arg15, A: Ala36, A: Arg37, A: Asp38, A: Hoh1007, A: Hoh1016, conact list: Atom Atom Distance (A) Co O A:Gly12 4.35 Co N A:Gly12 4.65 Co C A:Gly12 3.99 Co CA A:Gly12 3.63 Co N A:Ala13 4.48 Co N A:Ser14 4.19 Co CB A:Ser14 4.02 Co OG A:Ser14 3.04 Co CA A:Ser14 4.62 Co N A:Arg15 4.82 Co CD A:Arg15 4.70 Co CZ A:Arg15 4.30 Co CG A:Arg15 4.36 Co NE A:Arg15 4.07 Co NH2 A:Arg15 4.33 Co C A:Ala36 4.71 Co CB A:Ala36 3.86 Co CA A:Ala36 4.27 Co N A:Arg37 4.09 Co N A:Asp38 4.56 Co CB A:Asp38 4.81 Co O A:Hoh1007 4.95 Co O A:Hoh1016 3.33 interactive model: Cobalt binding site 2 out of 2 in 2ehd Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Cobalt in the PDB 2ehd. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Cobalt atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: B: Ser14, B: Arg15, B: Ala36, B: Arg37, B: Asp38, conact list: Atom Atom Distance (A) Co CB B:Ser14 4.74 Co OG B:Ser14 3.62 Co NE B:Arg15 4.83 Co C B:Ala36 4.56 Co CB B:Ala36 4.11 Co CA B:Ala36 4.67 Co N B:Arg37 3.59 Co CB B:Arg37 4.04 Co C B:Arg37 4.33 Co CG B:Arg37 4.79 Co CA B:Arg37 4.15 Co N B:Asp38 3.52 Co CB B:Asp38 3.95 Co CA B:Asp38 4.37 interactive model: