Nickel in the structure of High Resolution Structure Of the Oxidized State of [Nife]Hydrogenase From Desulufovibrio Vulgaris Miyazaki F (pdb 1wuk)

The binding sites of Nickel atom in the structure of High Resolution Structure Of the Oxidized State of [Nife]Hydrogenase From Desulufovibrio Vulgaris Miyazaki F (pdb code 1wuk). This binding sites where shown with 5.0 Angstroms radius around Nickel atom. The 1wuk structure was solved by H.OGATA, S.HIROTA, A.NAKAHARA, H.KOMORI, N.SHIBATA, T.KATO, K.KANO, Y.HIGUCHI, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 20.0-1.1 Space group P212121 a (A) 98.291 b (A) 125.843 c (A) 66.440 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 9.6 Rfree (%) 12.3 Nickel Binding Sites: Nickel binding site 1 out of 1 in 1wuk Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Nickel in the PDB 1wuk. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Nickel atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: L: Cys81, L: Val83, L: Cys84, L: Arg479, L: Cso546, L: Cys549, L: Nfo1004, conact list: Atom Atom Distance (A) Ni CB L:Cys81 3.11 Ni SG L:Cys81 2.22 Ni CA L:Cys81 4.54 Ni CB L:Val83 4.59 Ni C L:Val83 4.81 Ni N L:Cys84 3.67 Ni CB L:Cys84 3.38 Ni SG L:Cys84 2.28 Ni C L:Cys84 4.88 Ni CA L:Cys84 4.08 Ni CD L:Arg479 4.70 Ni CZ L:Arg479 4.68 Ni NE L:Arg479 4.72 Ni NH1 L:Arg479 4.36 Ni CB L:Cso546 3.29 Ni SG L:Cso546 2.14 Ni OD L:Cso546 2.94 Ni CA L:Cso546 4.65 Ni N L:Cys549 4.73 Ni CB L:Cys549 3.63 Ni SG L:Cys549 2.54 Ni CA L:Cys549 4.69 Ni NI L:Nfo1004 0.00 Ni N2 L:Nfo1004 4.83 Ni C1 L:Nfo1004 3.74 Ni O1 L:Nfo1004 4.65 Ni C3 L:Nfo1004 4.19 Ni FE L:Nfo1004 2.67 Ni O4 L:Nfo1004 1.63 Ni C2 L:Nfo1004 3.87 interactive model: