Nickel in the structure of Structure Of the Unready Oxidized Form of [Nife] Hydrogenase (pdb 1yq9)

The binding sites of Nickel atom in the structure of Structure Of the Unready Oxidized Form of [Nife] Hydrogenase (pdb code 1yq9). This binding sites where shown with 5.0 Angstroms radius around Nickel atom. The 1yq9 structure was solved by A.VOLBEDA, L.MARTIN, C.CAVAZZA, M.MATHO, B.W.FABER, W.ROSEBOOM, S.P.ALBRACHT, E.GARCIN, M.ROUSSET, J.C.FONTECILLA-CAMPS, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 13.0-2.4 Space group P1 a (A) 62.750 b (A) 93.440 c (A) 69.030 alpha (°) 89.33 beta (°) 102.41 gamma (°) 90.95 Rfactor (%) 13.2 Rfree (%) 18.3 Nickel Binding Sites: Nickel binding site 1 out of 2 in 1yq9 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Nickel in the PDB 1yq9. 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: H: Cys65, H: Val67, H: Cys68, H: Arg463, H: Cys530, H: Cys533, H: Fco537, H: Per539, conact list: Atom Atom Distance (A) Ni CB H:Cys65 2.98 Ni SG H:Cys65 2.17 Ni C H:Cys65 4.92 Ni CA H:Cys65 4.44 Ni N H:Val67 4.82 Ni CB H:Val67 4.42 Ni C H:Val67 4.70 Ni CA H:Val67 4.89 Ni N H:Cys68 3.65 Ni CB H:Cys68 3.66 Ni SG H:Cys68 2.52 Ni C H:Cys68 4.98 Ni CA H:Cys68 4.23 Ni CD H:Arg463 4.74 Ni CZ H:Arg463 4.99 Ni NE H:Arg463 4.94 Ni NH1 H:Arg463 4.75 Ni CB H:Cys530 3.33 Ni SG H:Cys530 2.23 Ni CA H:Cys530 4.75 Ni N H:Cys533 4.59 Ni CB H:Cys533 3.63 Ni SG H:Cys533 2.62 Ni CA H:Cys533 4.62 Ni N1 H:Fco537 4.85 Ni C1 H:Fco537 3.98 Ni C3 H:Fco537 4.51 Ni FE H:Fco537 2.97 Ni C2 H:Fco537 4.19 Ni O1 H:Per539 1.89 Ni O2 H:Per539 1.99 interactive model: Nickel binding site 2 out of 2 in 1yq9 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Nickel in the PDB 1yq9. 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: I: Cys65, I: Val67, I: Cys68, I: Arg463, I: Cys530, I: Cys533, I: Fco537, I: Per539, conact list: Atom Atom Distance (A) Ni CB I:Cys65 3.02 Ni SG I:Cys65 2.23 Ni C I:Cys65 4.88 Ni CA I:Cys65 4.48 Ni N I:Val67 4.76 Ni CB I:Val67 4.40 Ni C I:Val67 4.73 Ni CA I:Val67 4.88 Ni N I:Cys68 3.68 Ni CB I:Cys68 3.67 Ni SG I:Cys68 2.52 Ni C I:Cys68 4.96 Ni CA I:Cys68 4.25 Ni CD I:Arg463 4.83 Ni CZ I:Arg463 5.00 Ni NH1 I:Arg463 4.75 Ni CB I:Cys530 3.31 Ni SG I:Cys530 2.23 Ni CA I:Cys530 4.74 Ni N I:Cys533 4.64 Ni CB I:Cys533 3.69 Ni SG I:Cys533 2.67 Ni CA I:Cys533 4.67 Ni N1 I:Fco537 4.94 Ni C1 I:Fco537 4.02 Ni C3 I:Fco537 4.44 Ni FE I:Fco537 2.91 Ni C2 I:Fco537 4.15 Ni O1 I:Per539 1.89 Ni O2 I:Per539 2.22 interactive model: