Nickel in the structure of Crystal Structure of Nisod D3A Mutant At 1.9 A (pdb 3g50)

The binding sites of Nickel atom in the structure of Crystal Structure of Nisod D3A Mutant At 1.9 A (pdb code 3g50). This binding sites where shown with 5.0 Angstroms radius around Nickel atom. The 3g50 structure was solved by S.C.GARMAN, A.I.GUCE, R.W.HERBST, P.A.BRYNGELSON, D.E.CABELLI, K.A.HIGGINS, K.C.RYAN, M.J.MARONEY, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 21.6-1.9 Space group C2221 a (A) 59.988 b (A) 112.274 c (A) 111.695 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 18.6 Rfree (%) 24 Nickel Binding Sites: Nickel binding site 1 out of 2 in 3g50 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Nickel in the PDB 3g50. 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: A: His1, A: Cys2, A: Ala3, A: Cys6, A: Gly7, A: Val8, A: Tyr9, A: Hoh128, conact list: Atom Atom Distance (A) Ni O A:His1 4.26 Ni N A:His1 2.33 Ni CB A:His1 4.29 Ni ND1 A:His1 3.80 Ni CD2 A:His1 4.91 Ni C A:His1 3.18 Ni CE1 A:His1 4.44 Ni CG A:His1 4.13 Ni CA A:His1 3.27 Ni N A:Cys2 2.46 Ni CB A:Cys2 3.01 Ni SG A:Cys2 2.37 Ni C A:Cys2 3.99 Ni CA A:Cys2 3.22 Ni N A:Ala3 3.90 Ni N A:Cys6 4.07 Ni CB A:Cys6 3.57 Ni SG A:Cys6 2.47 Ni C A:Cys6 4.85 Ni CA A:Cys6 4.34 Ni N A:Gly7 4.74 Ni O A:Val8 4.57 Ni N A:Val8 4.78 Ni CE2 A:Tyr9 4.89 Ni CZ A:Tyr9 4.48 Ni CE1 A:Tyr9 4.92 Ni OH A:Tyr9 4.24 Ni O A:Hoh128 3.79 interactive model: Nickel binding site 2 out of 2 in 3g50 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Nickel in the PDB 3g50. 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: C: His1, C: Cys2, C: Ala3, C: Cys6, C: Gly7, C: Val8, C: Tyr9, conact list: Atom Atom Distance (A) Ni O C:His1 4.40 Ni N C:His1 2.14 Ni CB C:His1 4.45 Ni CD2 C:His1 4.54 Ni C C:His1 3.38 Ni CG C:His1 4.55 Ni CA C:His1 3.23 Ni O C:Cys2 4.87 Ni N C:Cys2 3.00 Ni CB C:Cys2 4.10 Ni SG C:Cys2 3.08 Ni C C:Cys2 4.19 Ni CA C:Cys2 3.90 Ni N C:Ala3 4.23 Ni N C:Cys6 4.37 Ni CB C:Cys6 3.47 Ni SG C:Cys6 2.81 Ni C C:Cys6 4.87 Ni CA C:Cys6 4.39 Ni N C:Gly7 4.70 Ni O C:Val8 4.45 Ni N C:Val8 4.81 Ni CE2 C:Tyr9 4.74 Ni CZ C:Tyr9 4.33 Ni CE1 C:Tyr9 4.81 Ni OH C:Tyr9 4.02 interactive model: