Nickel in the structure of Structure Of A Double Methionine Mutant of Ni-Fe Hydrogenase (pdb 3cur)

The binding sites of Nickel atom in the structure of Structure Of A Double Methionine Mutant of Ni-Fe Hydrogenase (pdb code 3cur). This binding sites where shown with 5.0 Angstroms radius around Nickel atom. The 3cur structure was solved by A.VOLBEDA, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 25.0-2.4 Space group P1211 a (A) 64.600 b (A) 99.900 c (A) 183.000 alpha (°) 90.00 beta (°) 91.60 gamma (°) 90.00 Rfactor (%) 15 Rfree (%) 19.4 Nickel Binding Sites: Nickel binding site 1 out of 3 in 3cur Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Nickel in the PDB 3cur. 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: Glu25, H: Cys72, H: Met74, H: Cys75, H: Arg476, H: Cys543, H: Cys546, H: Fco550, H: Per552, conact list: Atom Atom Distance (A) Ni CG H:Glu25 4.94 Ni CB H:Cys72 2.89 Ni SG H:Cys72 2.25 Ni C H:Cys72 4.83 Ni CA H:Cys72 4.34 Ni N H:Met74 4.73 Ni CB H:Met74 4.46 Ni C H:Met74 4.61 Ni CA H:Met74 4.82 Ni O H:Cys75 4.90 Ni N H:Cys75 3.53 Ni CB H:Cys75 3.46 Ni SG H:Cys75 2.36 Ni C H:Cys75 4.80 Ni CA H:Cys75 4.07 Ni CD H:Arg476 4.83 Ni CZ H:Arg476 4.88 Ni NE H:Arg476 4.94 Ni NH1 H:Arg476 4.65 Ni CB H:Cys543 3.24 Ni CB H:Cys543 3.24 Ni SG H:Cys543 2.22 Ni SG H:Cys543 2.75 Ni CA H:Cys543 4.65 Ni N H:Cys546 4.64 Ni CB H:Cys546 3.62 Ni SG H:Cys546 2.56 Ni CA H:Cys546 4.62 Ni N1 H:Fco550 4.68 Ni C1 H:Fco550 3.80 Ni C3 H:Fco550 4.34 Ni FE H:Fco550 2.79 Ni C2 H:Fco550 4.09 Ni O1 H:Per552 1.89 Ni O2 H:Per552 2.14 interactive model: Nickel binding site 2 out of 3 in 3cur Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Nickel in the PDB 3cur. 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: Glu25, I: Cys72, I: Met74, I: Cys75, I: Arg476, I: Cys543, I: Cys546, I: Fco550, I: Per552, conact list: Atom Atom Distance (A) Ni CG I:Glu25 4.98 Ni CB I:Cys72 2.87 Ni SG I:Cys72 2.19 Ni C I:Cys72 4.83 Ni CA I:Cys72 4.33 Ni N I:Met74 4.79 Ni CB I:Met74 4.52 Ni C I:Met74 4.60 Ni CA I:Met74 4.86 Ni O I:Cys75 4.69 Ni N I:Cys75 3.49 Ni CB I:Cys75 3.34 Ni SG I:Cys75 2.31 Ni C I:Cys75 4.66 Ni CA I:Cys75 3.96 Ni CD I:Arg476 4.89 Ni CZ I:Arg476 4.96 Ni NH1 I:Arg476 4.73 Ni CB I:Cys543 3.44 Ni SG I:Cys543 2.11 Ni CA I:Cys543 4.79 Ni N I:Cys546 4.66 Ni CB I:Cys546 3.58 Ni SG I:Cys546 2.56 Ni CA I:Cys546 4.61 Ni N1 I:Fco550 4.72 Ni C1 I:Fco550 3.87 Ni C3 I:Fco550 4.31 Ni FE I:Fco550 2.80 Ni C2 I:Fco550 4.11 Ni O1 I:Per552 1.90 Ni O2 I:Per552 2.22 interactive model: Nickel binding site 3 out of 3 in 3cur Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Nickel in the PDB 3cur. 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: J: Glu25, J: Cys72, J: Met74, J: Cys75, J: Arg476, J: Cys543, J: Cys546, J: Fco550, J: Per552, conact list: Atom Atom Distance (A) Ni CG J:Glu25 4.94 Ni CB J:Cys72 2.96 Ni SG J:Cys72 2.21 Ni C J:Cys72 4.92 Ni CA J:Cys72 4.43 Ni N J:Met74 4.90 Ni CB J:Met74 4.50 Ni C J:Met74 4.68 Ni CA J:Met74 4.93 Ni O J:Cys75 4.88 Ni N J:Cys75 3.58 Ni CB J:Cys75 3.44 Ni SG J:Cys75 2.33 Ni C J:Cys75 4.81 Ni CA J:Cys75 4.07 Ni CD J:Arg476 4.80 Ni CZ J:Arg476 4.89 Ni NE J:Arg476 4.93 Ni NH1 J:Arg476 4.64 Ni CB J:Cys543 3.28 Ni CB J:Cys543 3.27 Ni SG J:Cys543 2.21 Ni SG J:Cys543 2.85 Ni CA J:Cys543 4.67 Ni N J:Cys546 4.57 Ni CB J:Cys546 3.56 Ni SG J:Cys546 2.60 Ni CA J:Cys546 4.56 Ni N1 J:Fco550 4.65 Ni C1 J:Fco550 3.75 Ni C3 J:Fco550 4.28 Ni FE J:Fco550 2.75 Ni C2 J:Fco550 4.00 Ni O1 J:Per552 1.90 Ni O2 J:Per552 2.12 interactive model: