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 |
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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:
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