Nickel in PDB 6nw0: Crystal Structure Desulfovibrio Desulfuricans Nickel-Substituted Rubredoxin

The structure of Crystal Structure Desulfovibrio Desulfuricans Nickel-Substituted Rubredoxin, PDB code: 6nw0 was solved by J.W.Slater, S.C.Marguet, M.E.Gray, M.Sotomayor, H.S.Shafaat, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	32.53 / 1.85
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	53.290, 51.436, 39.697, 90.00, 128.00, 90.00
R / Rfree (%)	16.3 / 22.2

The binding sites of Nickel atom in the Crystal Structure Desulfovibrio Desulfuricans Nickel-Substituted Rubredoxin (pdb code 6nw0). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the Crystal Structure Desulfovibrio Desulfuricans Nickel-Substituted Rubredoxin, PDB code: 6nw0:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in the Crystal Structure Desulfovibrio Desulfuricans Nickel-Substituted Rubredoxin


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Crystal Structure Desulfovibrio Desulfuricans Nickel-Substituted Rubredoxin within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni101 b:12.3 occ:1.00 SG A:CYS9 2.2 12.0 1.0 SG A:CYS35 2.3 14.8 1.0 SG A:CYS32 2.3 11.3 1.0 SG A:CYS6 2.3 11.4 1.0 CB A:CYS6 3.1 12.6 1.0 CB A:CYS32 3.1 11.9 1.0 CB A:CYS9 3.3 12.5 1.0 CB A:CYS35 3.3 13.0 1.0 N A:CYS35 3.7 13.3 1.0 N A:CYS9 3.7 14.2 1.0 CA A:CYS9 4.0 13.1 1.0 CA A:CYS35 4.1 13.4 1.0 CG2 A:VAL37 4.2 12.2 1.0 CB A:TYR11 4.5 12.4 1.0 CB A:VAL8 4.5 16.1 1.0 CA A:CYS32 4.6 13.0 1.0 CA A:CYS6 4.6 13.2 1.0 CB A:VAL34 4.6 13.4 1.0 C A:CYS9 4.7 12.7 1.0 C A:CYS35 4.7 13.0 1.0 C A:VAL8 4.7 15.4 1.0 C A:VAL34 4.8 14.2 1.0 N A:GLY36 4.8 13.5 1.0 N A:TYR11 4.8 12.5 1.0 N A:GLY10 4.8 14.6 1.0 CZ A:PHE42 4.9 12.9 1.0

Nickel binding site 2 out of 2 in the Crystal Structure Desulfovibrio Desulfuricans Nickel-Substituted Rubredoxin


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Crystal Structure Desulfovibrio Desulfuricans Nickel-Substituted Rubredoxin within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni101 b:13.4 occ:1.00 SG B:CYS6 2.2 14.8 1.0 SG B:CYS35 2.3 13.2 1.0 SG B:CYS9 2.3 13.7 1.0 SG B:CYS32 2.3 12.6 1.0 CB B:CYS6 3.1 13.4 1.0 CB B:CYS32 3.1 11.8 1.0 CB B:CYS35 3.3 13.2 1.0 CB B:CYS9 3.4 11.4 1.0 N B:CYS9 3.6 11.1 1.0 N B:CYS35 3.7 12.7 1.0 CA B:CYS9 4.0 11.7 1.0 CA B:CYS35 4.1 13.8 1.0 CB B:TYR11 4.4 15.2 1.0 CG1 B:VAL37 4.4 11.8 1.0 CA B:CYS6 4.5 13.5 1.0 CB B:VAL8 4.5 12.6 1.0 CA B:CYS32 4.6 12.3 1.0 C B:CYS9 4.6 11.0 1.0 CB B:VAL34 4.6 13.3 1.0 C B:VAL8 4.7 12.8 1.0 N B:GLY10 4.7 12.6 1.0 N B:TYR11 4.8 14.4 1.0 CZ B:PHE42 4.8 13.9 1.0 C B:VAL34 4.8 12.9 1.0 C B:CYS35 4.8 13.3 1.0 N B:GLY36 4.9 14.2 1.0 CG1 B:VAL8 4.9 12.8 1.0 CA B:VAL8 5.0 12.9 1.0 N B:VAL8 5.0 12.6 1.0

J.W.Slater, S.C.Marguet, M.E.Gray, H.A.Monaco, M.Sotomayor, H.S.Shafaat. The Power of the Secondary Sphere: Modulating Hydrogenase Activity in Nickel-Substituted Rubredoxin Acs Catalysis 2019.
ISSN: ESSN 2155-5435
DOI: 10.1021/ACSCATAL.9B01720