Nickel in PDB 6nw1: Crystal Structure Desulfovibrio Desulfuricans Nickel-Substituted Rubredoxin V37N

The structure of Crystal Structure Desulfovibrio Desulfuricans Nickel-Substituted Rubredoxin V37N, PDB code: 6nw1 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)	26.81 / 1.86
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	23.718, 25.401, 29.084, 111.50, 94.43, 97.52
R / Rfree (%)	12.3 / 18.8

The binding sites of Nickel atom in the Crystal Structure Desulfovibrio Desulfuricans Nickel-Substituted Rubredoxin V37N (pdb code 6nw1). 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 V37N, PDB code: 6nw1:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in the Crystal Structure Desulfovibrio Desulfuricans Nickel-Substituted Rubredoxin V37N


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 V37N within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni101 b:2.6 occ:1.00 SG A:CYS32 2.3 2.2 1.0 SG A:CYS6 2.3 3.0 1.0 SG A:CYS9 2.3 3.1 1.0 SG A:CYS35 2.3 2.8 1.0 CB A:CYS32 3.1 2.4 1.0 CB A:CYS6 3.1 3.2 1.0 CB A:CYS9 3.2 3.1 1.0 CB A:CYS35 3.3 2.7 1.0 N A:CYS35 3.7 2.7 1.0 N A:CYS9 3.8 3.3 1.0 CA A:CYS9 4.0 3.2 1.0 CA A:CYS35 4.0 2.7 1.0 CB A:ASN37 4.3 3.5 1.0 CB A:TYR11 4.3 2.7 1.0 CA A:CYS32 4.5 2.5 1.0 CB A:VAL34 4.5 2.5 1.0 CA A:CYS6 4.5 3.3 1.0 C A:CYS9 4.7 3.1 1.0 C A:CYS35 4.7 2.8 1.0 N A:TYR11 4.7 2.8 1.0 N A:ASN37 4.7 3.3 1.0 C A:VAL34 4.8 2.6 1.0 CB A:VAL8 4.8 3.6 1.0 C A:VAL8 4.8 3.5 1.0 N A:GLY10 4.8 3.0 1.0 N A:GLY36 4.8 2.9 1.0 CZ A:PHE42 4.9 4.1 1.0 N A:VAL8 5.0 3.9 1.0

Nickel binding site 2 out of 2 in the Crystal Structure Desulfovibrio Desulfuricans Nickel-Substituted Rubredoxin V37N


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 V37N within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni101 b:1.9 occ:1.00 SG B:CYS9 2.3 2.8 1.0 SG B:CYS35 2.3 1.7 1.0 SG B:CYS32 2.3 2.1 1.0 SG B:CYS6 2.3 2.1 1.0 CB B:CYS32 3.0 2.3 1.0 CB B:CYS6 3.2 2.3 1.0 CB B:CYS9 3.3 2.7 1.0 CB B:CYS35 3.3 1.8 1.0 N B:CYS35 3.7 1.9 1.0 N B:CYS9 3.8 2.8 1.0 CA B:CYS9 4.0 2.7 1.0 CA B:CYS35 4.0 1.9 1.0 CB B:ASN37 4.3 2.2 1.0 CB B:TYR11 4.4 2.8 1.0 CA B:CYS32 4.5 2.4 1.0 CA B:CYS6 4.6 2.4 1.0 C B:CYS35 4.7 1.9 1.0 C B:CYS9 4.7 2.7 1.0 CB B:VAL34 4.7 2.0 1.0 N B:TYR11 4.7 2.8 1.0 N B:ASN37 4.7 2.2 1.0 N B:GLY36 4.7 2.0 1.0 N B:GLY10 4.8 2.7 1.0 CB B:VAL8 4.8 2.9 1.0 C B:VAL34 4.8 2.0 1.0 C B:VAL8 4.9 2.9 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