Nickel in PDB 1yq9: Structure of the Unready Oxidized Form of [Nife] Hydrogenase

All present enzymatic activity of Structure of the Unready Oxidized Form of [Nife] Hydrogenase:
1.12.2.1;

The structure of Structure of the Unready Oxidized Form of [Nife] Hydrogenase, PDB code: 1yq9 was solved by A.Volbeda, L.Martin, C.Cavazza, M.Matho, B.W.Faber, W.Roseboom, S.P.Albracht, E.Garcin, M.Rousset, J.C.Fontecilla-Camps, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	13.00 / 2.35
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	62.750, 93.440, 69.030, 89.33, 102.41, 90.95
R / Rfree (%)	13.2 / 18.3

The structure of Structure of the Unready Oxidized Form of [Nife] Hydrogenase also contains other interesting chemical elements:

Magnesium	(Mg)	2 atoms
Iron	(Fe)	24 atoms

The binding sites of Nickel atom in the Structure of the Unready Oxidized Form of [Nife] Hydrogenase (pdb code 1yq9). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the Structure of the Unready Oxidized Form of [Nife] Hydrogenase, PDB code: 1yq9:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in the Structure of the Unready Oxidized Form of [Nife] Hydrogenase


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Structure of the Unready Oxidized Form of [Nife] Hydrogenase within 5.0Å range: probe atom residue distance (Å) B Occ H:Ni538 b:17.1 occ:1.00 O1 H:PER539 1.9 18.7 1.0 O2 H:PER539 2.0 24.3 0.7 SG H:CYS65 2.2 17.5 1.0 SG H:CYS530 2.2 17.9 1.0 SG H:CYS68 2.5 10.4 1.0 SG H:CYS533 2.6 12.3 1.0 FE H:FCO537 3.0 11.1 1.0 CB H:CYS65 3.0 13.1 1.0 CB H:CYS530 3.3 13.9 1.0 CB H:CYS533 3.6 12.7 1.0 N H:CYS68 3.6 13.9 1.0 CB H:CYS68 3.7 14.5 1.0 C1 H:FCO537 4.0 12.5 1.0 C2 H:FCO537 4.2 11.5 1.0 CA H:CYS68 4.2 14.1 1.0 CB H:VAL67 4.4 11.1 1.0 CA H:CYS65 4.4 12.6 1.0 C3 H:FCO537 4.5 13.5 1.0 N H:CYS533 4.6 10.9 1.0 CA H:CYS533 4.6 12.5 1.0 C H:VAL67 4.7 13.5 1.0 CD H:ARG463 4.7 12.5 1.0 NH1 H:ARG463 4.8 14.1 1.0 CA H:CYS530 4.8 13.5 1.0 N H:VAL67 4.8 11.5 1.0 N1 H:FCO537 4.8 13.0 1.0 CA H:VAL67 4.9 11.2 1.0 C H:CYS65 4.9 12.7 1.0 NE H:ARG463 4.9 13.6 1.0 C H:CYS68 5.0 15.4 1.0 CZ H:ARG463 5.0 13.4 1.0

Nickel binding site 2 out of 2 in the Structure of the Unready Oxidized Form of [Nife] Hydrogenase


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Structure of the Unready Oxidized Form of [Nife] Hydrogenase within 5.0Å range: probe atom residue distance (Å) B Occ I:Ni538 b:16.4 occ:1.00 O1 I:PER539 1.9 18.8 1.0 O2 I:PER539 2.2 24.0 0.7 SG I:CYS530 2.2 19.3 1.0 SG I:CYS65 2.2 17.1 1.0 SG I:CYS68 2.5 12.1 1.0 SG I:CYS533 2.7 11.8 1.0 FE I:FCO537 2.9 11.7 1.0 CB I:CYS65 3.0 13.9 1.0 CB I:CYS530 3.3 13.8 1.0 CB I:CYS68 3.7 14.5 1.0 N I:CYS68 3.7 13.6 1.0 CB I:CYS533 3.7 12.9 1.0 C1 I:FCO537 4.0 11.9 1.0 C2 I:FCO537 4.1 12.7 1.0 CA I:CYS68 4.3 13.4 1.0 CB I:VAL67 4.4 11.4 1.0 C3 I:FCO537 4.4 13.7 1.0 CA I:CYS65 4.5 13.1 1.0 N I:CYS533 4.6 11.3 1.0 CA I:CYS533 4.7 12.5 1.0 C I:VAL67 4.7 13.0 1.0 CA I:CYS530 4.7 13.8 1.0 NH1 I:ARG463 4.8 14.9 1.0 N I:VAL67 4.8 12.4 1.0 CD I:ARG463 4.8 11.4 1.0 CA I:VAL67 4.9 11.2 1.0 C I:CYS65 4.9 13.2 1.0 N1 I:FCO537 4.9 12.7 1.0 C I:CYS68 5.0 15.8 1.0 CZ I:ARG463 5.0 14.1 1.0

A.Volbeda, L.Martin, C.Cavazza, M.Matho, B.W.Faber, W.Roseboom, S.P.Albracht, E.Garcin, M.Rousset, J.C.Fontecilla-Camps. Structural Differences Between the Ready and Unready Oxidized States of [Nife] Hydrogenases. J.Biol.Inorg.Chem. V. 10 239 2005.
ISSN: ISSN 0949-8257
PubMed: 15803334
DOI: 10.1007/S00775-005-0632-X