Nickel in PDB 1yqw: Structure of the Oxidized Unready Form of Ni-Fe Hydrogenase

All present enzymatic activity of Structure of the Oxidized Unready Form of Ni-Fe Hydrogenase:
1.12.2.1;

The structure of Structure of the Oxidized Unready Form of Ni-Fe Hydrogenase, PDB code: 1yqw was solved by A.Volbeda, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 1.83
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	64.410, 99.700, 182.830, 90.00, 91.42, 90.00
R / Rfree (%)	14.6 / 18.5

The structure of Structure of the Oxidized Unready Form of Ni-Fe Hydrogenase also contains other interesting chemical elements:

Magnesium	(Mg)	3 atoms
Iron	(Fe)	39 atoms

The binding sites of Nickel atom in the Structure of the Oxidized Unready Form of Ni-Fe Hydrogenase (pdb code 1yqw). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 3 binding sites of Nickel where determined in the Structure of the Oxidized Unready Form of Ni-Fe Hydrogenase, PDB code: 1yqw:
Jump to Nickel binding site number: 1; 2; 3;

Nickel binding site 1 out of 3 in the Structure of the Oxidized Unready Form of Ni-Fe 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 Oxidized Unready Form of Ni-Fe Hydrogenase within 5.0Å range: probe atom residue distance (Å) B Occ Q:Ni551 b:15.0 occ:1.00 O Q:HOH564 1.8 12.2 0.3 O1 Q:PER552 1.9 14.9 1.0 O2 Q:PER552 2.1 15.9 0.7 SG Q:CYS72 2.2 11.4 1.0 SG Q:CYS543 2.3 13.9 0.7 SG Q:CYS546 2.5 11.3 1.0 SG Q:CYS75 2.5 12.0 1.0 CB Q:CYS72 2.9 9.5 1.0 FE Q:FCO550 2.9 10.2 1.0 SG Q:CYS543 3.2 13.2 0.3 CB Q:CYS543 3.3 8.8 1.0 CB Q:CYS546 3.5 9.1 1.0 CB Q:CYS75 3.6 11.0 1.0 N Q:CYS75 3.6 7.4 1.0 C1 Q:FCO550 3.9 8.1 1.0 CA Q:CYS75 4.2 10.3 1.0 C2 Q:FCO550 4.2 9.5 1.0 CA Q:CYS72 4.3 8.9 1.0 CB Q:VAL74 4.4 10.2 1.0 C3 Q:FCO550 4.4 7.4 1.0 CA Q:CYS546 4.5 10.2 1.0 N Q:CYS546 4.6 7.5 1.0 CA Q:CYS543 4.7 10.1 1.0 C Q:VAL74 4.7 8.0 1.0 N Q:VAL74 4.7 9.3 1.0 C Q:CYS72 4.8 10.3 1.0 NH1 Q:ARG476 4.8 13.8 1.0 N1 Q:FCO550 4.8 9.3 1.0 CD Q:ARG476 4.8 7.2 1.0 C Q:CYS75 4.9 9.5 1.0 CA Q:VAL74 4.9 8.3 1.0 CG Q:GLU25 4.9 10.2 1.0 O Q:CYS75 5.0 11.6 1.0 NE Q:ARG476 5.0 8.9 1.0

Nickel binding site 2 out of 3 in the Structure of the Oxidized Unready Form of Ni-Fe 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 Oxidized Unready Form of Ni-Fe Hydrogenase within 5.0Å range: probe atom residue distance (Å) B Occ R:Ni551 b:14.2 occ:1.00 O R:HOH557 1.9 9.4 0.5 O1 R:PER552 1.9 14.2 1.0 O2 R:PER552 2.1 16.3 0.5 SG R:CYS72 2.2 12.4 1.0 SG R:CYS543 2.3 12.9 0.7 SG R:CYS546 2.5 9.4 1.0 SG R:CYS75 2.5 12.0 1.0 SG R:CYS543 2.8 15.4 0.3 FE R:FCO550 2.8 9.7 1.0 CB R:CYS72 2.9 10.9 1.0 CB R:CYS543 3.2 8.1 1.0 CB R:CYS75 3.5 9.3 1.0 CB R:CYS546 3.6 9.1 1.0 N R:CYS75 3.6 8.9 1.0 C1 R:FCO550 3.9 5.5 1.0 C2 R:FCO550 4.1 7.2 1.0 CA R:CYS75 4.1 9.7 1.0 C3 R:FCO550 4.4 7.8 1.0 CA R:CYS72 4.4 11.3 1.0 CB R:VAL74 4.5 12.4 1.0 CA R:CYS546 4.5 9.3 1.0 N R:CYS546 4.6 10.5 1.0 NH1 R:ARG476 4.6 10.2 1.0 CA R:CYS543 4.7 8.9 1.0 C R:VAL74 4.7 9.2 1.0 CD R:ARG476 4.7 12.2 1.0 N1 R:FCO550 4.8 8.0 1.0 N R:VAL74 4.8 10.7 1.0 C R:CYS75 4.8 11.8 1.0 C R:CYS72 4.9 10.8 1.0 CA R:VAL74 4.9 8.5 1.0 CZ R:ARG476 4.9 12.1 1.0 NE R:ARG476 4.9 11.8 1.0 O R:CYS75 4.9 11.9 1.0

Nickel binding site 3 out of 3 in the Structure of the Oxidized Unready Form of Ni-Fe Hydrogenase


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Structure of the Oxidized Unready Form of Ni-Fe Hydrogenase within 5.0Å range: probe atom residue distance (Å) B Occ S:Ni551 b:15.1 occ:1.00 O S:HOH557 1.8 10.3 0.3 O1 S:PER552 1.9 12.1 1.0 O2 S:PER552 2.0 12.1 0.7 SG S:CYS72 2.1 16.2 1.0 SG S:CYS543 2.2 12.1 0.7 SG S:CYS75 2.5 12.7 1.0 SG S:CYS546 2.5 9.0 1.0 CB S:CYS72 2.9 10.0 1.0 FE S:FCO550 2.9 11.9 1.0 SG S:CYS543 3.1 11.5 0.3 CB S:CYS543 3.3 9.6 1.0 CB S:CYS546 3.5 10.3 1.0 CB S:CYS75 3.6 12.3 1.0 N S:CYS75 3.7 9.0 1.0 C1 S:FCO550 3.9 8.4 1.0 C2 S:FCO550 4.2 11.3 1.0 CA S:CYS75 4.2 10.1 1.0 CA S:CYS72 4.4 9.3 1.0 CA S:CYS546 4.4 9.9 1.0 C3 S:FCO550 4.5 13.0 1.0 N S:CYS546 4.5 10.5 1.0 CB S:VAL74 4.6 10.9 1.0 CA S:CYS543 4.7 8.6 1.0 C S:VAL74 4.8 9.0 1.0 N1 S:FCO550 4.8 9.5 1.0 C S:CYS72 4.8 9.4 1.0 CD S:ARG476 4.8 8.7 1.0 NH1 S:ARG476 4.8 18.3 1.0 C S:CYS75 4.9 12.8 1.0 N S:VAL74 4.9 10.3 1.0 O S:CYS75 4.9 13.3 1.0 CG S:GLU25 4.9 9.4 1.0 CA S:VAL74 5.0 9.9 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