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

Enzymatic activity of 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;

Protein crystallography data

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

Other elements in 1yq9:

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

Nickel Binding Sites:

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 1yq9

Go back to Nickel Binding Sites List in 1yq9
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 1yq9

Go back to Nickel Binding Sites List in 1yq9
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

Reference:

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
Page generated: Thu Oct 29 06:16:22 2020
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