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Nickel in PDB 1frv: Crystal Structure of the Oxidized Form of Ni-Fe Hydrogenase

Enzymatic activity of Crystal Structure of the Oxidized Form of Ni-Fe Hydrogenase

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

Protein crystallography data

The structure of Crystal Structure of the Oxidized Form of Ni-Fe Hydrogenase, PDB code: 1frv was solved by A.Volbeda, M.Frey, J.C.Fontecilla-Camps, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 8.00 / 2.85
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 63.600, 93.900, 69.200, 89.80, 102.90, 90.80
R / Rfree (%) 17.8 / n/a

Nickel Binding Sites:

The binding sites of Nickel atom in the Crystal Structure of the Oxidized Form of Ni-Fe Hydrogenase (pdb code 1frv). 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 of the Oxidized Form of Ni-Fe Hydrogenase, PDB code: 1frv:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in 1frv

Go back to Nickel Binding Sites List in 1frv
Nickel binding site 1 out of 2 in the Crystal Structure of the Oxidized 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 Crystal Structure of the Oxidized Form of Ni-Fe Hydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni538

b:25.3
occ:1.00
SG B:CYS65 2.0 14.6 1.0
SG B:CYS68 2.2 17.9 1.0
SG B:CYS530 2.4 27.0 1.0
SG B:CYS533 2.6 16.4 1.0
FE B:FEL537 2.7 12.8 1.0
CB B:CYS68 3.2 11.3 1.0
CG2 B:VAL67 3.3 8.9 1.0
CB B:CYS530 3.7 18.1 1.0
CB B:CYS65 3.7 7.6 1.0
N B:CYS68 3.7 6.9 1.0
O2 B:FEL537 3.8 5.2 1.0
CA B:CYS68 4.0 7.5 1.0
O1 B:FEL537 4.1 13.1 1.0
CB B:CYS533 4.1 13.8 1.0
O3 B:FEL537 4.4 11.5 1.0
NH1 B:ARG463 4.7 4.4 1.0
O B:CYS68 4.7 8.3 1.0
CB B:VAL67 4.7 7.3 1.0
C B:CYS68 4.8 7.3 1.0
CA B:CYS65 4.8 4.9 1.0
N B:VAL67 4.9 3.7 1.0
C B:VAL67 4.9 6.9 1.0
CZ B:ARG463 4.9 5.3 1.0
CA B:CYS530 4.9 13.2 1.0

Nickel binding site 2 out of 2 in 1frv

Go back to Nickel Binding Sites List in 1frv
Nickel binding site 2 out of 2 in the Crystal Structure of the Oxidized 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 Crystal Structure of the Oxidized Form of Ni-Fe Hydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ni538

b:27.6
occ:1.00
SG D:CYS68 2.4 16.6 1.0
SG D:CYS530 2.5 23.9 1.0
SG D:CYS533 2.5 12.0 1.0
SG D:CYS65 2.5 21.2 1.0
FE D:FEL537 2.6 12.0 1.0
CB D:CYS68 3.3 12.2 1.0
CB D:CYS530 3.4 17.1 1.0
N D:CYS68 3.6 9.2 1.0
CB D:CYS65 3.6 13.8 1.0
O1 D:FEL537 3.8 13.9 1.0
O2 D:FEL537 3.9 17.3 1.0
CA D:CYS68 4.0 10.1 1.0
CB D:CYS533 4.1 11.1 1.0
C D:VAL67 4.6 9.1 1.0
CG2 D:VAL67 4.6 9.0 1.0
N D:VAL67 4.6 8.1 1.0
O3 D:FEL537 4.7 17.2 1.0
CA D:CYS530 4.8 14.6 1.0
NE D:ARG463 4.8 6.4 1.0
CD D:ARG463 4.8 7.7 1.0
CA D:VAL67 4.9 8.6 1.0
CA D:CYS65 4.9 9.1 1.0
CG D:GLU18 4.9 13.1 1.0
N D:CYS533 4.9 9.8 1.0
C D:CYS68 4.9 10.4 1.0
CG1 D:VAL67 5.0 9.7 1.0
CB D:VAL67 5.0 8.9 1.0
CZ D:ARG463 5.0 5.5 1.0
CA D:CYS533 5.0 10.7 1.0

Reference:

A.Volbeda, M.H.Charon, C.Piras, E.C.Hatchikian, M.Frey, J.C.Fontecilla-Camps. Crystal Structure of the Nickel-Iron Hydrogenase From Desulfovibrio Gigas. Nature V. 373 580 1995.
ISSN: ISSN 0028-0836
PubMed: 7854413
DOI: 10.1038/373580A0
Page generated: Fri Sep 25 07:52:41 2020
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