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Nickel in PDB 6rtp: The 3D Structure of [Nifese] Hydrogenase G50T Variant From Desulfovibrio Vulgaris Hildenborough at 1.10 Angstrom Resolution

Enzymatic activity of The 3D Structure of [Nifese] Hydrogenase G50T Variant From Desulfovibrio Vulgaris Hildenborough at 1.10 Angstrom Resolution

All present enzymatic activity of The 3D Structure of [Nifese] Hydrogenase G50T Variant From Desulfovibrio Vulgaris Hildenborough at 1.10 Angstrom Resolution:
1.12.7.2;

Protein crystallography data

The structure of The 3D Structure of [Nifese] Hydrogenase G50T Variant From Desulfovibrio Vulgaris Hildenborough at 1.10 Angstrom Resolution, PDB code: 6rtp was solved by P.M.Matias, S.Zacarias, I.Pereita, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.38 / 1.10
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 106.138, 62.712, 110.240, 90.00, 105.11, 90.00
R / Rfree (%) 13.9 / 15.8

Other elements in 6rtp:

The structure of The 3D Structure of [Nifese] Hydrogenase G50T Variant From Desulfovibrio Vulgaris Hildenborough at 1.10 Angstrom Resolution also contains other interesting chemical elements:

Iron (Fe) 18 atoms
Chlorine (Cl) 1 atom

Nickel Binding Sites:

The binding sites of Nickel atom in the The 3D Structure of [Nifese] Hydrogenase G50T Variant From Desulfovibrio Vulgaris Hildenborough at 1.10 Angstrom Resolution (pdb code 6rtp). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total only one binding site of Nickel was determined in the The 3D Structure of [Nifese] Hydrogenase G50T Variant From Desulfovibrio Vulgaris Hildenborough at 1.10 Angstrom Resolution, PDB code: 6rtp:

Nickel binding site 1 out of 1 in 6rtp

Go back to Nickel Binding Sites List in 6rtp
Nickel binding site 1 out of 1 in the The 3D Structure of [Nifese] Hydrogenase G50T Variant From Desulfovibrio Vulgaris Hildenborough at 1.10 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of The 3D Structure of [Nifese] Hydrogenase G50T Variant From Desulfovibrio Vulgaris Hildenborough at 1.10 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni502

b:12.2
occ:0.67
 S B:H2S504 2.0 13.8 0.8
SG B:CYS492 2.2 10.9 1.0
SG B:CSD75 2.2 14.1 0.7
SG B:CYS78 2.3 12.4 1.0
FE B:FCO501 2.3 12.7 1.0
SE B:SEC489 2.4 10.3 0.5
SE B:SEC489 2.5 20.7 0.4
HB2 B:CSD75 3.0 14.8 1.0
CB B:CSD75 3.1 12.3 1.0
OD1 B:CSD75 3.1 12.3 0.7
OD2 B:CSD75 3.1 13.4 0.5
C1 B:FCO501 3.1 12.2 1.0
SE B:SEC489 3.2 15.2 0.2
CB B:SEC489 3.3 13.4 0.2
HB2 B:CYS492 3.3 11.4 1.0
HB3 B:CSD75 3.3 14.8 1.0
C2 B:FCO501 3.3 10.6 1.0
HB3 B:CYS78 3.4 11.8 1.0
CB B:CYS492 3.4 9.5 1.0
CB B:SEC489 3.5 16.6 0.4
CB B:CYS78 3.5 9.8 1.0
H B:CYS78 3.6 12.2 1.0
CB B:SEC489 3.6 10.0 0.5
H B:CYS492 3.8 11.5 1.0
HD2 B:ARG422 3.9 11.6 1.0
N1 B:FCO501 4.0 12.5 1.0
HB3 B:CYS492 4.0 11.4 1.0
C3 B:FCO501 4.0 14.2 1.0
HB B:VAL77 4.1 12.5 1.0
HE2 B:HIS82 4.1 11.9 1.0
N B:CYS78 4.2 10.1 1.0
HB2 B:CYS78 4.2 11.8 1.0
N2 B:FCO501 4.3 10.0 1.0
CA B:CYS78 4.4 9.4 1.0
N B:CYS492 4.4 9.6 1.0
CA B:CYS492 4.4 8.8 1.0
HH11 B:ARG422 4.5 12.5 1.0
CA B:CSD75 4.5 11.2 1.0
HA B:CYS492 4.6 10.6 1.0
CD B:ARG422 4.7 9.7 1.0
HD3 B:ARG422 4.7 11.6 1.0
CA B:SEC489 4.8 11.4 0.2
H B:VAL77 4.8 11.0 1.0
HD2 B:HIS82 4.8 11.6 1.0
CA B:SEC489 4.8 12.8 0.4
O B:SEC489 4.8 11.3 0.4
NE2 B:HIS82 4.8 9.9 1.0
O B:SEC489 4.9 10.3 0.5
HA B:CSD75 4.9 13.4 1.0
CA B:SEC489 4.9 9.0 0.5
NH1 B:ARG422 5.0 10.4 1.0
HG22 B:ILE74 5.0 11.2 1.0

Reference:

S.Zacarias, A.Temporao, M.Del Barrio, V.Fourmond, C.Leger, P.M.Matias, I.A.C.Pereira. A Hydrophilic Channel Is Involved in Oxidative Inactivation of A [Nifese] Hydrogenase Acs Catalysis 2019.
ISSN: ESSN 2155-5435
DOI: 10.1021/ACSCATAL.9B02347
Page generated: Mon Aug 18 21:30:24 2025

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