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Nickel in PDB 5jsh: The 3D Structure of Recombinant [Nifese] Hydrogenase From Desulfovibrio Vulgaris Hildenborough in the Oxidized State at 1.30 Angstrom

Enzymatic activity of The 3D Structure of Recombinant [Nifese] Hydrogenase From Desulfovibrio Vulgaris Hildenborough in the Oxidized State at 1.30 Angstrom

All present enzymatic activity of The 3D Structure of Recombinant [Nifese] Hydrogenase From Desulfovibrio Vulgaris Hildenborough in the Oxidized State at 1.30 Angstrom:
1.12.7.2;

Protein crystallography data

The structure of The 3D Structure of Recombinant [Nifese] Hydrogenase From Desulfovibrio Vulgaris Hildenborough in the Oxidized State at 1.30 Angstrom, PDB code: 5jsh was solved by M.C.Marques, I.A.C.Pereira, P.M.Matias, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 51.82 / 1.30
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 106.220, 63.460, 111.080, 90.00, 105.15, 90.00
R / Rfree (%) 11.3 / 13.5

Other elements in 5jsh:

The structure of The 3D Structure of Recombinant [Nifese] Hydrogenase From Desulfovibrio Vulgaris Hildenborough in the Oxidized State at 1.30 Angstrom 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 Recombinant [Nifese] Hydrogenase From Desulfovibrio Vulgaris Hildenborough in the Oxidized State at 1.30 Angstrom (pdb code 5jsh). 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 Recombinant [Nifese] Hydrogenase From Desulfovibrio Vulgaris Hildenborough in the Oxidized State at 1.30 Angstrom, PDB code: 5jsh:

Nickel binding site 1 out of 1 in 5jsh

Go back to Nickel Binding Sites List in 5jsh
Nickel binding site 1 out of 1 in the The 3D Structure of Recombinant [Nifese] Hydrogenase From Desulfovibrio Vulgaris Hildenborough in the Oxidized State at 1.30 Angstrom


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 Recombinant [Nifese] Hydrogenase From Desulfovibrio Vulgaris Hildenborough in the Oxidized State at 1.30 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni602

b:14.7
occ:0.84
 S B:H2S604 2.0 16.3 1.0
SG B:CSD75 2.2 17.2 1.0
SG B:CYS492 2.2 11.2 1.0
SG B:CYS78 2.3 11.5 1.0
SE B:SEC489 2.3 13.4 0.5
SE B:SEC489 2.4 15.5 0.3
FE B:FCO601 2.4 12.9 1.0
HB3 B:SEC489 2.9 16.0 0.2
OD1 B:CSD75 2.9 18.0 0.6
OD2 B:CSD75 3.0 15.6 1.0
SE B:SEC489 3.1 14.9 0.2
CB B:CSD75 3.2 13.1 1.0
C1 B:FCO601 3.2 13.1 1.0
CB B:SEC489 3.3 13.4 0.2
HB2 B:CYS492 3.3 12.1 1.0
HB2 B:SEC489 3.4 16.0 0.2
HB3 B:CYS78 3.4 10.5 1.0
HB3 B:SEC489 3.4 15.3 0.3
C2 B:FCO601 3.4 9.7 1.0
HB2 B:SEC489 3.4 14.5 0.5
CB B:CYS492 3.4 10.1 1.0
CB B:SEC489 3.5 12.8 0.3
CB B:CYS78 3.5 8.8 1.0
H B:CYS78 3.6 11.0 1.0
CB B:SEC489 3.6 12.1 0.5
HB2 B:SEC489 3.8 15.3 0.3
H B:CYS492 3.8 10.4 1.0
HD2 B:ARG422 3.9 13.8 1.0
HB3 B:SEC489 4.0 14.5 0.5
HB B:VAL77 4.0 12.0 1.0
HB3 B:CYS492 4.1 12.1 1.0
N1 B:FCO601 4.1 13.7 1.0
C3 B:FCO601 4.1 15.9 1.0
N B:CYS78 4.1 9.2 1.0
HE2 B:HIS82 4.2 13.8 1.0
HB2 B:CYS78 4.2 10.5 1.0
N2 B:FCO601 4.4 9.4 1.0
CA B:CYS78 4.4 9.0 1.0
N B:CYS492 4.4 8.7 1.0
CA B:CYS492 4.5 8.9 1.0
HH11 B:ARG422 4.6 12.9 1.0
CA B:CSD75 4.6 10.2 1.0
HA B:CYS492 4.7 10.7 1.0
CD B:ARG422 4.7 11.5 1.0
HD3 B:ARG422 4.7 13.8 1.0
H B:VAL77 4.7 10.8 1.0
CA B:SEC489 4.8 11.8 0.2
CA B:SEC489 4.8 11.5 0.3
HD2 B:HIS82 4.9 12.4 1.0
CA B:SEC489 4.9 10.5 0.5
NE2 B:HIS82 4.9 11.5 1.0
O B:SEC489 4.9 11.3 0.5
CB B:VAL77 4.9 10.0 1.0
NH1 B:ARG422 5.0 10.8 1.0
O B:SEC489 5.0 11.3 0.3

Reference:

M.C.Marques, C.Tapia, O.Gutierrez-Sanz, A.R.Ramos, K.L.Keller, J.D.Wall, A.L.De Lacey, P.M.Matias, I.A.C.Pereira. The Direct Role of Selenocysteine in [Nifese] Hydrogenase Maturation and Catalysis. Nat. Chem. Biol. V. 13 544 2017.
ISSN: ESSN 1552-4469
PubMed: 28319099
DOI: 10.1038/NCHEMBIO.2335
Page generated: Wed Dec 16 01:41:22 2020

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