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Nickel in PDB 6z8j: Structure of [Nifese] Hydrogenase From Desulfovibrio Vulgaris Hildenborough Pressurized with Oxygen Gas - Structure WTO2

Enzymatic activity of Structure of [Nifese] Hydrogenase From Desulfovibrio Vulgaris Hildenborough Pressurized with Oxygen Gas - Structure WTO2

All present enzymatic activity of Structure of [Nifese] Hydrogenase From Desulfovibrio Vulgaris Hildenborough Pressurized with Oxygen Gas - Structure WTO2:
1.12.7.2;

Protein crystallography data

The structure of Structure of [Nifese] Hydrogenase From Desulfovibrio Vulgaris Hildenborough Pressurized with Oxygen Gas - Structure WTO2, PDB code: 6z8j was solved by S.Zacarias, A.Temporao, P.Carpentier, P.Van Der Linden, 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) 42.41 / 1.09
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 74.864, 93.988, 98.612, 90.00, 93.16, 90.00
R / Rfree (%) 14 / 16.4

Other elements in 6z8j:

The structure of Structure of [Nifese] Hydrogenase From Desulfovibrio Vulgaris Hildenborough Pressurized with Oxygen Gas - Structure WTO2 also contains other interesting chemical elements:

Iron (Fe) 36 atoms
Chlorine (Cl) 2 atoms

Nickel Binding Sites:

The binding sites of Nickel atom in the Structure of [Nifese] Hydrogenase From Desulfovibrio Vulgaris Hildenborough Pressurized with Oxygen Gas - Structure WTO2 (pdb code 6z8j). 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 [Nifese] Hydrogenase From Desulfovibrio Vulgaris Hildenborough Pressurized with Oxygen Gas - Structure WTO2, PDB code: 6z8j:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in 6z8j

Go back to Nickel Binding Sites List in 6z8j
Nickel binding site 1 out of 2 in the Structure of [Nifese] Hydrogenase From Desulfovibrio Vulgaris Hildenborough Pressurized with Oxygen Gas - Structure WTO2


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Structure of [Nifese] Hydrogenase From Desulfovibrio Vulgaris Hildenborough Pressurized with Oxygen Gas - Structure WTO2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni502

b:10.3
occ:0.83
 S B:H2S504 2.1 12.2 0.2
S B:H2S504 2.1 9.9 0.7
SG B:CYS492 2.2 9.6 1.0
SG B:CYS78 2.2 9.9 1.0
SG B:CSD75 2.2 12.1 1.0
SE B:SEC489 2.3 12.4 0.1
SE B:SEC489 2.4 9.2 0.7
FE B:FCO501 2.4 10.5 1.0
HB2 B:SEC489 2.8 14.2 0.2
SE B:SEC489 3.1 13.8 0.2
OD1 B:CSD75 3.1 12.6 0.8
HB2 B:CSD75 3.1 12.5 1.0
OD2 B:CSD75 3.1 12.0 1.0
C1 B:FCO501 3.2 10.5 1.0
CB B:CSD75 3.2 10.4 1.0
CB B:SEC489 3.2 11.9 0.2
HB2 B:CYS492 3.3 10.5 1.0
HB3 B:SEC489 3.3 14.2 0.2
HB3 B:CYS78 3.4 11.6 1.0
C2 B:FCO501 3.4 9.0 1.0
HB3 B:SEC489 3.4 10.5 0.7
HB2 B:SEC489 3.4 13.2 0.1
CB B:CYS492 3.4 8.8 1.0
HB3 B:CSD75 3.4 12.5 1.0
CB B:CYS78 3.5 9.7 1.0
CB B:SEC489 3.5 11.0 0.1
H B:CYS78 3.5 11.3 1.0
CB B:SEC489 3.5 8.7 0.7
H B:CYS492 3.8 10.3 1.0
HB3 B:SEC489 3.9 13.2 0.1
HD2 B:ARG422 3.9 10.7 1.0
HB2 B:SEC489 4.0 10.5 0.7
HB B:VAL77 4.0 12.0 1.0
HB3 B:CYS492 4.0 10.5 1.0
N1 B:FCO501 4.1 11.1 1.0
N B:CYS78 4.1 9.4 1.0
C3 B:FCO501 4.1 10.4 1.0
HB2 B:CYS78 4.2 11.6 1.0
N2 B:FCO501 4.3 9.3 1.0
CA B:CYS78 4.4 8.6 1.0
N B:CYS492 4.4 8.6 1.0
CA B:CYS492 4.4 8.9 1.0
HH11 B:ARG422 4.6 12.6 1.0
CA B:CSD75 4.6 9.5 1.0
HA B:CYS492 4.6 10.7 1.0
O B:SEC489 4.7 9.0 0.1
CA B:SEC489 4.7 10.2 0.2
CD B:ARG422 4.7 8.9 1.0
H B:VAL77 4.8 11.1 1.0
HD3 B:ARG422 4.8 10.7 1.0
CA B:SEC489 4.8 9.7 0.1
CA B:SEC489 4.8 8.4 0.7
NE2 B:HIS82 4.8 9.8 1.0
O B:SEC489 4.8 8.7 0.7
HD2 B:HIS82 4.9 11.8 1.0
HA B:CSD75 4.9 11.4 1.0
O B:SEC489 5.0 9.4 0.2
CB B:VAL77 5.0 10.0 1.0
NH1 B:ARG422 5.0 10.5 1.0

Nickel binding site 2 out of 2 in 6z8j

Go back to Nickel Binding Sites List in 6z8j
Nickel binding site 2 out of 2 in the Structure of [Nifese] Hydrogenase From Desulfovibrio Vulgaris Hildenborough Pressurized with Oxygen Gas - Structure WTO2


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Structure of [Nifese] Hydrogenase From Desulfovibrio Vulgaris Hildenborough Pressurized with Oxygen Gas - Structure WTO2 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ni502

b:10.2
occ:0.81
 S D:H2S504 2.0 12.3 0.2
S D:H2S504 2.1 9.4 0.6
SG D:CYS492 2.2 9.9 1.0
SG D:CSD75 2.2 12.1 1.0
SG D:CYS78 2.3 9.7 1.0
SE D:SEC489 2.3 13.7 0.2
SE D:SEC489 2.4 9.2 0.6
FE D:FCO501 2.4 10.7 1.0
HB2 D:SEC489 2.8 15.2 0.2
HB2 D:CSD75 3.0 12.1 1.0
OD1 D:CSD75 3.1 12.0 0.8
SE D:SEC489 3.1 14.6 0.2
OD2 D:CSD75 3.1 11.8 1.0
CB D:CSD75 3.1 10.1 1.0
C1 D:FCO501 3.2 11.1 1.0
CB D:SEC489 3.2 12.7 0.2
HB2 D:CYS492 3.3 11.6 1.0
HB3 D:CYS78 3.3 10.8 1.0
HB3 D:SEC489 3.3 15.2 0.2
C2 D:FCO501 3.4 9.3 1.0
HB3 D:SEC489 3.4 12.1 0.6
HB3 D:CSD75 3.4 12.1 1.0
HB2 D:SEC489 3.4 14.6 0.2
CB D:CYS492 3.4 9.6 1.0
CB D:CYS78 3.5 9.0 1.0
CB D:SEC489 3.5 12.1 0.2
H D:CYS78 3.5 10.6 1.0
CB D:SEC489 3.6 10.0 0.6
H D:CYS492 3.8 10.6 1.0
HB3 D:SEC489 3.9 14.6 0.2
HD2 D:ARG422 3.9 12.2 1.0
HB2 D:SEC489 4.0 12.1 0.6
HB D:VAL77 4.1 12.2 1.0
HB3 D:CYS492 4.1 11.6 1.0
N1 D:FCO501 4.1 11.3 1.0
N D:CYS78 4.1 8.8 1.0
C3 D:FCO501 4.2 10.9 1.0
HB2 D:CYS78 4.2 10.8 1.0
N2 D:FCO501 4.3 10.2 1.0
CA D:CYS78 4.4 8.9 1.0
N D:CYS492 4.4 8.8 1.0
CA D:CYS492 4.4 8.5 1.0
HH11 D:ARG422 4.6 12.5 1.0
CA D:CSD75 4.6 9.3 1.0
HA D:CYS492 4.6 10.2 1.0
CD D:ARG422 4.7 10.1 1.0
CA D:SEC489 4.7 11.3 0.2
O D:SEC489 4.8 10.3 0.2
H D:VAL77 4.8 10.7 1.0
HD3 D:ARG422 4.8 12.2 1.0
CA D:SEC489 4.8 11.0 0.2
O D:SEC489 4.8 9.8 0.6
CA D:SEC489 4.9 9.3 0.6
NE2 D:HIS82 4.9 9.5 1.0
HD2 D:HIS82 4.9 10.7 1.0
HA D:CSD75 4.9 11.2 1.0
O D:SEC489 4.9 10.7 0.2
CB D:VAL77 5.0 10.1 1.0
NH1 D:ARG422 5.0 10.4 1.0

Reference:

S.Zacarias, A.Temporao, P.Carpentier, P.Van Der Linden, I.A.C.Pereira, P.M.Matias. Exploring the Gas Access Routes in A [Nifese] Hydrogenase Using Crystals Pressurized with Krypton and Oxygen. J.Biol.Inorg.Chem. V. 25 863 2020.
ISSN: ESSN 1432-1327
PubMed: 32865640
DOI: 10.1007/S00775-020-01814-Y
Page generated: Thu Oct 10 09:03:12 2024

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