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Nickel in PDB 6z8m: Structure of [Nifese] Hydrogenase G491S Variant From Desulfovibrio Vulgaris Hildenborough Pressurized with Oxygen Gas - Structure G491S- O2

Enzymatic activity of Structure of [Nifese] Hydrogenase G491S Variant From Desulfovibrio Vulgaris Hildenborough Pressurized with Oxygen Gas - Structure G491S- O2

All present enzymatic activity of Structure of [Nifese] Hydrogenase G491S Variant From Desulfovibrio Vulgaris Hildenborough Pressurized with Oxygen Gas - Structure G491S- O2:
1.12.7.2;

Protein crystallography data

The structure of Structure of [Nifese] Hydrogenase G491S Variant From Desulfovibrio Vulgaris Hildenborough Pressurized with Oxygen Gas - Structure G491S- O2, PDB code: 6z8m 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) 53.33 / 1.02
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 105.993, 62.639, 110.532, 90.00, 105.21, 90.00
R / Rfree (%) 13.4 / 15.1

Other elements in 6z8m:

The structure of Structure of [Nifese] Hydrogenase G491S Variant From Desulfovibrio Vulgaris Hildenborough Pressurized with Oxygen Gas - Structure G491S- O2 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 Structure of [Nifese] Hydrogenase G491S Variant From Desulfovibrio Vulgaris Hildenborough Pressurized with Oxygen Gas - Structure G491S- O2 (pdb code 6z8m). 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 G491S Variant From Desulfovibrio Vulgaris Hildenborough Pressurized with Oxygen Gas - Structure G491S- O2, PDB code: 6z8m:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in 6z8m

Go back to Nickel Binding Sites List in 6z8m
Nickel binding site 1 out of 2 in the Structure of [Nifese] Hydrogenase G491S Variant From Desulfovibrio Vulgaris Hildenborough Pressurized with Oxygen Gas - Structure G491S- O2


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 G491S Variant From Desulfovibrio Vulgaris Hildenborough Pressurized with Oxygen Gas - Structure G491S- O2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni502

b:10.6
occ:0.15
 NI B:NI502 0.0 10.6 0.1
NI B:NI502 1.2 9.9 0.7
S B:H2S504 1.6 9.7 0.7
S B:H2S504 1.6 10.6 0.1
SG B:CYS75 1.9 9.6 0.5
SG B:CYS75 2.0 11.2 0.5
OD1 B:CYS75 2.0 9.6 0.3
SE B:SEC489 2.2 12.1 0.5
SE B:SEC489 2.6 10.0 0.2
SG B:CYS78 2.7 10.1 1.0
HB B:VAL77 2.7 11.1 1.0
SE B:SEC489 2.7 7.9 0.3
H B:CYS78 2.8 10.5 1.0
OD2 B:CYS75 2.9 9.1 0.4
HB3 B:CYS78 3.1 11.2 1.0
HB2 B:CYS75 3.2 11.6 0.5
CB B:CYS75 3.2 9.7 0.5
CB B:CYS75 3.2 10.4 0.5
HB2 B:SEC489 3.3 12.0 0.2
N B:CYS78 3.3 8.7 1.0
HB3 B:CYS75 3.3 12.4 0.5
HB3 B:SEC489 3.4 10.4 0.3
SG B:CYS492 3.4 9.3 1.0
CB B:CYS78 3.4 9.4 1.0
FE B:FCO501 3.4 10.6 1.0
HB2 B:CYS75 3.4 12.4 0.5
CB B:SEC489 3.6 8.7 0.3
CB B:SEC489 3.6 10.0 0.2
CB B:VAL77 3.7 9.2 1.0
H B:VAL77 3.7 9.7 1.0
CB B:SEC489 3.7 11.4 0.5
HB2 B:SEC489 3.8 10.4 0.3
HB3 B:CYS75 3.8 11.6 0.5
HB3 B:SEC489 3.9 12.0 0.2
CA B:CYS78 3.9 8.3 1.0
C2 B:FCO501 4.0 9.4 1.0
HB3 B:SEC489 4.0 13.7 0.5
HB2 B:SEC489 4.0 13.7 0.5
C B:VAL77 4.1 8.4 1.0
HG12 B:VAL77 4.1 12.2 1.0
HD2 B:ARG422 4.1 10.6 1.0
HG3 B:GLU28 4.1 12.4 1.0
CA B:VAL77 4.2 8.1 1.0
HB2 B:CYS78 4.2 11.2 1.0
HH11 B:ARG422 4.3 11.8 1.0
C1 B:FCO501 4.3 10.6 1.0
N B:VAL77 4.3 8.1 1.0
CG1 B:VAL77 4.3 10.1 1.0
HB2 B:CYS492 4.4 10.4 1.0
CA B:CYS75 4.4 9.1 0.5
HG11 B:VAL77 4.4 12.2 1.0
NH1 B:ARG422 4.5 9.8 1.0
HG23 B:VAL77 4.5 12.3 1.0
CA B:CYS75 4.5 8.9 0.5
C B:CYS75 4.6 8.7 0.5
CG2 B:VAL77 4.6 10.2 1.0
CB B:CYS492 4.6 8.7 1.0
H B:CYS492 4.6 10.1 1.0
HA B:CYS75 4.6 10.9 0.5
O B:CYS75 4.7 8.5 0.5
HG21 B:VAL77 4.7 12.3 1.0
HA B:CYS78 4.7 10.0 1.0
N2 B:FCO501 4.7 9.1 1.0
HH12 B:ARG422 4.8 11.8 1.0
HA B:CYS75 4.8 10.7 0.5
C B:CYS75 4.8 9.0 0.5
CZ B:ARG422 4.8 8.7 1.0
CD B:ARG422 4.8 8.9 1.0
HB3 B:GLU28 4.8 12.1 1.0
C B:CYS78 4.8 8.3 1.0
NE B:ARG422 4.9 9.1 1.0
CA B:SEC489 4.9 9.6 0.2
CG B:GLU28 5.0 10.3 1.0
HA B:SEC489 5.0 12.7 0.5
CA B:SEC489 5.0 10.6 0.5
HD3 B:ARG422 5.0 10.6 1.0
HA B:SEC489 5.0 11.5 0.2

Nickel binding site 2 out of 2 in 6z8m

Go back to Nickel Binding Sites List in 6z8m
Nickel binding site 2 out of 2 in the Structure of [Nifese] Hydrogenase G491S Variant From Desulfovibrio Vulgaris Hildenborough Pressurized with Oxygen Gas - Structure G491S- O2


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 G491S Variant From Desulfovibrio Vulgaris Hildenborough Pressurized with Oxygen Gas - Structure G491S- O2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni502

b:9.9
occ:0.70
 NI B:NI502 0.0 9.9 0.7
NI B:NI502 1.2 10.6 0.1
S B:H2S504 1.6 10.6 0.1
S B:H2S504 2.2 9.7 0.7
SG B:CYS492 2.2 9.3 1.0
SG B:CYS75 2.2 9.6 0.5
SG B:CYS78 2.2 10.1 1.0
SE B:SEC489 2.4 12.1 0.5
SE B:SEC489 2.4 7.9 0.3
FE B:FCO501 2.4 10.6 1.0
SG B:CYS75 2.6 11.2 0.5
OD1 B:CYS75 2.9 9.6 0.3
HB2 B:SEC489 2.9 12.0 0.2
SE B:SEC489 3.0 10.0 0.2
HB2 B:CYS75 3.0 11.6 0.5
CB B:CYS75 3.1 9.7 0.5
OD2 B:CYS75 3.1 9.1 0.4
HB3 B:CYS75 3.1 12.4 0.5
HB2 B:CYS75 3.2 12.4 0.5
CB B:CYS75 3.2 10.4 0.5
CB B:SEC489 3.3 10.0 0.2
C1 B:FCO501 3.3 10.6 1.0
HB3 B:CYS75 3.3 11.6 0.5
HB2 B:CYS492 3.3 10.4 1.0
HB3 B:CYS78 3.3 11.2 1.0
HB3 B:SEC489 3.4 12.0 0.2
HB2 B:SEC489 3.4 13.7 0.5
C2 B:FCO501 3.4 9.4 1.0
CB B:CYS492 3.4 8.7 1.0
CB B:CYS78 3.5 9.4 1.0
H B:CYS78 3.5 10.5 1.0
CB B:SEC489 3.5 11.4 0.5
HB3 B:SEC489 3.5 10.4 0.3
CB B:SEC489 3.7 8.7 0.3
HB3 B:SEC489 3.9 13.7 0.5
H B:CYS492 3.9 10.1 1.0
HB B:VAL77 4.0 11.1 1.0
HD2 B:ARG422 4.0 10.6 1.0
HB3 B:CYS492 4.1 10.4 1.0
N B:CYS78 4.1 8.7 1.0
C3 B:FCO501 4.1 10.9 1.0
HE2 B:HIS82 4.1 11.4 1.0
HB2 B:SEC489 4.2 10.4 0.3
HB2 B:CYS78 4.2 11.2 1.0
N1 B:FCO501 4.2 10.8 1.0
CA B:CYS78 4.4 8.3 1.0
N2 B:FCO501 4.4 9.1 1.0
CA B:CYS492 4.4 8.1 1.0
N B:CYS492 4.5 8.4 1.0
CA B:CYS75 4.5 9.1 0.5
HH11 B:ARG422 4.5 11.8 1.0
HA B:CYS492 4.6 9.7 1.0
CA B:CYS75 4.7 8.9 0.5
O B:SEC489 4.7 9.1 0.3
H B:VAL77 4.7 9.7 1.0
CA B:SEC489 4.8 9.6 0.2
CD B:ARG422 4.8 8.9 1.0
CA B:SEC489 4.8 10.6 0.5
HD3 B:ARG422 4.8 10.6 1.0
NE2 B:HIS82 4.8 9.5 1.0
HD2 B:HIS82 4.9 10.7 1.0
HA B:CYS75 4.9 10.9 0.5
CB B:VAL77 4.9 9.2 1.0
CA B:SEC489 4.9 8.7 0.3
O B:SEC489 4.9 9.0 0.5
NH1 B:ARG422 4.9 9.8 1.0
HG3 B:GLU28 5.0 12.4 1.0
HG22 B:ILE74 5.0 10.3 1.0
C B:CYS75 5.0 8.7 0.5

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: Mon Aug 18 21:42:01 2025

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