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Nickel in PDB 6z9g: Structure of [Nifese] Hydrogenase G491A Variant From Desulfovibrio Vulgaris Hildenborough Pressurized with Oxygen Gas - Structure G491A- O2

Enzymatic activity of Structure of [Nifese] Hydrogenase G491A Variant From Desulfovibrio Vulgaris Hildenborough Pressurized with Oxygen Gas - Structure G491A- O2

All present enzymatic activity of Structure of [Nifese] Hydrogenase G491A Variant From Desulfovibrio Vulgaris Hildenborough Pressurized with Oxygen Gas - Structure G491A- O2:
1.12.7.2;

Protein crystallography data

The structure of Structure of [Nifese] Hydrogenase G491A Variant From Desulfovibrio Vulgaris Hildenborough Pressurized with Oxygen Gas - Structure G491A- O2, PDB code: 6z9g 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) 61.20 / 1.76
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 120.306, 93.815, 126.951, 90.00, 105.20, 90.00
R / Rfree (%) 19.2 / 24

Other elements in 6z9g:

The structure of Structure of [Nifese] Hydrogenase G491A Variant From Desulfovibrio Vulgaris Hildenborough Pressurized with Oxygen Gas - Structure G491A- O2 also contains other interesting chemical elements:

Iron (Fe) 72 atoms
Chlorine (Cl) 4 atoms

Nickel Binding Sites:

The binding sites of Nickel atom in the Structure of [Nifese] Hydrogenase G491A Variant From Desulfovibrio Vulgaris Hildenborough Pressurized with Oxygen Gas - Structure G491A- O2 (pdb code 6z9g). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 4 binding sites of Nickel where determined in the Structure of [Nifese] Hydrogenase G491A Variant From Desulfovibrio Vulgaris Hildenborough Pressurized with Oxygen Gas - Structure G491A- O2, PDB code: 6z9g:
Jump to Nickel binding site number: 1; 2; 3; 4;

Nickel binding site 1 out of 4 in 6z9g

Go back to Nickel Binding Sites List in 6z9g
Nickel binding site 1 out of 4 in the Structure of [Nifese] Hydrogenase G491A Variant From Desulfovibrio Vulgaris Hildenborough Pressurized with Oxygen Gas - Structure G491A- 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 G491A Variant From Desulfovibrio Vulgaris Hildenborough Pressurized with Oxygen Gas - Structure G491A- O2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni501

b:18.7
occ:0.77
 S B:H2S503 1.9 11.1 0.7
SG B:CSD75 2.2 11.2 0.6
SG B:CYS492 2.3 12.7 1.0
SG B:CSD75 2.3 19.7 0.4
SG B:CYS78 2.3 16.3 1.0
SE B:SEC489 2.4 19.9 0.4
FE B:FCO500 2.5 14.5 1.0
SE B:SEC489 2.6 18.4 0.3
HB2 B:CSD75 2.9 17.6 0.6
HB2 B:CSD75 2.9 17.7 0.4
CB B:CSD75 2.9 14.6 0.6
SE B:SEC489 3.0 15.0 0.3
HB3 B:CSD75 3.0 17.6 0.6
CB B:CSD75 3.0 14.7 0.4
OD1 B:CSD75 3.1 11.1 0.6
HB3 B:CSD75 3.1 17.7 0.4
OD2 B:CSD75 3.2 20.5 0.6
HB3 B:CYS78 3.4 18.6 1.0
CB B:SEC489 3.4 22.4 0.3
HB2 B:CYS492 3.4 15.8 1.0
C1 B:FCO500 3.4 11.1 1.0
C2 B:FCO500 3.4 6.5 1.0
H B:CYS78 3.5 17.4 1.0
CB B:SEC489 3.5 22.1 0.4
CB B:CYS492 3.5 13.1 1.0
CB B:CYS78 3.5 15.5 1.0
CB B:SEC489 3.7 24.0 0.3
HB B:VAL77 3.8 10.2 1.0
H B:CYS492 4.0 10.5 1.0
N B:CYS78 4.1 14.5 1.0
HE2 B:HIS82 4.1 15.9 1.0
HB3 B:CYS492 4.2 15.8 1.0
HD2 B:ARG422 4.2 17.7 1.0
C3 B:FCO500 4.2 11.4 1.0
HB2 B:CYS78 4.3 18.6 1.0
N1 B:FCO500 4.3 13.4 1.0
CA B:CYS78 4.4 20.2 1.0
CA B:CSD75 4.4 17.3 0.6
N2 B:FCO500 4.5 7.1 1.0
CA B:CSD75 4.5 17.2 0.4
H B:VAL77 4.5 13.2 1.0
N B:CYS492 4.5 8.7 1.0
CA B:CYS492 4.5 14.0 1.0
HH11 B:ARG422 4.6 17.4 1.0
HG3 B:GLU28 4.7 24.0 1.0
HA B:CYS492 4.7 16.8 1.0
HA B:CSD75 4.8 20.7 0.4
CB B:VAL77 4.8 8.4 1.0
HB3 B:ALA491 4.8 13.5 1.0
HD2 B:HIS82 4.8 10.6 1.0
NE2 B:HIS82 4.8 13.2 1.0
CA B:SEC489 4.8 21.2 0.3
HA B:CSD75 4.9 20.8 0.6
HG22 B:ILE74 4.9 14.0 1.0
O B:SEC489 4.9 22.8 0.4
CA B:SEC489 4.9 21.1 0.4
CD B:ARG422 5.0 14.7 1.0
NH1 B:ARG422 5.0 14.4 1.0

Nickel binding site 2 out of 4 in 6z9g

Go back to Nickel Binding Sites List in 6z9g
Nickel binding site 2 out of 4 in the Structure of [Nifese] Hydrogenase G491A Variant From Desulfovibrio Vulgaris Hildenborough Pressurized with Oxygen Gas - Structure G491A- 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 G491A Variant From Desulfovibrio Vulgaris Hildenborough Pressurized with Oxygen Gas - Structure G491A- O2 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ni501

b:19.2
occ:0.81
 S D:H2S503 1.9 10.2 0.7
SG D:CSD75 2.2 13.8 0.6
SG D:CYS492 2.3 13.1 1.0
SG D:CSD75 2.3 17.0 0.4
SG D:CYS78 2.4 12.2 1.0
SE D:SEC489 2.4 21.0 0.4
FE D:FCO500 2.5 13.2 1.0
SE D:SEC489 2.6 21.4 0.3
HB2 D:CSD75 2.9 12.5 0.6
HB2 D:CSD75 2.9 12.6 0.4
CB D:CSD75 2.9 10.4 0.6
CB D:CSD75 3.0 10.5 0.4
SE D:SEC489 3.0 17.2 0.3
HB3 D:CSD75 3.0 12.5 0.6
HB3 D:CSD75 3.0 12.6 0.4
OD2 D:CSD75 3.1 21.7 0.6
OD1 D:CSD75 3.2 9.6 0.6
HB2 D:CYS492 3.4 18.8 1.0
HB3 D:CYS78 3.4 15.7 1.0
C1 D:FCO500 3.4 13.2 1.0
CB D:SEC489 3.4 24.0 0.3
H D:CYS78 3.5 12.2 1.0
C2 D:FCO500 3.5 10.6 1.0
CB D:CYS492 3.5 15.6 1.0
CB D:SEC489 3.5 24.1 0.4
CB D:CYS78 3.5 13.1 1.0
CB D:SEC489 3.8 24.4 0.3
HB D:VAL77 3.9 10.1 1.0
H D:CYS492 4.0 12.3 1.0
N D:CYS78 4.1 10.1 1.0
C3 D:FCO500 4.2 17.9 1.0
HB3 D:CYS492 4.2 18.8 1.0
HE2 D:HIS82 4.2 15.4 1.0
HD2 D:ARG422 4.2 14.9 1.0
N1 D:FCO500 4.3 12.8 1.0
HB2 D:CYS78 4.3 15.7 1.0
CA D:CYS78 4.4 17.1 1.0
CA D:CSD75 4.4 15.4 0.6
CA D:CSD75 4.5 15.3 0.4
N2 D:FCO500 4.5 8.1 1.0
CA D:CYS492 4.5 15.8 1.0
H D:VAL77 4.5 9.8 1.0
N D:CYS492 4.5 10.3 1.0
HH11 D:ARG422 4.6 13.7 1.0
HA D:CYS492 4.6 19.0 1.0
HA D:CSD75 4.8 18.4 0.4
HD2 D:HIS82 4.8 13.2 1.0
HG3 D:GLU28 4.8 27.4 1.0
CB D:VAL77 4.8 8.4 1.0
HA D:CSD75 4.8 18.5 0.6
HB3 D:ALA491 4.8 15.6 1.0
NE2 D:HIS82 4.9 12.8 1.0
CA D:SEC489 4.9 23.7 0.3
O D:SEC489 4.9 22.2 0.3
CA D:SEC489 4.9 23.8 0.4
NH1 D:ARG422 4.9 11.3 1.0
HG22 D:ILE74 5.0 13.2 1.0
O D:SEC489 5.0 22.1 0.4
C D:VAL77 5.0 8.8 1.0
CD D:ARG422 5.0 12.4 1.0
C D:CSD75 5.0 9.8 0.6

Nickel binding site 3 out of 4 in 6z9g

Go back to Nickel Binding Sites List in 6z9g
Nickel binding site 3 out of 4 in the Structure of [Nifese] Hydrogenase G491A Variant From Desulfovibrio Vulgaris Hildenborough Pressurized with Oxygen Gas - Structure G491A- O2


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Structure of [Nifese] Hydrogenase G491A Variant From Desulfovibrio Vulgaris Hildenborough Pressurized with Oxygen Gas - Structure G491A- O2 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ni501

b:21.1
occ:0.84
 S F:H2S503 1.9 11.9 0.7
SG F:CSD75 2.3 16.0 0.5
SG F:CYS492 2.3 14.1 1.0
SG F:CSD75 2.3 15.0 0.5
SG F:CYS78 2.3 15.8 1.0
SE F:SEC489 2.3 22.7 0.4
FE F:FCO500 2.5 16.1 1.0
SE F:SEC489 2.7 22.1 0.3
HB2 F:CSD75 2.7 20.5 0.5
SE F:SEC489 2.8 20.1 0.3
HB2 F:CSD75 2.8 20.6 0.5
CB F:CSD75 2.9 17.0 0.5
CB F:CSD75 2.9 17.1 0.5
HB3 F:CSD75 2.9 20.6 0.5
OD2 F:CSD75 3.1 20.1 0.5
HB3 F:CSD75 3.1 20.5 0.5
OD1 F:CSD75 3.3 12.3 0.5
CB F:SEC489 3.3 25.2 0.3
HB3 F:CYS78 3.4 16.3 1.0
C1 F:FCO500 3.4 18.4 1.0
HB2 F:CYS492 3.4 17.1 1.0
H F:CYS78 3.4 18.8 1.0
CB F:SEC489 3.5 24.9 0.4
C2 F:FCO500 3.5 20.4 1.0
CB F:CYS78 3.5 13.5 1.0
CB F:CYS492 3.5 14.2 1.0
CB F:SEC489 3.7 25.9 0.3
HB F:VAL77 3.8 10.2 1.0
N F:CYS78 4.0 15.6 1.0
H F:CYS492 4.0 11.7 1.0
C3 F:FCO500 4.1 16.4 1.0
HE2 F:HIS82 4.1 15.8 1.0
HD2 F:ARG422 4.2 18.2 1.0
HB3 F:CYS492 4.2 17.1 1.0
HB2 F:CYS78 4.2 16.3 1.0
N1 F:FCO500 4.3 16.8 1.0
CA F:CSD75 4.4 10.8 0.5
CA F:CYS78 4.4 16.3 1.0
CA F:CSD75 4.4 10.8 0.5
H F:VAL77 4.4 9.7 1.0
N2 F:FCO500 4.4 8.9 1.0
CA F:CYS492 4.5 11.7 1.0
HH11 F:ARG422 4.5 24.9 1.0
N F:CYS492 4.6 9.7 1.0
HG3 F:GLU28 4.7 31.2 1.0
HA F:CYS492 4.7 14.0 1.0
HA F:CSD75 4.7 12.9 0.5
CB F:VAL77 4.8 8.4 1.0
CA F:SEC489 4.8 26.7 0.3
C F:CSD75 4.8 11.6 0.5
CA F:SEC489 4.9 26.7 0.4
HA F:CSD75 4.9 13.0 0.5
NE2 F:HIS82 4.9 13.2 1.0
NH1 F:ARG422 4.9 20.7 1.0
HD2 F:HIS82 4.9 6.7 1.0
HB3 F:ALA491 4.9 24.8 1.0
CD F:ARG422 5.0 15.2 1.0
C F:VAL77 5.0 10.5 1.0
O F:CSD75 5.0 11.6 0.5
C F:CYS78 5.0 5.9 1.0
C F:CSD75 5.0 11.3 0.5

Nickel binding site 4 out of 4 in 6z9g

Go back to Nickel Binding Sites List in 6z9g
Nickel binding site 4 out of 4 in the Structure of [Nifese] Hydrogenase G491A Variant From Desulfovibrio Vulgaris Hildenborough Pressurized with Oxygen Gas - Structure G491A- O2


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of Structure of [Nifese] Hydrogenase G491A Variant From Desulfovibrio Vulgaris Hildenborough Pressurized with Oxygen Gas - Structure G491A- O2 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Ni501

b:22.4
occ:0.79
 S H:H2S503 1.9 21.8 0.8
SG H:CYS492 2.2 15.2 1.0
SE H:SEC489 2.3 30.9 0.4
SG H:OCS75 2.3 19.4 0.7
SG H:CYS78 2.3 20.3 1.0
SG H:OCS75 2.4 23.0 0.3
FE H:FCO500 2.5 19.3 1.0
SE H:SEC489 2.6 30.7 0.3
HB2 H:OCS75 2.7 27.1 0.3
SE H:SEC489 2.7 27.4 0.3
CB H:OCS75 2.8 22.5 0.3
HB2 H:OCS75 2.9 27.3 0.7
HB3 H:OCS75 2.9 27.3 0.7
CB H:OCS75 2.9 22.7 0.7
HB3 H:OCS75 3.0 27.1 0.3
OD1 H:OCS75 3.1 15.9 0.3
CB H:SEC489 3.3 37.2 0.3
CB H:SEC489 3.4 37.5 0.4
HB2 H:CYS492 3.4 29.0 1.0
OD3 H:OCS75 3.5 19.1 0.3
C1 H:FCO500 3.5 25.9 1.0
CB H:CYS492 3.5 24.2 1.0
H H:CYS78 3.5 22.8 1.0
HB3 H:CYS78 3.5 22.5 1.0
CB H:SEC489 3.6 37.6 0.3
C2 H:FCO500 3.6 28.5 1.0
CB H:CYS78 3.6 18.7 1.0
HB H:VAL77 3.9 12.3 1.0
H H:CYS492 3.9 17.0 1.0
N H:CYS78 4.1 19.0 1.0
HB3 H:CYS492 4.2 29.0 1.0
HE2 H:HIS82 4.2 20.3 1.0
C3 H:FCO500 4.2 14.8 1.0
HD2 H:ARG422 4.3 25.2 1.0
N1 H:FCO500 4.3 21.9 1.0
HB2 H:CYS78 4.3 22.5 1.0
CA H:OCS75 4.4 14.0 0.3
CA H:OCS75 4.4 13.9 0.7
N H:CYS492 4.4 14.2 1.0
H H:VAL77 4.4 14.6 1.0
CA H:CYS78 4.5 20.5 1.0
CA H:CYS492 4.5 16.3 1.0
HA H:CYS492 4.6 19.6 1.0
N2 H:FCO500 4.6 16.7 1.0
HG3 H:GLU28 4.6 33.1 1.0
HB3 H:ALA491 4.7 18.7 1.0
CA H:SEC489 4.7 34.9 0.3
HA H:OCS75 4.7 16.7 0.7
CA H:SEC489 4.8 34.8 0.4
HD2 H:HIS82 4.8 7.2 1.0
CB H:VAL77 4.8 10.3 1.0
HH11 H:ARG422 4.8 33.9 1.0
O H:SEC489 4.9 37.1 0.4
C H:OCS75 4.9 15.4 0.3
HA H:OCS75 4.9 16.8 0.3
NE2 H:HIS82 4.9 16.9 1.0
CA H:SEC489 4.9 34.6 0.3
O H:SEC489 5.0 37.1 0.3
HG22 H:ILE74 5.0 15.8 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 09:05:01 2024

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