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Nickel in PDB 6z8o: Structure of [Nifese] Hydrogenase G491A Variant From Desulfovibrio Vulgaris Hildenborough Pressurized with Krypton Gas - Structure G491A-Kr

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

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

Protein crystallography data

The structure of Structure of [Nifese] Hydrogenase G491A Variant From Desulfovibrio Vulgaris Hildenborough Pressurized with Krypton Gas - Structure G491A-Kr, PDB code: 6z8o 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) 39.12 / 2.20
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 63.716, 97.022, 121.318, 90.00, 104.66, 90.00
R / Rfree (%) 22.6 / 27.5

Other elements in 6z8o:

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

Krypton (Kr) 20 atoms
Iron (Fe) 36 atoms
Chlorine (Cl) 2 atoms

Nickel Binding Sites:

The binding sites of Nickel atom in the Structure of [Nifese] Hydrogenase G491A Variant From Desulfovibrio Vulgaris Hildenborough Pressurized with Krypton Gas - Structure G491A-Kr (pdb code 6z8o). 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 G491A Variant From Desulfovibrio Vulgaris Hildenborough Pressurized with Krypton Gas - Structure G491A-Kr, PDB code: 6z8o:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in 6z8o

Go back to Nickel Binding Sites List in 6z8o
Nickel binding site 1 out of 2 in the Structure of [Nifese] Hydrogenase G491A Variant From Desulfovibrio Vulgaris Hildenborough Pressurized with Krypton Gas - Structure G491A-Kr


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 Krypton Gas - Structure G491A-Kr within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni502

b:23.5
occ:0.78
 S B:H2S504 2.1 31.5 0.9
SG B:CYS492 2.3 28.2 1.0
SE B:SEC489 2.3 35.4 0.4
SG B:CYS75 2.3 30.5 1.0
SG B:CYS78 2.3 31.7 1.0
SE B:SEC489 2.3 36.7 0.1
FE B:FCO501 2.4 21.7 1.0
SE B:SEC489 2.6 36.8 0.5
CB B:CYS75 3.0 31.0 1.0
HB2 B:CYS75 3.0 38.6 1.0
HB3 B:CYS75 3.1 38.6 1.0
HB2 B:CYS492 3.3 36.0 1.0
C1 B:FCO501 3.3 30.3 1.0
CB B:SEC489 3.3 39.2 0.5
CB B:SEC489 3.4 38.2 0.4
CB B:CYS492 3.5 28.8 1.0
C2 B:FCO501 3.5 28.9 1.0
CB B:SEC489 3.5 39.0 0.1
H B:CYS78 3.7 33.1 1.0
CB B:CYS78 3.8 31.5 1.0
HB3 B:CYS78 3.8 39.2 1.0
HB B:VAL77 3.9 39.0 1.0
H B:CYS492 3.9 35.9 1.0
HB3 B:CYS492 4.1 36.0 1.0
C3 B:FCO501 4.1 34.7 1.0
HD2 B:ARG422 4.1 45.0 1.0
N1 B:FCO501 4.2 33.4 1.0
HE2 B:HIS82 4.3 31.1 1.0
N B:CYS78 4.4 26.4 1.0
N B:CYS492 4.4 28.7 1.0
HB2 B:CYS78 4.4 39.2 1.0
CA B:CYS492 4.5 33.9 1.0
N2 B:FCO501 4.5 30.3 1.0
CA B:CYS75 4.5 25.0 1.0
H B:VAL77 4.5 34.8 1.0
HA B:CYS492 4.6 42.1 1.0
CA B:CYS78 4.7 36.5 1.0
CA B:SEC489 4.8 39.2 0.5
HG3 B:GLU28 4.8 45.3 1.0
HA B:CYS75 4.8 31.4 1.0
O B:SEC489 4.8 38.4 0.4
CA B:SEC489 4.8 39.2 0.4
CB B:VAL77 4.9 31.3 1.0
CD B:ARG422 4.9 36.3 1.0
HD3 B:ARG422 4.9 45.0 1.0
CA B:SEC489 4.9 39.3 0.1
HD2 B:HIS82 4.9 32.7 1.0
NE2 B:HIS82 5.0 24.7 1.0
HB1 B:ALA491 5.0 38.2 1.0
O B:SEC489 5.0 38.2 0.1

Nickel binding site 2 out of 2 in 6z8o

Go back to Nickel Binding Sites List in 6z8o
Nickel binding site 2 out of 2 in the Structure of [Nifese] Hydrogenase G491A Variant From Desulfovibrio Vulgaris Hildenborough Pressurized with Krypton Gas - Structure G491A-Kr


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 Krypton Gas - Structure G491A-Kr within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ni502

b:22.1
occ:0.81
 S D:H2S504 2.1 38.2 0.6
SG D:CYS78 2.3 32.9 1.0
SE D:SEC489 2.3 39.5 0.4
SG D:CYS492 2.3 31.7 1.0
SE D:SEC489 2.3 41.6 0.2
SG D:CYS75 2.3 32.7 1.0
FE D:FCO501 2.6 20.6 1.0
SE D:SEC489 2.6 38.2 0.4
HB3 D:CYS75 2.9 38.4 1.0
CB D:CYS75 3.0 30.8 1.0
HB2 D:CYS75 3.0 38.4 1.0
HB2 D:CYS492 3.3 40.6 1.0
CB D:SEC489 3.4 38.7 0.4
C1 D:FCO501 3.4 33.0 1.0
CB D:CYS492 3.5 32.7 1.0
CB D:SEC489 3.5 38.6 0.4
C2 D:FCO501 3.5 32.7 1.0
H D:CYS78 3.5 46.0 1.0
HB3 D:CYS78 3.6 48.5 1.0
CB D:SEC489 3.6 38.5 0.2
CB D:CYS78 3.6 39.2 1.0
H D:CYS492 3.9 41.2 1.0
HB3 D:CYS492 4.1 40.6 1.0
HB D:VAL77 4.1 39.5 1.0
HE2 D:HIS82 4.1 32.3 1.0
HD2 D:ARG422 4.2 44.8 1.0
N D:CYS78 4.2 37.1 1.0
N1 D:FCO501 4.3 34.5 1.0
C3 D:FCO501 4.4 37.1 1.0
HB2 D:CYS78 4.4 48.5 1.0
N2 D:FCO501 4.4 34.7 1.0
N D:CYS492 4.4 33.2 1.0
CA D:CYS75 4.4 27.1 1.0
CA D:CYS78 4.5 30.9 1.0
CA D:CYS492 4.5 32.7 1.0
H D:VAL77 4.6 29.7 1.0
HA D:CYS492 4.6 40.7 1.0
O D:SEC489 4.7 35.1 0.2
HB3 D:ALA491 4.7 48.6 1.0
O D:SEC489 4.7 35.0 0.4
CA D:SEC489 4.8 36.1 0.4
HA D:CYS75 4.8 34.0 1.0
HG3 D:GLU28 4.8 51.5 1.0
HD2 D:HIS82 4.8 34.2 1.0
NE2 D:HIS82 4.8 25.7 1.0
CA D:SEC489 4.9 36.1 0.4
CD D:ARG422 4.9 36.2 1.0
HD3 D:ARG422 4.9 44.8 1.0
O D:SEC489 4.9 34.5 0.4
HG22 D:ILE74 4.9 34.1 1.0
CA D:SEC489 5.0 36.1 0.2
O D:CYS78 5.0 29.6 1.0
C D:CYS78 5.0 27.9 1.0
NE D:ARG422 5.0 36.3 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 09:04:58 2024

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