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Nickel in PDB 6za1: Structure of [Nifese] Hydrogenase G491A Variant From Desulfovibrio Vulgaris Hildenborough Pressurized with Oxygen Gas - Structure G491A- O2-Hd

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

All present enzymatic activity of Structure of [Nifese] Hydrogenase G491A Variant From Desulfovibrio Vulgaris Hildenborough Pressurized with Oxygen Gas - Structure G491A- O2-Hd:
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-Hd, PDB code: 6za1 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) 50.95 / 1.37
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 106.156, 63.415, 110.044, 90.00, 104.79, 90.00
R / Rfree (%) 14.3 / 16.3

Other elements in 6za1:

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

Iron (Fe) 18 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-Hd (pdb code 6za1). 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 Structure of [Nifese] Hydrogenase G491A Variant From Desulfovibrio Vulgaris Hildenborough Pressurized with Oxygen Gas - Structure G491A- O2-Hd, PDB code: 6za1:

Nickel binding site 1 out of 1 in 6za1

Go back to Nickel Binding Sites List in 6za1
Nickel binding site 1 out of 1 in the Structure of [Nifese] Hydrogenase G491A Variant From Desulfovibrio Vulgaris Hildenborough Pressurized with Oxygen Gas - Structure G491A- O2-Hd


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-Hd within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni502

b:24.3
occ:0.79
S B:H2S504 2.0 25.1 1.0
SG B:CYS492 2.2 16.7 1.0
SE B:SEC489 2.3 25.4 0.4
SG B:CSD75 2.3 21.4 0.4
SG B:CYS78 2.3 17.6 1.0
SG B:CSD75 2.3 22.0 0.6
SE B:SEC489 2.4 18.1 0.2
FE B:FCO501 2.4 18.3 1.0
HB2 B:SEC489 3.0 24.0 0.2
SE B:SEC489 3.0 26.4 0.2
OD2 B:CSD75 3.0 24.2 0.4
HB2 B:CSD75 3.1 22.1 0.6
CB B:CSD75 3.1 18.4 0.6
HB3 B:CSD75 3.2 22.1 0.6
CB B:CSD75 3.2 17.9 0.4
HB2 B:SEC489 3.2 23.9 0.2
OD1 B:CSD75 3.2 21.0 0.4
SE B:SEC489 3.3 29.1 0.2
C1 B:FCO501 3.3 19.7 1.0
HB2 B:CYS492 3.4 19.0 1.0
HB3 B:CYS78 3.4 18.4 1.0
CB B:SEC489 3.5 20.0 0.2
HB2 B:SEC489 3.5 24.2 0.4
C2 B:FCO501 3.5 17.2 1.0
CB B:CYS492 3.5 15.8 1.0
CB B:SEC489 3.5 19.9 0.2
H B:CYS78 3.5 19.5 1.0
CB B:SEC489 3.5 20.1 0.4
CB B:CYS78 3.6 15.3 1.0
HB3 B:SEC489 3.6 23.9 0.2
HB3 B:SEC489 3.7 23.9 0.2
CB B:SEC489 3.7 19.9 0.2
HB3 B:SEC489 3.8 24.0 0.2
HD2 B:ARG422 3.9 20.1 1.0
HB3 B:SEC489 3.9 24.2 0.4
H B:CYS492 3.9 18.2 1.0
HB B:VAL77 3.9 19.4 1.0
C3 B:FCO501 4.1 20.6 1.0
N B:CYS78 4.1 16.2 1.0
HB3 B:CYS492 4.1 19.0 1.0
HE2 B:HIS82 4.2 20.6 1.0
N1 B:FCO501 4.2 19.4 1.0
HB2 B:SEC489 4.3 23.9 0.2
HB2 B:CYS78 4.3 18.4 1.0
CA B:CYS78 4.4 14.5 1.0
N B:CYS492 4.5 15.2 1.0
N2 B:FCO501 4.5 16.6 1.0
CA B:CYS492 4.5 14.9 1.0
HH11 B:ARG422 4.5 20.9 1.0
CA B:CSD75 4.6 16.8 0.4
CA B:CSD75 4.6 16.8 0.6
H B:VAL77 4.6 17.5 1.0
HA B:CYS492 4.7 17.9 1.0
CD B:ARG422 4.7 16.7 1.0
O B:SEC489 4.7 18.3 0.2
HB3 B:ALA491 4.8 20.5 1.0
HD3 B:ARG422 4.8 20.1 1.0
CA B:SEC489 4.8 18.8 0.2
CA B:SEC489 4.8 18.8 0.4
HD2 B:HIS82 4.9 20.3 1.0
CB B:VAL77 4.9 16.1 1.0
HA B:CSD75 4.9 20.2 0.6
NE2 B:HIS82 4.9 17.1 1.0
O B:CSD75 4.9 15.2 0.4
NH1 B:ARG422 4.9 17.4 1.0
C B:CSD75 4.9 16.4 0.4
HG3 B:GLU28 4.9 25.7 1.0
CA B:SEC489 5.0 18.8 0.2
CA B:SEC489 5.0 18.8 0.2
HG22 B:ILE74 5.0 18.8 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: Wed Dec 16 01:58:37 2020

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