Nickel in PDB 6z9o: Structure of [Nifese] Hydrogenase G491S Variant From Desulfovibrio Vulgaris Hildenborough Pressurized with Oxygen Gas - Structure G491A- O2-Ld

Enzymatic activity of Structure of [Nifese] Hydrogenase G491S Variant From Desulfovibrio Vulgaris Hildenborough Pressurized with Oxygen Gas - Structure G491A- O2-Ld

All present enzymatic activity of Structure of [Nifese] Hydrogenase G491S Variant From Desulfovibrio Vulgaris Hildenborough Pressurized with Oxygen Gas - Structure G491A- O2-Ld:
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 G491A- O2-Ld, PDB code: 6z9o 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) 50.98 / 1.53
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 106.096, 63.503, 109.942, 90.00, 104.74, 90.00
R / Rfree (%) 16.1 / 18.5

Other elements in 6z9o:

The structure of Structure of [Nifese] Hydrogenase G491S Variant From Desulfovibrio Vulgaris Hildenborough Pressurized with Oxygen Gas - Structure G491A- O2-Ld 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 G491S Variant From Desulfovibrio Vulgaris Hildenborough Pressurized with Oxygen Gas - Structure G491A- O2-Ld (pdb code 6z9o). 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 G491S Variant From Desulfovibrio Vulgaris Hildenborough Pressurized with Oxygen Gas - Structure G491A- O2-Ld, PDB code: 6z9o:

Nickel binding site 1 out of 1 in 6z9o

Go back to Nickel Binding Sites List in 6z9o
Nickel binding site 1 out of 1 in the Structure of [Nifese] Hydrogenase G491S Variant From Desulfovibrio Vulgaris Hildenborough Pressurized with Oxygen Gas - Structure G491A- O2-Ld


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 G491A- O2-Ld within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni502

b:28.7
occ:0.89
S B:H2S504 2.0 24.9 1.0
SG B:CYS492 2.3 18.4 1.0
SE B:SEC489 2.3 31.1 0.5
SG B:CSD75 2.3 23.8 0.6
SG B:CSD75 2.4 22.5 0.5
SG B:CYS78 2.4 18.8 1.0
SE B:SEC489 2.4 23.2 0.3
FE B:FCO501 2.4 20.5 1.0
HB2 B:CSD75 3.0 23.7 0.6
CB B:CSD75 3.1 19.7 0.6
CB B:CSD75 3.1 19.7 0.5
HB3 B:CSD75 3.1 23.7 0.6
OD2 B:CSD75 3.1 24.1 0.5
HB2 B:SEC489 3.2 28.1 0.2
SE B:SEC489 3.2 26.1 0.2
C1 B:FCO501 3.3 20.9 1.0
OD1 B:CSD75 3.3 21.9 0.5
HB2 B:CYS492 3.4 25.4 1.0
HB2 B:SEC489 3.4 28.4 0.5
HB3 B:CYS78 3.5 22.4 1.0
C2 B:FCO501 3.5 19.8 1.0
CB B:SEC489 3.5 23.6 0.5
CB B:CYS492 3.5 21.1 1.0
CB B:SEC489 3.5 23.4 0.2
H B:CYS78 3.6 20.2 1.0
CB B:CYS78 3.6 18.6 1.0
HB3 B:SEC489 3.6 28.5 0.3
HB3 B:SEC489 3.7 28.1 0.2
CB B:SEC489 3.8 23.7 0.3
HB3 B:SEC489 3.8 28.4 0.5
HB B:VAL77 4.0 22.2 1.0
HD2 B:ARG422 4.0 21.3 1.0
H B:CYS492 4.0 21.7 1.0
C3 B:FCO501 4.1 19.3 1.0
HB3 B:CYS492 4.1 25.4 1.0
N B:CYS78 4.2 16.8 1.0
HE2 B:HIS82 4.2 21.8 1.0
N1 B:FCO501 4.2 20.4 1.0
HB2 B:SEC489 4.3 28.5 0.3
HB2 B:CYS78 4.3 22.4 1.0
N2 B:FCO501 4.4 16.7 1.0
CA B:CYS78 4.5 16.2 1.0
N B:CYS492 4.5 18.1 1.0
CA B:CYS492 4.5 19.1 1.0
CA B:CSD75 4.5 18.8 0.6
CA B:CSD75 4.5 18.8 0.5
HH11 B:ARG422 4.6 20.8 1.0
H B:VAL77 4.6 20.1 1.0
HA B:CYS492 4.7 23.0 1.0
O B:SEC489 4.7 21.1 0.3
CD B:ARG422 4.8 17.7 1.0
HD3 B:ARG422 4.8 21.3 1.0
HA B:CSD75 4.8 22.6 0.6
CA B:SEC489 4.9 21.6 0.5
HB3 B:ALA491 4.9 21.5 1.0
CB B:VAL77 4.9 18.5 1.0
NE2 B:HIS82 4.9 18.1 1.0
HD2 B:HIS82 4.9 19.7 1.0
CA B:SEC489 5.0 21.6 0.2
NH1 B:ARG422 5.0 17.3 1.0
C B:CSD75 5.0 19.7 0.5
HG22 B:ILE74 5.0 21.5 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

Last articles

Zn in 7NA9
Zn in 7LZP
Zn in 7M1H
Zn in 7L6V
Zn in 7CM0
V in 7P8R
Ni in 7L19
Na in 7T88
Na in 7MJ5
Na in 7L00
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy