Atomistry » Nickel » PDB 6r44-6vwy » 6ru9
Atomistry »
  Nickel »
    PDB 6r44-6vwy »
      6ru9 »

Nickel in PDB 6ru9: The 3D Structure of [Nifese] Hydrogenase G491A Variant From Desulfovibrio Vulgaris Hildenborough at 1.36 Angstrom Resolution

Enzymatic activity of The 3D Structure of [Nifese] Hydrogenase G491A Variant From Desulfovibrio Vulgaris Hildenborough at 1.36 Angstrom Resolution

All present enzymatic activity of The 3D Structure of [Nifese] Hydrogenase G491A Variant From Desulfovibrio Vulgaris Hildenborough at 1.36 Angstrom Resolution:
1.12.7.2;

Protein crystallography data

The structure of The 3D Structure of [Nifese] Hydrogenase G491A Variant From Desulfovibrio Vulgaris Hildenborough at 1.36 Angstrom Resolution, PDB code: 6ru9 was solved by P.M.Matias, S.Zacarias, I.Pereita, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.33 / 1.36
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 60.445, 98.664, 63.885, 90.00, 105.36, 90.00
R / Rfree (%) 14.4 / 16.3

Other elements in 6ru9:

The structure of The 3D Structure of [Nifese] Hydrogenase G491A Variant From Desulfovibrio Vulgaris Hildenborough at 1.36 Angstrom Resolution also contains other interesting chemical elements:

Iron (Fe) 18 atoms

Nickel Binding Sites:

The binding sites of Nickel atom in the The 3D Structure of [Nifese] Hydrogenase G491A Variant From Desulfovibrio Vulgaris Hildenborough at 1.36 Angstrom Resolution (pdb code 6ru9). 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 The 3D Structure of [Nifese] Hydrogenase G491A Variant From Desulfovibrio Vulgaris Hildenborough at 1.36 Angstrom Resolution, PDB code: 6ru9:

Nickel binding site 1 out of 1 in 6ru9

Go back to Nickel Binding Sites List in 6ru9
Nickel binding site 1 out of 1 in the The 3D Structure of [Nifese] Hydrogenase G491A Variant From Desulfovibrio Vulgaris Hildenborough at 1.36 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of The 3D Structure of [Nifese] Hydrogenase G491A Variant From Desulfovibrio Vulgaris Hildenborough at 1.36 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni502

b:17.6
occ:0.80
S B:H2S504 2.0 23.3 0.8
SG B:CYS75 2.3 17.3 1.0
SG B:CYS78 2.3 15.7 1.0
SG B:CYS492 2.4 13.5 1.0
SE B:SEC489 2.4 27.4 0.8
FE B:FCO501 2.5 13.5 1.0
HB2 B:SEC489 3.0 25.3 0.2
HB3 B:CYS75 3.1 18.1 1.0
CB B:CYS75 3.1 15.0 1.0
HB2 B:CYS75 3.1 18.1 1.0
SE B:SEC489 3.2 30.5 0.2
H B:CYS78 3.3 15.9 1.0
HB3 B:CYS78 3.4 17.9 1.0
HB2 B:CYS492 3.4 12.7 1.0
C1 B:FCO501 3.5 10.3 1.0
CB B:SEC489 3.5 21.0 0.2
CB B:CYS78 3.5 14.8 1.0
C2 B:FCO501 3.6 12.8 1.0
CB B:CYS492 3.6 10.5 1.0
HB2 B:SEC489 3.6 23.5 0.8
CB B:SEC489 3.6 19.5 0.8
HB B:VAL77 3.7 16.1 1.0
HB3 B:SEC489 3.8 25.3 0.2
H B:CYS492 3.9 12.3 1.0
HB3 B:SEC489 3.9 23.5 0.8
N B:CYS78 3.9 13.2 1.0
HD2 B:ARG422 4.0 17.5 1.0
HE2 B:HIS82 4.2 16.5 1.0
C3 B:FCO501 4.2 14.5 1.0
HB3 B:CYS492 4.2 12.7 1.0
HB2 B:CYS78 4.3 17.9 1.0
CA B:CYS78 4.3 11.9 1.0
N1 B:FCO501 4.4 12.9 1.0
HH11 B:ARG422 4.4 19.8 1.0
H B:VAL77 4.4 15.5 1.0
N B:CYS492 4.5 10.2 1.0
CA B:CYS75 4.5 10.2 1.0
N2 B:FCO501 4.5 12.9 1.0
CA B:CYS492 4.6 9.6 1.0
HB3 B:ALA491 4.6 15.3 1.0
CB B:VAL77 4.6 13.3 1.0
HA B:CYS492 4.7 11.6 1.0
CD B:ARG422 4.8 14.5 1.0
HG3 B:GLU28 4.8 21.3 1.0
NH1 B:ARG422 4.8 16.4 1.0
HD3 B:ARG422 4.8 17.5 1.0
HD2 B:HIS82 4.8 16.2 1.0
HA B:CYS75 4.9 12.3 1.0
CA B:SEC489 4.9 14.8 0.2
C B:VAL77 4.9 13.5 1.0
NE2 B:HIS82 4.9 13.7 1.0
CA B:SEC489 4.9 13.8 0.8
HG12 B:VAL77 4.9 21.9 1.0
C B:CYS78 5.0 14.1 1.0

Reference:

S.Zacarias, A.Temporao, M.Del Barrio, V.Fourmond, C.Leger, P.M.Matias, I.A.C.Pereira. A Hydrophilic Channel Is Involved in Oxidative Inactivation of A [Nifese] Hydrogenase Acs Catalysis 2019.
ISSN: ESSN 2155-5435
DOI: 10.1021/ACSCATAL.9B02347
Page generated: Wed Dec 16 01:53:28 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy