Atomistry » Nickel » PDB 6vwz-6z8m » 6z7r
Atomistry »
  Nickel »
    PDB 6vwz-6z8m »
      6z7r »

Nickel in PDB 6z7r: Structure of [Nifese] Hydrogenase From Desulfovibrio Vulgaris Hildenborough Pressurized with Krypton Gas - Structure WTKR1

Enzymatic activity of Structure of [Nifese] Hydrogenase From Desulfovibrio Vulgaris Hildenborough Pressurized with Krypton Gas - Structure WTKR1

All present enzymatic activity of Structure of [Nifese] Hydrogenase From Desulfovibrio Vulgaris Hildenborough Pressurized with Krypton Gas - Structure WTKR1:
1.12.7.2;

Protein crystallography data

The structure of Structure of [Nifese] Hydrogenase From Desulfovibrio Vulgaris Hildenborough Pressurized with Krypton Gas - Structure WTKR1, PDB code: 6z7r 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) 58.05 / 1.77
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 75.125, 93.686, 98.433, 90.00, 93.26, 90.00
R / Rfree (%) 18.8 / 24.2

Other elements in 6z7r:

The structure of Structure of [Nifese] Hydrogenase From Desulfovibrio Vulgaris Hildenborough Pressurized with Krypton Gas - Structure WTKR1 also contains other interesting chemical elements:

Krypton (Kr) 42 atoms
Iron (Fe) 36 atoms
Chlorine (Cl) 2 atoms

Nickel Binding Sites:

The binding sites of Nickel atom in the Structure of [Nifese] Hydrogenase From Desulfovibrio Vulgaris Hildenborough Pressurized with Krypton Gas - Structure WTKR1 (pdb code 6z7r). 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 From Desulfovibrio Vulgaris Hildenborough Pressurized with Krypton Gas - Structure WTKR1, PDB code: 6z7r:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in 6z7r

Go back to Nickel Binding Sites List in 6z7r
Nickel binding site 1 out of 2 in the Structure of [Nifese] Hydrogenase From Desulfovibrio Vulgaris Hildenborough Pressurized with Krypton Gas - Structure WTKR1


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 From Desulfovibrio Vulgaris Hildenborough Pressurized with Krypton Gas - Structure WTKR1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni502

b:18.9
occ:0.89
 S B:H2S504 2.0 13.9 0.8
SG B:CYS492 2.2 12.7 1.0
SE B:SEC489 2.3 21.8 0.6
SG B:CSD75 2.3 17.9 1.0
SE B:SEC489 2.3 16.6 0.1
FE B:FCO501 2.3 17.6 1.0
SG B:CYS78 2.4 16.0 1.0
HB2 B:SEC489 2.8 21.0 0.3
OD1 B:CSD75 3.0 17.4 0.8
SE B:SEC489 3.0 26.9 0.3
HB2 B:CSD75 3.2 22.6 1.0
CB B:CSD75 3.2 18.7 1.0
HB2 B:CYS492 3.2 19.8 1.0
C1 B:FCO501 3.2 22.8 1.0
HB3 B:CSD75 3.3 22.6 1.0
CB B:SEC489 3.3 17.4 0.3
C2 B:FCO501 3.3 16.4 1.0
HB2 B:SEC489 3.3 20.9 0.1
HB3 B:CYS78 3.4 11.9 1.0
CB B:CYS492 3.4 16.4 1.0
OD2 B:CSD75 3.4 16.2 0.8
HB3 B:SEC489 3.5 21.0 0.3
CB B:SEC489 3.5 17.3 0.1
CB B:CYS78 3.5 9.8 1.0
HB3 B:SEC489 3.6 20.3 0.6
H B:CYS78 3.6 20.5 1.0
CB B:SEC489 3.7 16.8 0.6
HB3 B:SEC489 3.8 20.9 0.1
H B:CYS492 3.8 11.4 1.0
HE2 B:HIS82 3.9 28.7 1.0
HD2 B:CSD75 4.0 19.6 0.8
HB3 B:CYS492 4.0 19.8 1.0
HD2 B:ARG422 4.0 16.4 1.0
C3 B:FCO501 4.0 19.8 1.0
HB2 B:SEC489 4.1 20.3 0.6
N1 B:FCO501 4.1 11.8 1.0
HB B:VAL77 4.1 21.4 1.0
N B:CYS78 4.2 16.9 1.0
HB2 B:CYS78 4.2 11.9 1.0
N2 B:FCO501 4.3 17.7 1.0
N B:CYS492 4.4 9.4 1.0
CA B:CYS492 4.4 16.4 1.0
CA B:CYS78 4.5 14.9 1.0
CA B:CSD75 4.6 13.8 1.0
HH11 B:ARG422 4.6 15.8 1.0
HA B:CYS492 4.7 19.8 1.0
O B:SEC489 4.7 13.6 0.1
NE2 B:HIS82 4.7 23.8 1.0
HD3 B:ARG422 4.7 16.4 1.0
CD B:ARG422 4.8 13.5 1.0
CA B:SEC489 4.8 16.9 0.3
CA B:SEC489 4.8 16.9 0.1
O B:SEC489 4.8 12.6 0.6
H B:VAL77 4.9 14.4 1.0
HA B:CSD75 4.9 16.7 1.0
NH1 B:ARG422 5.0 13.1 1.0
CA B:SEC489 5.0 16.9 0.6
HG22 B:ILE74 5.0 24.9 1.0
HD2 B:HIS82 5.0 27.7 1.0

Nickel binding site 2 out of 2 in 6z7r

Go back to Nickel Binding Sites List in 6z7r
Nickel binding site 2 out of 2 in the Structure of [Nifese] Hydrogenase From Desulfovibrio Vulgaris Hildenborough Pressurized with Krypton Gas - Structure WTKR1


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 From Desulfovibrio Vulgaris Hildenborough Pressurized with Krypton Gas - Structure WTKR1 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ni502

b:21.2
occ:0.95
 S D:H2S504 2.0 15.6 0.8
SG D:CYS492 2.2 14.5 1.0
FE D:FCO501 2.3 17.8 1.0
SG D:CYS78 2.3 13.8 1.0
SE D:SEC489 2.3 29.8 0.3
SE D:SEC489 2.3 17.2 0.4
SG D:CSD75 2.3 19.9 1.0
HB2 D:SEC489 2.9 23.8 0.3
OD1 D:CSD75 3.0 16.6 0.8
HB2 D:CSD75 3.1 19.7 1.0
SE D:SEC489 3.1 24.1 0.3
C1 D:FCO501 3.2 27.4 1.0
CB D:CSD75 3.2 16.3 1.0
HB3 D:SEC489 3.2 23.8 0.3
CB D:SEC489 3.2 19.7 0.3
C2 D:FCO501 3.2 17.2 1.0
HB3 D:CYS78 3.3 6.8 1.0
HB2 D:CYS492 3.3 12.3 1.0
HB2 D:SEC489 3.3 24.2 0.3
HB3 D:SEC489 3.4 21.9 0.4
HB3 D:CSD75 3.4 19.7 1.0
CB D:SEC489 3.4 20.1 0.3
CB D:CYS78 3.4 6.0 1.0
CB D:CYS492 3.5 10.2 1.0
CB D:SEC489 3.5 18.1 0.4
H D:CYS78 3.6 13.7 1.0
OD2 D:CSD75 3.6 12.6 0.8
HB3 D:SEC489 3.7 24.2 0.3
HB2 D:SEC489 3.9 21.9 0.4
HD2 D:ARG422 4.0 22.6 1.0
H D:CYS492 4.0 16.1 1.0
HB D:VAL77 4.0 13.2 1.0
N1 D:FCO501 4.0 17.4 1.0
C3 D:FCO501 4.0 17.6 1.0
HB3 D:CYS492 4.1 12.3 1.0
HB2 D:CYS78 4.1 6.8 1.0
N D:CYS78 4.2 11.3 1.0
HE2 D:HIS82 4.2 16.6 1.0
HD2 D:CSD75 4.2 15.3 0.8
N2 D:FCO501 4.2 14.1 1.0
CA D:CYS78 4.4 6.0 1.0
N D:CYS492 4.5 13.3 1.0
CA D:CYS492 4.5 10.0 1.0
HD3 D:ARG422 4.6 22.6 1.0
CA D:CSD75 4.7 10.1 1.0
CD D:ARG422 4.7 18.7 1.0
H D:VAL77 4.7 16.6 1.0
HA D:CYS492 4.7 12.2 1.0
CA D:SEC489 4.8 19.5 0.3
CA D:SEC489 4.8 19.5 0.3
HH11 D:ARG422 4.8 25.8 1.0
O D:SEC489 4.9 17.3 0.3
CA D:SEC489 4.9 19.4 0.4
O D:SEC489 4.9 17.1 0.4
NE2 D:HIS82 4.9 13.7 1.0
CB D:VAL77 4.9 10.9 1.0
HG3 D:GLU28 5.0 22.0 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 09:02:23 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy