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

Nickel in PDB 6z8m: Structure of [Nifese] Hydrogenase G491S Variant From Desulfovibrio Vulgaris Hildenborough Pressurized with Oxygen Gas - Structure G491S- O2

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

All present enzymatic activity of Structure of [Nifese] Hydrogenase G491S Variant From Desulfovibrio Vulgaris Hildenborough Pressurized with Oxygen Gas - Structure G491S- O2:
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 G491S- O2, PDB code: 6z8m 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) 53.33 / 1.02
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 105.993, 62.639, 110.532, 90.00, 105.21, 90.00
R / Rfree (%) 13.4 / 15.1

Other elements in 6z8m:

The structure of Structure of [Nifese] Hydrogenase G491S Variant From Desulfovibrio Vulgaris Hildenborough Pressurized with Oxygen Gas - Structure G491S- O2 also contains other interesting chemical elements:

Iron (Fe) 18 atoms
Chlorine (Cl) 1 atom

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 G491S- O2 (pdb code 6z8m). 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 G491S Variant From Desulfovibrio Vulgaris Hildenborough Pressurized with Oxygen Gas - Structure G491S- O2, PDB code: 6z8m:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in 6z8m

Go back to Nickel Binding Sites List in 6z8m
Nickel binding site 1 out of 2 in the Structure of [Nifese] Hydrogenase G491S Variant From Desulfovibrio Vulgaris Hildenborough Pressurized with Oxygen Gas - Structure G491S- O2


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 G491S- O2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni502

b:10.6
occ:0.15
 NI B:NI502 0.0 10.6 0.1
NI B:NI502 1.2 9.9 0.7
S B:H2S504 1.6 9.7 0.7
S B:H2S504 1.6 10.6 0.1
SG B:CYS75 1.9 9.6 0.5
SG B:CYS75 2.0 11.2 0.5
OD1 B:CYS75 2.0 9.6 0.3
SE B:SEC489 2.2 12.1 0.5
SE B:SEC489 2.6 10.0 0.2
SG B:CYS78 2.7 10.1 1.0
HB B:VAL77 2.7 11.1 1.0
SE B:SEC489 2.7 7.9 0.3
H B:CYS78 2.8 10.5 1.0
OD2 B:CYS75 2.9 9.1 0.4
HB3 B:CYS78 3.1 11.2 1.0
HB2 B:CYS75 3.2 11.6 0.5
CB B:CYS75 3.2 9.7 0.5
CB B:CYS75 3.2 10.4 0.5
HB2 B:SEC489 3.3 12.0 0.2
N B:CYS78 3.3 8.7 1.0
HB3 B:CYS75 3.3 12.4 0.5
HB3 B:SEC489 3.4 10.4 0.3
SG B:CYS492 3.4 9.3 1.0
CB B:CYS78 3.4 9.4 1.0
FE B:FCO501 3.4 10.6 1.0
HB2 B:CYS75 3.4 12.4 0.5
CB B:SEC489 3.6 8.7 0.3
CB B:SEC489 3.6 10.0 0.2
CB B:VAL77 3.7 9.2 1.0
H B:VAL77 3.7 9.7 1.0
CB B:SEC489 3.7 11.4 0.5
HB2 B:SEC489 3.8 10.4 0.3
HB3 B:CYS75 3.8 11.6 0.5
HB3 B:SEC489 3.9 12.0 0.2
CA B:CYS78 3.9 8.3 1.0
C2 B:FCO501 4.0 9.4 1.0
HB3 B:SEC489 4.0 13.7 0.5
HB2 B:SEC489 4.0 13.7 0.5
C B:VAL77 4.1 8.4 1.0
HG12 B:VAL77 4.1 12.2 1.0
HD2 B:ARG422 4.1 10.6 1.0
HG3 B:GLU28 4.1 12.4 1.0
CA B:VAL77 4.2 8.1 1.0
HB2 B:CYS78 4.2 11.2 1.0
HH11 B:ARG422 4.3 11.8 1.0
C1 B:FCO501 4.3 10.6 1.0
N B:VAL77 4.3 8.1 1.0
CG1 B:VAL77 4.3 10.1 1.0
HB2 B:CYS492 4.4 10.4 1.0
CA B:CYS75 4.4 9.1 0.5
HG11 B:VAL77 4.4 12.2 1.0
NH1 B:ARG422 4.5 9.8 1.0
HG23 B:VAL77 4.5 12.3 1.0
CA B:CYS75 4.5 8.9 0.5
C B:CYS75 4.6 8.7 0.5
CG2 B:VAL77 4.6 10.2 1.0
CB B:CYS492 4.6 8.7 1.0
H B:CYS492 4.6 10.1 1.0
HA B:CYS75 4.6 10.9 0.5
O B:CYS75 4.7 8.5 0.5
HG21 B:VAL77 4.7 12.3 1.0
HA B:CYS78 4.7 10.0 1.0
N2 B:FCO501 4.7 9.1 1.0
HH12 B:ARG422 4.8 11.8 1.0
HA B:CYS75 4.8 10.7 0.5
C B:CYS75 4.8 9.0 0.5
CZ B:ARG422 4.8 8.7 1.0
CD B:ARG422 4.8 8.9 1.0
HB3 B:GLU28 4.8 12.1 1.0
C B:CYS78 4.8 8.3 1.0
NE B:ARG422 4.9 9.1 1.0
CA B:SEC489 4.9 9.6 0.2
CG B:GLU28 5.0 10.3 1.0
HA B:SEC489 5.0 12.7 0.5
CA B:SEC489 5.0 10.6 0.5
HD3 B:ARG422 5.0 10.6 1.0
HA B:SEC489 5.0 11.5 0.2

Nickel binding site 2 out of 2 in 6z8m

Go back to Nickel Binding Sites List in 6z8m
Nickel binding site 2 out of 2 in the Structure of [Nifese] Hydrogenase G491S Variant From Desulfovibrio Vulgaris Hildenborough Pressurized with Oxygen Gas - Structure G491S- O2


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 G491S Variant From Desulfovibrio Vulgaris Hildenborough Pressurized with Oxygen Gas - Structure G491S- O2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni502

b:9.9
occ:0.70
 NI B:NI502 0.0 9.9 0.7
NI B:NI502 1.2 10.6 0.1
S B:H2S504 1.6 10.6 0.1
S B:H2S504 2.2 9.7 0.7
SG B:CYS492 2.2 9.3 1.0
SG B:CYS75 2.2 9.6 0.5
SG B:CYS78 2.2 10.1 1.0
SE B:SEC489 2.4 12.1 0.5
SE B:SEC489 2.4 7.9 0.3
FE B:FCO501 2.4 10.6 1.0
SG B:CYS75 2.6 11.2 0.5
OD1 B:CYS75 2.9 9.6 0.3
HB2 B:SEC489 2.9 12.0 0.2
SE B:SEC489 3.0 10.0 0.2
HB2 B:CYS75 3.0 11.6 0.5
CB B:CYS75 3.1 9.7 0.5
OD2 B:CYS75 3.1 9.1 0.4
HB3 B:CYS75 3.1 12.4 0.5
HB2 B:CYS75 3.2 12.4 0.5
CB B:CYS75 3.2 10.4 0.5
CB B:SEC489 3.3 10.0 0.2
C1 B:FCO501 3.3 10.6 1.0
HB3 B:CYS75 3.3 11.6 0.5
HB2 B:CYS492 3.3 10.4 1.0
HB3 B:CYS78 3.3 11.2 1.0
HB3 B:SEC489 3.4 12.0 0.2
HB2 B:SEC489 3.4 13.7 0.5
C2 B:FCO501 3.4 9.4 1.0
CB B:CYS492 3.4 8.7 1.0
CB B:CYS78 3.5 9.4 1.0
H B:CYS78 3.5 10.5 1.0
CB B:SEC489 3.5 11.4 0.5
HB3 B:SEC489 3.5 10.4 0.3
CB B:SEC489 3.7 8.7 0.3
HB3 B:SEC489 3.9 13.7 0.5
H B:CYS492 3.9 10.1 1.0
HB B:VAL77 4.0 11.1 1.0
HD2 B:ARG422 4.0 10.6 1.0
HB3 B:CYS492 4.1 10.4 1.0
N B:CYS78 4.1 8.7 1.0
C3 B:FCO501 4.1 10.9 1.0
HE2 B:HIS82 4.1 11.4 1.0
HB2 B:SEC489 4.2 10.4 0.3
HB2 B:CYS78 4.2 11.2 1.0
N1 B:FCO501 4.2 10.8 1.0
CA B:CYS78 4.4 8.3 1.0
N2 B:FCO501 4.4 9.1 1.0
CA B:CYS492 4.4 8.1 1.0
N B:CYS492 4.5 8.4 1.0
CA B:CYS75 4.5 9.1 0.5
HH11 B:ARG422 4.5 11.8 1.0
HA B:CYS492 4.6 9.7 1.0
CA B:CYS75 4.7 8.9 0.5
O B:SEC489 4.7 9.1 0.3
H B:VAL77 4.7 9.7 1.0
CA B:SEC489 4.8 9.6 0.2
CD B:ARG422 4.8 8.9 1.0
CA B:SEC489 4.8 10.6 0.5
HD3 B:ARG422 4.8 10.6 1.0
NE2 B:HIS82 4.8 9.5 1.0
HD2 B:HIS82 4.9 10.7 1.0
HA B:CYS75 4.9 10.9 0.5
CB B:VAL77 4.9 9.2 1.0
CA B:SEC489 4.9 8.7 0.3
O B:SEC489 4.9 9.0 0.5
NH1 B:ARG422 4.9 9.8 1.0
HG3 B:GLU28 5.0 12.4 1.0
HG22 B:ILE74 5.0 10.3 1.0
C B:CYS75 5.0 8.7 0.5

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 09:03:36 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy