Atomistry » Nickel » PDB 5mdk-5ph1 » 5odi
Atomistry »
  Nickel »
    PDB 5mdk-5ph1 »
      5odi »

Nickel in PDB 5odi: Heterodisulfide Reductase / [Nife]-Hydrogenase Complex From Methanothermococcus Thermolithotrophicus Cocrystallized with Com-Sh

Enzymatic activity of Heterodisulfide Reductase / [Nife]-Hydrogenase Complex From Methanothermococcus Thermolithotrophicus Cocrystallized with Com-Sh

All present enzymatic activity of Heterodisulfide Reductase / [Nife]-Hydrogenase Complex From Methanothermococcus Thermolithotrophicus Cocrystallized with Com-Sh:
1.12.1.2; 1.8.98.1;

Protein crystallography data

The structure of Heterodisulfide Reductase / [Nife]-Hydrogenase Complex From Methanothermococcus Thermolithotrophicus Cocrystallized with Com-Sh, PDB code: 5odi was solved by T.Wagner, J.Koch, U.Ermler, S.Shima, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.54 / 2.40
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 370.528, 97.077, 135.149, 90.00, 109.43, 90.00
R / Rfree (%) 20.2 / 24.1

Other elements in 5odi:

The structure of Heterodisulfide Reductase / [Nife]-Hydrogenase Complex From Methanothermococcus Thermolithotrophicus Cocrystallized with Com-Sh also contains other interesting chemical elements:

Iron (Fe) 112 atoms

Nickel Binding Sites:

The binding sites of Nickel atom in the Heterodisulfide Reductase / [Nife]-Hydrogenase Complex From Methanothermococcus Thermolithotrophicus Cocrystallized with Com-Sh (pdb code 5odi). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the Heterodisulfide Reductase / [Nife]-Hydrogenase Complex From Methanothermococcus Thermolithotrophicus Cocrystallized with Com-Sh, PDB code: 5odi:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in 5odi

Go back to Nickel Binding Sites List in 5odi
Nickel binding site 1 out of 2 in the Heterodisulfide Reductase / [Nife]-Hydrogenase Complex From Methanothermococcus Thermolithotrophicus Cocrystallized with Com-Sh


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Heterodisulfide Reductase / [Nife]-Hydrogenase Complex From Methanothermococcus Thermolithotrophicus Cocrystallized with Com-Sh within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ni501

b:29.8
occ:1.00
NI F:NFU501 0.0 29.8 1.0
SG F:CYS64 2.2 27.1 1.0
SG F:CYS442 2.2 38.2 1.0
SG F:CYS61 2.5 33.8 1.0
FE F:NFU501 2.6 33.4 1.0
SG F:CYS445 2.9 34.7 1.0
CB F:CYS61 3.0 30.7 1.0
CB F:CYS445 3.2 31.4 1.0
CB F:CYS442 3.2 35.4 1.0
C2 F:NFU501 3.2 34.9 1.0
C1 F:NFU501 3.3 41.7 1.0
CB F:CYS64 3.5 24.6 1.0
N F:CYS64 3.9 21.3 1.0
N2 F:NFU501 4.0 39.3 1.0
N1 F:NFU501 4.1 36.9 1.0
C3 F:NFU501 4.3 38.2 1.0
CA F:CYS64 4.3 22.4 1.0
CA F:CYS445 4.5 33.0 1.0
CA F:CYS61 4.5 29.7 1.0
CD F:ARG375 4.5 33.8 1.0
CB F:ILE63 4.6 27.4 1.0
NH1 F:ARG375 4.6 26.4 1.0
CA F:CYS442 4.6 35.5 1.0
C F:ILE63 4.9 26.2 1.0
NE2 F:HIS68 4.9 23.6 1.0
N F:ILE63 5.0 26.5 1.0
N F:CYS445 5.0 34.3 1.0
NE F:ARG375 5.0 52.8 1.0
C F:CYS61 5.0 28.0 1.0

Nickel binding site 2 out of 2 in 5odi

Go back to Nickel Binding Sites List in 5odi
Nickel binding site 2 out of 2 in the Heterodisulfide Reductase / [Nife]-Hydrogenase Complex From Methanothermococcus Thermolithotrophicus Cocrystallized with Com-Sh


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Heterodisulfide Reductase / [Nife]-Hydrogenase Complex From Methanothermococcus Thermolithotrophicus Cocrystallized with Com-Sh within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Ni501

b:34.5
occ:1.00
NI L:NFU501 0.0 34.5 1.0
SG L:CYS442 2.1 34.9 1.0
SG L:CYS64 2.3 33.2 1.0
SG L:CYS61 2.5 42.9 1.0
SG L:CYS445 2.6 35.4 1.0
FE L:NFU501 2.6 29.4 1.0
CB L:CYS442 3.1 32.1 1.0
CB L:CYS61 3.1 38.8 1.0
CB L:CYS445 3.2 31.5 1.0
C2 L:NFU501 3.3 34.6 1.0
C1 L:NFU501 3.4 30.8 1.0
CB L:CYS64 3.7 31.2 1.0
N2 L:NFU501 4.1 41.5 1.0
N L:CYS64 4.1 28.3 1.0
N1 L:NFU501 4.2 28.4 1.0
CD L:ARG375 4.4 38.9 1.0
C3 L:NFU501 4.4 37.7 1.0
CA L:CYS445 4.5 31.3 1.0
CA L:CYS442 4.5 32.1 1.0
CA L:CYS64 4.5 31.3 1.0
NH1 L:ARG375 4.6 62.4 1.0
CA L:CYS61 4.6 38.1 1.0
CB L:ILE63 4.6 30.0 1.0
NE L:ARG375 4.8 42.9 1.0
N L:CYS445 4.9 28.8 1.0
O L:CYS442 4.9 30.4 1.0
CZ L:ARG375 4.9 57.1 1.0

Reference:

T.Wagner, J.Koch, U.Ermler, S.Shima. Methanogenic Heterodisulfide Reductase (Hdrabc-Mvhagd) Uses Two Noncubane [4FE-4S] Clusters For Reduction. Science V. 357 699 2017.
ISSN: ESSN 1095-9203
PubMed: 28818947
DOI: 10.1126/SCIENCE.AAN0425
Page generated: Wed Dec 16 01:42:28 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