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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: Thu Oct 10 06:43:41 2024

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