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Nickel in PDB 5odc: Heterodisulfide Reductase / [Nife]-Hydrogenase Complex From Methanothermococcus Thermolithotrophicus at 2.3 A Resolution

Enzymatic activity of Heterodisulfide Reductase / [Nife]-Hydrogenase Complex From Methanothermococcus Thermolithotrophicus at 2.3 A Resolution

All present enzymatic activity of Heterodisulfide Reductase / [Nife]-Hydrogenase Complex From Methanothermococcus Thermolithotrophicus at 2.3 A Resolution:
1.12.99.6; 1.8.98.1;

Protein crystallography data

The structure of Heterodisulfide Reductase / [Nife]-Hydrogenase Complex From Methanothermococcus Thermolithotrophicus at 2.3 A Resolution, PDB code: 5odc 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) 49.22 / 2.30
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 378.047, 98.446, 137.884, 90.00, 110.70, 90.00
R / Rfree (%) 17.8 / 20

Other elements in 5odc:

The structure of Heterodisulfide Reductase / [Nife]-Hydrogenase Complex From Methanothermococcus Thermolithotrophicus at 2.3 A Resolution also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms
Iron (Fe) 110 atoms
Calcium (Ca) 2 atoms
Sodium (Na) 2 atoms

Nickel Binding Sites:

The binding sites of Nickel atom in the Heterodisulfide Reductase / [Nife]-Hydrogenase Complex From Methanothermococcus Thermolithotrophicus at 2.3 A Resolution (pdb code 5odc). 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 at 2.3 A Resolution, PDB code: 5odc:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in 5odc

Go back to Nickel Binding Sites List in 5odc
Nickel binding site 1 out of 2 in the Heterodisulfide Reductase / [Nife]-Hydrogenase Complex From Methanothermococcus Thermolithotrophicus at 2.3 A Resolution


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 at 2.3 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ni504

b:36.7
occ:1.00
 NI F:NFU504 0.0 36.7 1.0
SG F:CYS442 2.2 37.1 1.0
SG F:CYS64 2.3 28.1 1.0
SG F:CYS61 2.3 30.8 1.0
SG F:CYS445 2.6 31.5 1.0
FE F:NFU504 2.6 42.6 1.0
CB F:CYS61 3.0 27.7 1.0
CB F:CYS442 3.2 32.9 1.0
CB F:CYS445 3.4 27.4 1.0
C2 F:NFU504 3.4 34.4 1.0
C1 F:NFU504 3.4 38.9 1.0
CB F:CYS64 3.5 24.9 1.0
N F:CYS64 3.9 24.2 1.0
N2 F:NFU504 4.2 30.3 1.0
N1 F:NFU504 4.3 33.6 1.0
CA F:CYS64 4.3 24.9 1.0
C3 F:NFU504 4.4 40.2 1.0
CA F:CYS61 4.5 28.0 1.0
NH1 F:ARG375 4.6 26.8 1.0
CB F:ILE63 4.6 26.7 1.0
CA F:CYS445 4.6 27.4 1.0
CD F:ARG375 4.6 36.5 1.0
CA F:CYS442 4.6 32.4 1.0
N F:CYS445 4.8 27.9 1.0
C F:ILE63 4.9 28.1 1.0
N F:ILE63 4.9 25.2 1.0
C F:CYS64 5.0 29.8 1.0

Nickel binding site 2 out of 2 in 5odc

Go back to Nickel Binding Sites List in 5odc
Nickel binding site 2 out of 2 in the Heterodisulfide Reductase / [Nife]-Hydrogenase Complex From Methanothermococcus Thermolithotrophicus at 2.3 A Resolution


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 at 2.3 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Ni502

b:36.7
occ:1.00
 NI L:NFU502 0.0 36.7 1.0
SG L:CYS442 2.1 38.5 1.0
SG L:CYS64 2.3 32.9 1.0
SG L:CYS61 2.3 35.2 1.0
SG L:CYS445 2.6 37.7 1.0
FE L:NFU502 2.6 42.2 1.0
CB L:CYS61 3.0 31.0 1.0
CB L:CYS442 3.2 35.5 1.0
C1 L:NFU502 3.4 37.8 1.0
CB L:CYS445 3.4 34.2 1.0
C2 L:NFU502 3.4 43.5 1.0
CB L:CYS64 3.5 30.0 1.0
N L:CYS64 3.9 30.2 1.0
N1 L:NFU502 4.2 32.6 1.0
N2 L:NFU502 4.3 44.3 1.0
CA L:CYS64 4.3 30.4 1.0
C3 L:NFU502 4.3 41.3 1.0
CA L:CYS61 4.5 31.4 1.0
CB L:ILE63 4.6 32.6 1.0
NH1 L:ARG375 4.6 27.7 1.0
CA L:CYS445 4.6 34.1 1.0
CD L:ARG375 4.6 39.7 1.0
CA L:CYS442 4.6 35.4 1.0
N L:CYS445 4.8 33.9 1.0
C L:ILE63 4.9 33.1 1.0
N L:ILE63 4.9 32.6 1.0
C L:CYS61 5.0 38.0 1.0
OE1 L:GLU13 5.0 47.5 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 06:43:15 2024

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