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Sodium 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:

Nickel (Ni) 2 atoms
Magnesium (Mg) 2 atoms
Iron (Fe) 110 atoms
Calcium (Ca) 2 atoms

Sodium Binding Sites:

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

Sodium binding site 1 out of 2 in 5odc

Go back to Sodium Binding Sites List in 5odc
Sodium 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 Sodium with other atoms in the Na 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
A:Na702

b:49.7
occ:1.00
 OD2 A:ASP164 3.6 51.1 1.0
O G:HOH918 3.8 47.6 1.0
OD2 A:ASP205 4.0 47.0 1.0
OD1 A:ASP164 4.1 46.7 1.0
CD2 A:LEU160 4.2 37.1 1.0
CG A:ASP164 4.3 45.8 1.0
CD1 A:LEU160 4.5 37.0 1.0
CB A:ASP205 4.6 39.9 1.0
CG A:ASP205 4.6 51.0 1.0
CG A:LEU160 4.7 35.4 1.0
CB A:LEU160 4.7 29.4 1.0

Sodium binding site 2 out of 2 in 5odc

Go back to Sodium Binding Sites List in 5odc
Sodium 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 Sodium with other atoms in the Na 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
G:Na702

b:43.8
occ:1.00
 O G:VAL212 2.5 40.1 1.0
O G:HOH876 2.6 39.9 1.0
O G:VAL206 2.8 38.3 1.0
C G:ALA207 3.2 41.8 1.0
O G:ALA207 3.3 43.5 1.0
N G:HIS209 3.5 37.8 1.0
O G:HIS209 3.5 42.9 1.0
C G:VAL212 3.5 40.9 1.0
N G:LYS208 3.6 38.6 1.0
CA G:ALA207 3.7 36.1 1.0
C G:VAL206 3.8 38.7 1.0
CB G:VAL212 4.1 40.8 1.0
CA G:LYS208 4.1 38.5 1.0
N G:LEU214 4.1 37.9 1.0
C G:LYS208 4.2 42.4 1.0
N G:ALA207 4.2 36.5 1.0
CA G:HIS209 4.3 36.5 1.0
CA G:VAL212 4.3 37.7 1.0
C G:HIS209 4.3 42.0 1.0
CG1 G:VAL212 4.4 40.1 1.0
N G:LYS213 4.4 37.4 1.0
CB G:LEU214 4.4 35.8 1.0
CB G:HIS209 4.5 35.8 1.0
CA G:LYS213 4.5 37.5 1.0
C G:LYS213 4.7 41.3 1.0
N G:VAL212 4.8 39.0 1.0
CA G:LEU214 4.9 36.9 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: Mon Oct 7 23:10:42 2024

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