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Calcium 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
Sodium (Na) 2 atoms

Calcium Binding Sites:

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

Calcium binding site 1 out of 2 in 5odc

Go back to Calcium Binding Sites List in 5odc
Calcium 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 Calcium with other atoms in the Ca 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:Ca501

b:31.6
occ:1.00
 O F:HOH611 2.1 29.8 1.0
O F:LEU395 2.1 34.0 1.0
OE2 F:GLU42 2.1 48.5 1.0
O F:HOH634 2.2 44.2 1.0
O F:HOH612 2.2 31.6 1.0
NE2 F:HIS448 2.3 32.7 1.0
CD F:GLU42 3.1 47.9 1.0
CE1 F:HIS448 3.2 32.4 1.0
C F:LEU395 3.3 34.3 1.0
CD2 F:HIS448 3.3 32.7 1.0
OE1 F:GLU42 3.3 30.5 1.0
NZ F:LYS273 3.9 53.7 1.0
N F:LEU395 3.9 31.7 1.0
CA F:LEU395 4.0 30.6 1.0
CB F:LEU395 4.2 29.7 1.0
OE2 F:GLU264 4.2 30.1 1.0
OD1 F:ASN394 4.3 27.5 1.0
O F:HOH624 4.3 26.0 1.0
N F:VAL396 4.3 31.8 1.0
CG F:GLU42 4.4 43.5 1.0
ND1 F:HIS448 4.4 33.4 1.0
CG F:HIS448 4.4 31.6 1.0
O F:HOH607 4.5 28.4 1.0
OE1 F:GLU264 4.5 48.1 1.0
CA F:VAL396 4.6 31.1 1.0
CD F:GLU264 4.8 52.2 1.0
CE F:LYS273 4.9 44.0 1.0

Calcium binding site 2 out of 2 in 5odc

Go back to Calcium Binding Sites List in 5odc
Calcium 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 Calcium with other atoms in the Ca 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:Ca501

b:38.6
occ:1.00
 O L:HOH606 2.1 53.3 1.0
O L:LEU395 2.2 38.4 1.0
O L:HOH613 2.2 38.2 1.0
OE2 L:GLU42 2.2 53.4 1.0
NE2 L:HIS448 2.4 44.1 1.0
O L:HOH623 2.6 35.9 1.0
CD L:GLU42 3.1 48.6 1.0
CE1 L:HIS448 3.1 43.6 1.0
C L:LEU395 3.3 40.3 1.0
OE1 L:GLU42 3.4 43.1 1.0
CD2 L:HIS448 3.6 43.8 1.0
NZ L:LYS273 3.8 57.6 1.0
N L:LEU395 4.0 42.4 1.0
CA L:LEU395 4.1 39.6 1.0
OE2 L:GLU264 4.2 39.4 1.0
CB L:LEU395 4.3 37.9 1.0
OD1 L:ASN394 4.3 45.7 1.0
N L:VAL396 4.3 36.8 1.0
ND1 L:HIS448 4.4 43.7 1.0
OE1 L:GLU264 4.4 60.5 1.0
CG L:GLU42 4.5 40.3 1.0
CG L:HIS448 4.6 42.5 1.0
CA L:VAL396 4.6 36.2 1.0
O L:HOH603 4.7 22.5 1.0
CD L:GLU264 4.8 52.0 1.0
CE L:LYS273 4.8 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: Mon Jul 15 09:46:34 2024

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