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Xenon in PDB 7tsj: Xenon-Bound Structure of Carbon Monoxide Dehydrogenase (Codh) From Desulfovibrio Vulgaris

Enzymatic activity of Xenon-Bound Structure of Carbon Monoxide Dehydrogenase (Codh) From Desulfovibrio Vulgaris

All present enzymatic activity of Xenon-Bound Structure of Carbon Monoxide Dehydrogenase (Codh) From Desulfovibrio Vulgaris:
1.2.7.4;

Protein crystallography data

The structure of Xenon-Bound Structure of Carbon Monoxide Dehydrogenase (Codh) From Desulfovibrio Vulgaris, PDB code: 7tsj was solved by A.Biester, C.L.Drennan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.72 / 2.10
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 113.892, 100.87, 65.384, 90, 124.88, 90
R / Rfree (%) 16.7 / 20.6

Other elements in 7tsj:

The structure of Xenon-Bound Structure of Carbon Monoxide Dehydrogenase (Codh) From Desulfovibrio Vulgaris also contains other interesting chemical elements:

Iron (Fe) 9 atoms
Nickel (Ni) 1 atom

Xenon Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Xenon atom in the Xenon-Bound Structure of Carbon Monoxide Dehydrogenase (Codh) From Desulfovibrio Vulgaris (pdb code 7tsj). This binding sites where shown within 5.0 Angstroms radius around Xenon atom.
In total 12 binding sites of Xenon where determined in the Xenon-Bound Structure of Carbon Monoxide Dehydrogenase (Codh) From Desulfovibrio Vulgaris, PDB code: 7tsj:
Jump to Xenon binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Xenon binding site 1 out of 12 in 7tsj

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Xenon binding site 1 out of 12 in the Xenon-Bound Structure of Carbon Monoxide Dehydrogenase (Codh) From Desulfovibrio Vulgaris


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 1 of Xenon-Bound Structure of Carbon Monoxide Dehydrogenase (Codh) From Desulfovibrio Vulgaris within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Xe704

b:36.7
occ:0.40
 CD1 A:LEU573 3.6 41.1 1.0
CB A:ALA558 3.7 33.3 1.0
CE1 A:PHE86 3.9 42.9 1.0
CA A:ALA558 3.9 28.6 1.0
CZ A:PHE86 3.9 44.1 1.0
CE1 A:PHE601 3.9 43.2 1.0
O A:ALA558 4.0 30.4 1.0
CG A:PRO577 4.1 44.8 1.0
CZ A:PHE601 4.2 42.9 1.0
CB A:ALA561 4.3 34.8 1.0
C A:ALA558 4.4 30.2 1.0
CB A:PRO577 4.4 41.4 1.0
CD A:PRO577 4.5 43.5 1.0
CD1 A:PHE601 4.6 42.9 1.0
CZ2 A:TRP552 4.7 39.2 1.0
XE A:XE705 4.7 51.2 0.3
CH2 A:TRP552 4.7 36.0 1.0
CD1 A:ILE90 4.8 36.3 1.0
CG A:LEU573 4.8 39.5 1.0
CD2 A:LEU573 4.9 37.3 1.0

Xenon binding site 2 out of 12 in 7tsj

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Xenon binding site 2 out of 12 in the Xenon-Bound Structure of Carbon Monoxide Dehydrogenase (Codh) From Desulfovibrio Vulgaris


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 2 of Xenon-Bound Structure of Carbon Monoxide Dehydrogenase (Codh) From Desulfovibrio Vulgaris within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Xe705

b:51.2
occ:0.30
 CB A:PHE601 3.6 41.8 1.0
CG A:PHE601 3.6 42.8 1.0
CD A:PRO577 3.6 43.5 1.0
CG A:PRO577 3.7 44.8 1.0
CB A:ALA589 3.8 43.8 1.0
CD2 A:PHE601 3.9 41.6 1.0
CD1 A:LEU573 4.0 41.1 1.0
CD1 A:PHE601 4.1 42.9 1.0
CD1 A:ILE579 4.2 43.6 1.0
CG2 A:VAL603 4.2 43.2 1.0
CD2 A:LEU590 4.4 45.8 1.0
CE2 A:PHE601 4.6 46.8 1.0
XE A:XE704 4.7 36.7 0.4
CE1 A:PHE601 4.8 43.2 1.0

Xenon binding site 3 out of 12 in 7tsj

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Xenon binding site 3 out of 12 in the Xenon-Bound Structure of Carbon Monoxide Dehydrogenase (Codh) From Desulfovibrio Vulgaris


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 3 of Xenon-Bound Structure of Carbon Monoxide Dehydrogenase (Codh) From Desulfovibrio Vulgaris within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Xe706

b:57.7
occ:0.30
 CB A:ALA589 3.6 43.8 1.0
CD2 A:LEU213 3.7 51.9 1.0
CA A:ALA589 3.9 48.0 1.0
CE2 A:PHE86 4.0 48.3 1.0
CD1 A:LEU213 4.2 52.9 1.0
CE A:MET562 4.2 42.0 1.0
N A:ALA589 4.3 46.0 1.0
CG A:LEU213 4.4 50.9 1.0
CD1 A:LEU593 4.4 40.5 1.0
CE2 A:PHE601 4.4 46.8 1.0
CD2 A:PHE86 4.6 44.2 1.0
CB A:LEU213 4.6 45.0 1.0
CZ A:PHE86 4.7 44.1 1.0
O A:VAL585 4.7 45.2 1.0
CD2 A:PHE601 4.8 41.6 1.0
CG A:MET588 4.9 50.1 1.0
C A:MET588 4.9 48.1 1.0
CG1 A:VAL585 4.9 45.0 1.0
CG A:LEU593 5.0 46.9 1.0

Xenon binding site 4 out of 12 in 7tsj

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Xenon binding site 4 out of 12 in the Xenon-Bound Structure of Carbon Monoxide Dehydrogenase (Codh) From Desulfovibrio Vulgaris


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 4 of Xenon-Bound Structure of Carbon Monoxide Dehydrogenase (Codh) From Desulfovibrio Vulgaris within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Xe707

b:55.8
occ:0.30
 CG2 A:VAL214 3.7 43.6 1.0
SD A:MET588 3.8 61.8 1.0
CB A:LEU213 3.9 45.0 1.0
CG A:MET588 4.0 50.1 1.0
CD2 A:LEU593 4.0 43.8 1.0
O A:THR210 4.2 45.7 1.0
N A:VAL214 4.2 40.7 1.0
CG2 A:THR210 4.3 54.3 1.0
C A:LEU213 4.5 41.0 1.0
CA A:VAL214 4.7 41.3 1.0
CD1 A:LEU213 4.7 52.9 1.0
CE A:MET588 4.8 55.4 1.0
CB A:VAL214 4.8 43.7 1.0
CA A:LEU213 4.8 42.9 1.0
CA A:THR210 4.9 51.4 1.0
CG1 A:VAL596 4.9 49.4 1.0
C A:THR210 4.9 50.2 1.0
CG A:LEU213 5.0 50.9 1.0

Xenon binding site 5 out of 12 in 7tsj

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Xenon binding site 5 out of 12 in the Xenon-Bound Structure of Carbon Monoxide Dehydrogenase (Codh) From Desulfovibrio Vulgaris


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 5 of Xenon-Bound Structure of Carbon Monoxide Dehydrogenase (Codh) From Desulfovibrio Vulgaris within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Xe708

b:50.2
occ:0.30
 CG2 A:VAL446 3.5 48.8 1.0
CG2 A:THR571 3.6 36.4 1.0
CA A:ALA561 3.7 34.0 1.0
CB A:ALA561 3.8 34.8 1.0
OG A:SER549 3.9 52.6 1.0
CB A:SER549 4.0 42.2 1.0
N A:ALA561 4.0 34.0 1.0
CB A:ALA547 4.1 35.8 1.0
CG2 A:ILE560 4.2 34.4 1.0
C A:SER548 4.2 40.1 1.0
N A:SER549 4.3 36.0 1.0
N A:SER548 4.3 37.1 1.0
O A:SER548 4.4 42.5 1.0
C A:ILE560 4.6 30.7 1.0
CA A:SER548 4.7 36.9 1.0
CA A:SER549 4.7 40.0 1.0
C A:ALA547 4.8 37.9 1.0
O A:ILE560 4.8 30.2 1.0
O A:ALA557 4.8 33.1 1.0
O A:HIS572 4.9 38.3 1.0
CD2 A:LEU573 4.9 37.3 1.0
CB A:VAL446 4.9 50.6 1.0
CB A:THR571 4.9 39.5 1.0

Xenon binding site 6 out of 12 in 7tsj

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Xenon binding site 6 out of 12 in the Xenon-Bound Structure of Carbon Monoxide Dehydrogenase (Codh) From Desulfovibrio Vulgaris


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 6 of Xenon-Bound Structure of Carbon Monoxide Dehydrogenase (Codh) From Desulfovibrio Vulgaris within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Xe709

b:45.6
occ:0.70
 O A:GLY546 3.5 36.2 1.0
CG2 A:ILE525 3.7 39.6 1.0
N A:GLY444 3.8 38.1 1.0
O A:PHE442 3.9 42.6 1.0
CB A:VAL545 4.0 39.4 1.0
SG A:CYS529 4.1 45.4 1.0
CG1 A:VAL545 4.2 43.3 1.0
CD1 A:LEU474 4.2 38.5 1.0
C A:PHE442 4.2 43.4 1.0
CB A:PHE442 4.3 44.1 1.0
XE A:XE710 4.3 61.8 0.5
C A:VAL443 4.3 40.5 1.0
N A:GLY546 4.4 41.4 1.0
CA A:VAL443 4.4 38.7 1.0
CA A:GLY444 4.5 36.6 1.0
N A:VAL443 4.5 39.9 1.0
C A:GLY546 4.5 36.6 1.0
CA A:VAL545 4.7 43.6 1.0
CG2 A:VAL545 5.0 40.0 1.0
CA A:PHE442 5.0 45.3 1.0

Xenon binding site 7 out of 12 in 7tsj

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Xenon binding site 7 out of 12 in the Xenon-Bound Structure of Carbon Monoxide Dehydrogenase (Codh) From Desulfovibrio Vulgaris


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 7 of Xenon-Bound Structure of Carbon Monoxide Dehydrogenase (Codh) From Desulfovibrio Vulgaris within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Xe710

b:61.8
occ:0.50
 CG A:LEU528 3.9 41.1 1.0
CD2 A:LEU528 3.9 39.8 1.0
CD1 A:LEU532 4.0 49.9 1.0
CG A:PHE442 4.0 47.9 1.0
SG A:CYS529 4.0 45.4 1.0
CD1 A:PHE442 4.0 51.9 1.0
CB A:PHE442 4.2 44.1 1.0
XE A:XE709 4.3 45.6 0.7
CG1 A:VAL545 4.3 43.3 1.0
CD1 A:LEU474 4.3 38.5 1.0
CD2 A:PHE442 4.5 48.3 1.0
CB A:LEU528 4.5 41.0 1.0
N A:CYS529 4.5 41.8 1.0
CE1 A:PHE442 4.6 53.4 1.0
CA A:CYS529 4.7 42.9 1.0
C A:LEU528 4.8 41.7 1.0
CE2 A:PHE442 5.0 51.6 1.0

Xenon binding site 8 out of 12 in 7tsj

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Xenon binding site 8 out of 12 in the Xenon-Bound Structure of Carbon Monoxide Dehydrogenase (Codh) From Desulfovibrio Vulgaris


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 8 of Xenon-Bound Structure of Carbon Monoxide Dehydrogenase (Codh) From Desulfovibrio Vulgaris within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Xe711

b:71.0
occ:0.50
 CD1 A:LEU536 3.9 48.9 1.0
CG1 A:VAL434 4.1 55.9 1.0
CD A:PRO544 4.1 44.6 1.0
CB A:VAL434 4.3 56.5 1.0
CG2 A:VAL434 4.3 51.5 1.0
CG A:PRO544 4.4 48.8 1.0
CD2 A:LEU543 4.6 45.5 1.0
CG1 A:ILE431 4.7 59.3 1.0
CD1 A:LEU532 4.7 49.9 1.0
CG2 A:ILE431 4.8 63.1 1.0
CB A:LEU532 4.9 47.9 1.0
CA A:ILE431 4.9 59.3 1.0
CE1 A:PHE442 5.0 53.4 1.0
CD2 A:LEU532 5.0 54.9 1.0

Xenon binding site 9 out of 12 in 7tsj

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Xenon binding site 9 out of 12 in the Xenon-Bound Structure of Carbon Monoxide Dehydrogenase (Codh) From Desulfovibrio Vulgaris


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 9 of Xenon-Bound Structure of Carbon Monoxide Dehydrogenase (Codh) From Desulfovibrio Vulgaris within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Xe712

b:59.8
occ:0.40
 CE2 A:PHE442 3.6 51.6 1.0
CD2 A:LEU430 3.9 57.5 1.0
CD2 A:LEU528 4.0 39.8 1.0
CD2 A:PHE442 4.0 48.3 1.0
XE A:XE713 4.0 74.2 0.4
SD A:MET472 4.1 55.8 1.0
CG2 A:ILE419 4.1 44.2 1.0
CD1 A:LEU514 4.2 48.1 1.0
CD2 A:LEU474 4.2 40.4 1.0
CD1 A:ILE419 4.3 45.4 1.0
CZ A:PHE442 4.5 57.0 1.0
CD1 A:LEU430 4.5 59.6 1.0
CG1 A:ILE419 4.9 42.8 1.0
CG A:LEU430 4.9 56.4 1.0
CD1 A:LEU474 4.9 38.5 1.0

Xenon binding site 10 out of 12 in 7tsj

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Xenon binding site 10 out of 12 in the Xenon-Bound Structure of Carbon Monoxide Dehydrogenase (Codh) From Desulfovibrio Vulgaris


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 10 of Xenon-Bound Structure of Carbon Monoxide Dehydrogenase (Codh) From Desulfovibrio Vulgaris within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Xe713

b:74.2
occ:0.40
 XE A:XE714 3.4 50.6 0.3
CD1 A:LEU430 3.6 59.6 1.0
CD1 A:LEU508 3.9 63.2 1.0
SD A:MET472 4.0 55.8 1.0
XE A:XE712 4.0 59.8 0.4
CE A:MET472 4.1 46.1 1.0
CD2 A:LEU423 4.2 54.0 1.0
CD1 A:ILE439 4.4 56.1 1.0
CG A:LEU430 4.7 56.4 1.0
CD2 A:LEU430 4.8 57.5 1.0
CG1 A:VAL504 4.8 54.7 1.0
CD1 A:LEU423 4.9 53.7 1.0
CE2 A:PHE442 5.0 51.6 1.0

Reference:

A.Biester, S.Dementin, C.L.Drennan. Visualizing the Gas Channel of A Monofunctional Carbon Monoxide Dehydrogenase. J.Inorg.Biochem. V. 230 11774 2022.
ISSN: ISSN 0162-0134
PubMed: 35278753
DOI: 10.1016/J.JINORGBIO.2022.111774
Page generated: Sat Oct 12 20:08:36 2024

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