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Xenon in PDB 9kul: Bovine Heart Cytochrome C Oxidase in the Xenon-Bound Fully Oxidized State Under Anaerobic Condition

Enzymatic activity of Bovine Heart Cytochrome C Oxidase in the Xenon-Bound Fully Oxidized State Under Anaerobic Condition

All present enzymatic activity of Bovine Heart Cytochrome C Oxidase in the Xenon-Bound Fully Oxidized State Under Anaerobic Condition:
7.1.1.9;

Protein crystallography data

The structure of Bovine Heart Cytochrome C Oxidase in the Xenon-Bound Fully Oxidized State Under Anaerobic Condition, PDB code: 9kul was solved by K.Muramoto, K.Shinzawa-Itoh, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.00 / 1.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 181.9, 204, 178, 90, 90, 90
R / Rfree (%) 12 / 15.5

Other elements in 9kul:

The structure of Bovine Heart Cytochrome C Oxidase in the Xenon-Bound Fully Oxidized State Under Anaerobic Condition also contains other interesting chemical elements:

Iron (Fe) 4 atoms
Magnesium (Mg) 2 atoms
Copper (Cu) 6 atoms
Zinc (Zn) 2 atoms
Sodium (Na) 2 atoms

Xenon Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 14;

Binding sites:

The binding sites of Xenon atom in the Bovine Heart Cytochrome C Oxidase in the Xenon-Bound Fully Oxidized State Under Anaerobic Condition (pdb code 9kul). This binding sites where shown within 5.0 Angstroms radius around Xenon atom.
In total 14 binding sites of Xenon where determined in the Bovine Heart Cytochrome C Oxidase in the Xenon-Bound Fully Oxidized State Under Anaerobic Condition, PDB code: 9kul:
Jump to Xenon binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Xenon binding site 1 out of 14 in 9kul

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Xenon binding site 1 out of 14 in the Bovine Heart Cytochrome C Oxidase in the Xenon-Bound Fully Oxidized State Under Anaerobic Condition


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 1 of Bovine Heart Cytochrome C Oxidase in the Xenon-Bound Fully Oxidized State Under Anaerobic Condition within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Xe616

b:43.4
occ:1.00
 OG A:SER149 3.4 34.0 1.0
CD2 A:LEU150 3.7 36.8 1.0
CZ A:PHE68 3.8 31.3 1.0
CB A:PHE67 3.9 30.8 1.0
CG A:PHE67 4.0 29.1 1.0
CD2 A:PHE67 4.0 30.6 1.0
CG A:LEU150 4.2 31.9 1.0
CE2 A:PHE68 4.2 32.4 1.0
CD1 A:PHE63 4.2 31.3 1.0
CB A:PHE63 4.2 29.4 1.0
N A:LEU150 4.2 31.0 1.0
CB A:SER149 4.3 29.6 1.0
C A:SER149 4.3 29.4 1.0
O A:SER149 4.3 30.5 1.0
CA A:LEU150 4.3 29.8 1.0
OG A:SER108 4.4 30.1 1.0
CE1 A:PHE68 4.4 28.9 1.0
CG A:PHE63 4.4 30.0 1.0
CB A:ALA153 4.6 31.9 1.0
CE2 A:PHE67 4.7 31.2 1.0
CD1 A:PHE67 4.7 30.8 1.0
O A:PHE63 4.7 28.7 1.0
CB A:LEU150 4.9 29.7 1.0
O A:HOH2034 4.9 60.5 1.0
CE1 A:PHE63 4.9 29.1 1.0
CA A:SER149 4.9 30.9 1.0
CD1 A:LEU112 4.9 38.2 1.0
CA A:PHE63 5.0 27.3 1.0

Xenon binding site 2 out of 14 in 9kul

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Xenon binding site 2 out of 14 in the Bovine Heart Cytochrome C Oxidase in the Xenon-Bound Fully Oxidized State Under Anaerobic Condition


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 2 of Bovine Heart Cytochrome C Oxidase in the Xenon-Bound Fully Oxidized State Under Anaerobic Condition within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Xe617

b:42.4
occ:0.82
 O A:LEU150 3.5 32.5 1.0
CA A:ALA203 3.8 29.9 1.0
N A:ALA203 3.8 29.8 1.0
CD2 A:LEU202 3.8 33.7 1.0
CD1 A:ILE206 3.9 31.2 1.0
CB A:ALA203 4.0 30.9 1.0
O A:LEU199 4.0 29.5 1.0
C A:LEU150 4.0 30.8 1.0
CG A:LEU202 4.0 28.5 1.0
CA A:GLY154 4.1 30.6 1.0
C38 G:PEK101 4.2 77.5 1.0
CA A:HIS151 4.3 30.0 1.0
CB A:LEU202 4.4 28.7 1.0
N A:HIS151 4.4 30.8 1.0
CD2 A:LEU199 4.4 32.4 1.0
C A:LEU202 4.4 28.4 1.0
CD2 A:HIS151 4.6 41.1 1.0
N A:GLY154 4.6 29.8 1.0
CG1 A:ILE206 4.7 30.4 1.0
CB A:LEU150 4.7 29.7 1.0
O A:HIS151 4.8 30.9 1.0
O A:LEU202 4.8 30.0 1.0
C A:LEU199 5.0 30.9 1.0
CA A:LEU150 5.0 29.8 1.0
C A:HIS151 5.0 32.2 1.0

Xenon binding site 3 out of 14 in 9kul

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Xenon binding site 3 out of 14 in the Bovine Heart Cytochrome C Oxidase in the Xenon-Bound Fully Oxidized State Under Anaerobic Condition


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 3 of Bovine Heart Cytochrome C Oxidase in the Xenon-Bound Fully Oxidized State Under Anaerobic Condition within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Xe618

b:47.6
occ:0.15
 CD2 A:LEU113 2.6 34.1 0.5
CD2 A:LEU112 3.3 73.0 1.0
CG A:LEU113 3.6 34.2 0.5
CA A:LEU113 4.0 37.2 0.5
CD1 A:LEU112 4.1 38.2 1.0
CB A:ALA60 4.1 32.0 1.0
N A:LEU113 4.1 32.9 0.5
CA A:LEU113 4.1 36.8 0.5
N A:LEU113 4.1 33.0 0.5
CG A:LEU112 4.2 39.6 1.0
O A:LEU112 4.2 33.4 1.0
C A:LEU112 4.3 33.7 1.0
CB A:LEU113 4.3 35.9 0.5
CG2 A:VAL64 4.3 30.0 1.0
CE1 A:PHE109 4.4 33.9 1.0
OG A:SER116 4.4 38.7 1.0
CB A:LEU112 4.7 34.1 1.0
CG1 A:VAL29 4.7 33.0 1.0
CD1 A:LEU113 4.8 40.7 0.5
CD1 A:LEU33 4.9 31.9 1.0
CD1 L:ILE39 4.9 48.3 1.0
CB A:SER116 4.9 33.4 1.0
CD1 A:PHE109 5.0 32.6 1.0

Xenon binding site 4 out of 14 in 9kul

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Xenon binding site 4 out of 14 in the Bovine Heart Cytochrome C Oxidase in the Xenon-Bound Fully Oxidized State Under Anaerobic Condition


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 4 of Bovine Heart Cytochrome C Oxidase in the Xenon-Bound Fully Oxidized State Under Anaerobic Condition within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Xe619

b:39.9
occ:0.21
 CD2 A:LEU33 3.8 32.3 1.0
CG2 L:ILE39 3.8 41.3 1.0
CB A:SER116 4.1 33.4 1.0
CB L:ILE39 4.2 38.5 1.0
CG1 A:VAL56 4.2 35.5 1.0
OG A:SER116 4.3 38.7 1.0
CG2 A:VAL57 4.3 33.3 1.0
CA A:VAL57 4.6 30.8 1.0
CB A:ALA60 4.7 32.0 1.0
O L:PRO36 4.7 34.8 1.0
N A:VAL57 4.8 29.9 1.0
O A:VAL56 4.8 31.6 1.0
CD1 L:ILE39 4.8 48.3 1.0
CG2 L:VAL40 4.8 43.2 1.0
CA L:PRO36 4.9 32.0 1.0
C A:VAL56 4.9 31.4 1.0
CB L:PRO36 4.9 32.7 1.0

Xenon binding site 5 out of 14 in 9kul

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Xenon binding site 5 out of 14 in the Bovine Heart Cytochrome C Oxidase in the Xenon-Bound Fully Oxidized State Under Anaerobic Condition


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 5 of Bovine Heart Cytochrome C Oxidase in the Xenon-Bound Fully Oxidized State Under Anaerobic Condition within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Xe620

b:46.4
occ:0.80
 CG1 A:VAL394 3.9 31.1 0.5
O A:HOH1937 3.9 32.2 1.0
CG2 A:ILE471 3.9 35.0 1.0
CG A:MET468 4.0 37.9 1.0
ND1 A:HIS413 4.2 34.5 1.0
CE A:MET390 4.2 53.5 1.0
CB A:ILE471 4.3 31.1 1.0
CG2 A:VAL394 4.5 30.0 0.5
CD1 A:ILE471 4.5 34.0 1.0
CE1 A:HIS413 4.6 35.6 1.0
CE2 A:PHE393 4.6 34.8 1.0
CD2 A:PHE393 4.6 34.5 1.0
CD1 A:LEU405 4.6 38.8 1.0
CA A:MET468 4.7 31.4 1.0
CG A:HIS413 4.7 31.1 1.0
CB A:MET468 4.7 34.5 1.0
O A:MET468 4.7 32.2 1.0
CB A:ALA410 4.8 31.4 1.0
CA A:ALA410 5.0 30.7 1.0

Xenon binding site 6 out of 14 in 9kul

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Xenon binding site 6 out of 14 in the Bovine Heart Cytochrome C Oxidase in the Xenon-Bound Fully Oxidized State Under Anaerobic Condition


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 6 of Bovine Heart Cytochrome C Oxidase in the Xenon-Bound Fully Oxidized State Under Anaerobic Condition within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Xe301

b:46.2
occ:0.43
 CG2 B:VAL31 3.3 44.8 1.0
CG2 A:ILE356 3.6 33.6 1.0
CG2 B:THR27 3.9 42.9 1.0
O A:LEU353 3.9 30.2 1.0
CD1 B:ILE76 4.0 39.0 1.0
CB A:ILE356 4.1 31.2 1.0
CG2 B:ILE30 4.1 46.8 1.0
O B:THR27 4.2 38.0 1.0
CD2 A:LEU353 4.2 34.0 1.0
N B:VAL31 4.4 36.1 1.0
C25 A:HEA602 4.5 36.6 1.0
CG2 A:VAL357 4.5 31.2 1.0
CB B:VAL31 4.5 37.8 1.0
CA B:VAL31 4.5 37.0 1.0
CB B:ILE30 4.6 45.1 1.0
N A:VAL357 4.7 29.6 1.0
CB A:LEU353 4.7 29.9 1.0
C A:LEU353 4.8 30.7 1.0
CA A:LEU353 4.8 29.5 1.0
C A:ILE356 4.9 31.5 1.0
C B:ILE30 4.9 37.3 1.0

Xenon binding site 7 out of 14 in 9kul

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Xenon binding site 7 out of 14 in the Bovine Heart Cytochrome C Oxidase in the Xenon-Bound Fully Oxidized State Under Anaerobic Condition


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 7 of Bovine Heart Cytochrome C Oxidase in the Xenon-Bound Fully Oxidized State Under Anaerobic Condition within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Xe325

b:44.8
occ:0.22
 C25 C:DMU324 0.8 63.1 0.6
C28 C:DMU324 1.3 58.8 0.6
C31 C:DMU324 1.9 51.9 0.6
C22 C:DMU324 2.0 59.3 0.6
C19 C:DMU324 3.0 48.9 0.6
C34 C:DMU324 3.3 39.8 0.6
CE C:MET33 3.4 42.6 0.5
SD C:MET33 3.7 39.1 0.5
CG2 C:THR32 4.0 38.1 1.0
O C:SER29 4.2 35.3 1.0
CE2 C:PHE37 4.2 47.1 1.0
C37 C:DMU324 4.3 39.6 0.6
CB C:THR32 4.3 33.5 1.0
CD2 C:PHE37 4.3 45.1 1.0
N C:MET33 4.4 34.3 0.5
C18 C:DMU324 4.4 57.7 0.6
N C:MET33 4.5 33.9 0.5
CB J:CYS49 4.6 42.5 1.0
CA C:MET33 4.7 37.4 0.5
CB J:ALA53 4.7 48.8 1.0
O J:CYS49 4.7 46.7 1.0
CA C:MET33 4.7 36.0 0.5
CB C:MET33 4.7 40.3 0.5
C C:THR32 4.8 35.6 1.0
CB C:MET33 4.8 42.6 0.5
C J:CYS49 4.8 44.6 1.0

Xenon binding site 8 out of 14 in 9kul

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Xenon binding site 8 out of 14 in the Bovine Heart Cytochrome C Oxidase in the Xenon-Bound Fully Oxidized State Under Anaerobic Condition


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 8 of Bovine Heart Cytochrome C Oxidase in the Xenon-Bound Fully Oxidized State Under Anaerobic Condition within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Xe616

b:43.9
occ:0.91
 OG N:SER149 3.4 36.0 1.0
CD2 N:LEU150 3.6 38.1 1.0
CZ N:PHE68 3.8 35.6 1.0
CB N:PHE67 3.9 32.4 1.0
CG N:PHE67 4.0 32.1 1.0
CD2 N:PHE67 4.0 32.6 1.0
CG N:LEU150 4.1 34.1 1.0
CD1 N:PHE63 4.2 32.6 1.0
CE2 N:PHE68 4.2 35.0 1.0
CB N:PHE63 4.2 31.5 1.0
N N:LEU150 4.3 32.1 1.0
C N:SER149 4.3 32.1 1.0
CB N:SER149 4.3 32.8 1.0
CA N:LEU150 4.3 32.7 1.0
CG N:PHE63 4.3 32.7 1.0
O N:SER149 4.3 32.3 1.0
CE1 N:PHE68 4.4 33.4 1.0
OG N:SER108 4.4 33.2 1.0
CB N:ALA153 4.6 34.0 1.0
CD1 N:PHE67 4.7 32.8 1.0
CE2 N:PHE67 4.8 32.8 1.0
O N:PHE63 4.8 32.4 1.0
CD1 N:LEU112 4.8 40.2 1.0
CB N:LEU150 4.8 32.1 1.0
CE1 N:PHE63 4.9 35.5 1.0
CA N:SER149 4.9 33.1 1.0

Xenon binding site 9 out of 14 in 9kul

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Xenon binding site 9 out of 14 in the Bovine Heart Cytochrome C Oxidase in the Xenon-Bound Fully Oxidized State Under Anaerobic Condition


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 9 of Bovine Heart Cytochrome C Oxidase in the Xenon-Bound Fully Oxidized State Under Anaerobic Condition within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Xe617

b:42.6
occ:0.78
 O N:LEU150 3.5 33.4 1.0
CA N:ALA203 3.8 32.4 1.0
N N:ALA203 3.8 32.3 1.0
CD2 N:LEU202 3.8 31.3 1.0
CB N:ALA203 3.9 31.9 1.0
CD1 N:ILE206 3.9 33.4 1.0
O N:LEU199 4.0 31.0 1.0
C N:LEU150 4.1 30.9 1.0
CG N:LEU202 4.1 31.2 1.0
CA N:GLY154 4.1 32.9 1.0
C38 T:PEK101 4.2 76.7 1.0
CA N:HIS151 4.2 31.5 1.0
CB N:LEU202 4.4 28.9 1.0
N N:HIS151 4.4 33.4 1.0
C N:LEU202 4.4 30.0 1.0
CD2 N:LEU199 4.4 32.8 1.0
CD2 N:HIS151 4.6 41.0 1.0
N N:GLY154 4.6 31.5 1.0
CG1 N:ILE206 4.8 32.6 1.0
CB N:LEU150 4.8 32.1 1.0
O N:HIS151 4.8 31.1 1.0
O N:LEU202 4.9 31.7 1.0
C N:HIS151 4.9 31.8 1.0
C N:LEU199 5.0 29.9 1.0
CA N:LEU150 5.0 32.7 1.0

Xenon binding site 10 out of 14 in 9kul

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Xenon binding site 10 out of 14 in the Bovine Heart Cytochrome C Oxidase in the Xenon-Bound Fully Oxidized State Under Anaerobic Condition


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 10 of Bovine Heart Cytochrome C Oxidase in the Xenon-Bound Fully Oxidized State Under Anaerobic Condition within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Xe618

b:48.7
occ:0.13
 CD2 N:LEU113 2.5 37.6 0.5
CD2 N:LEU112 3.2 76.1 1.0
CG N:LEU113 3.6 40.9 0.5
CA N:LEU113 4.0 38.8 0.5
CA N:LEU113 4.2 40.5 0.5
CB N:ALA60 4.2 35.1 1.0
N N:LEU113 4.2 35.3 0.5
N N:LEU113 4.2 34.0 0.5
CG N:LEU112 4.2 41.1 1.0
CD1 N:LEU112 4.2 40.2 1.0
CB N:LEU113 4.2 40.1 0.5
O N:LEU112 4.3 36.5 1.0
C N:LEU112 4.3 35.8 1.0
CG2 N:VAL64 4.3 35.0 1.0
CE1 N:PHE109 4.4 36.1 1.0
OG N:SER116 4.5 41.1 1.0
CG1 N:VAL29 4.7 35.6 1.0
CB N:LEU112 4.7 35.2 1.0
CD1 Y:ILE39 4.8 51.2 1.0
CD1 N:LEU113 4.8 44.6 0.5
CD1 N:LEU33 4.9 35.5 1.0
CD1 N:PHE109 4.9 36.1 1.0
CB N:LEU113 5.0 42.8 0.5

Reference:

K.Muramoto, T.Ide, K.Shinzawa-Itoh. The Binding Sites of Carbon Dioxide, Nitrous Oxide, and Xenon Reveal A Putative Exhaust Channel For Bovine Cytochrome C Oxidase. J.Biol.Chem. 10395 2025.
ISSN: ESSN 1083-351X
PubMed: 40543594
DOI: 10.1016/J.JBC.2025.110395
Page generated: Tue Aug 19 18:30:32 2025

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