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Copper 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:

Xenon (Xe) 14 atoms
Iron (Fe) 4 atoms
Magnesium (Mg) 2 atoms
Zinc (Zn) 2 atoms
Sodium (Na) 2 atoms

Copper Binding Sites:

The binding sites of Copper 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 Copper atom.
In total 6 binding sites of Copper where determined in the Bovine Heart Cytochrome C Oxidase in the Xenon-Bound Fully Oxidized State Under Anaerobic Condition, PDB code: 9kul:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6;

Copper binding site 1 out of 6 in 9kul

Go back to Copper Binding Sites List in 9kul
Copper binding site 1 out of 6 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 Copper with other atoms in the Cu 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:Cu603

b:30.0
occ:1.00
 ND1 A:HIS240 2.0 30.4 1.0
NE2 A:HIS291 2.0 28.3 1.0
NE2 A:HIS290 2.1 30.9 1.0
O2 A:PER606 2.3 37.8 1.0
O1 A:PER606 2.7 27.9 1.0
CE1 A:HIS291 3.0 27.7 1.0
CE1 A:HIS240 3.0 28.8 1.0
CG A:HIS240 3.0 28.1 1.0
CE1 A:HIS290 3.0 31.9 1.0
CD2 A:HIS291 3.0 26.9 1.0
CD2 A:HIS290 3.1 30.8 1.0
CB A:HIS240 3.3 29.0 1.0
CA A:HIS240 3.9 27.9 1.0
ND1 A:HIS291 4.1 27.4 1.0
NE2 A:HIS240 4.1 30.2 1.0
CD2 A:HIS240 4.1 27.6 1.0
CG A:HIS291 4.1 27.4 1.0
ND1 A:HIS290 4.2 29.9 1.0
CG A:HIS290 4.2 29.1 1.0
C1A A:HEA602 4.6 26.9 1.0
NA A:HEA602 4.6 28.0 1.0
C4A A:HEA602 4.7 26.5 1.0
N A:HIS240 4.7 28.7 1.0
CG2 A:VAL243 4.8 30.7 1.0
FE A:HEA602 4.9 28.9 1.0
C2A A:HEA602 4.9 26.3 1.0
C3A A:HEA602 5.0 27.3 1.0

Copper binding site 2 out of 6 in 9kul

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Copper binding site 2 out of 6 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 Copper with other atoms in the Cu 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
B:Cu302

b:31.3
occ:1.00
 CU1 B:CUA302 0.0 31.3 1.0
ND1 B:HIS161 2.1 32.2 1.0
SG B:CYS196 2.3 30.7 1.0
SD B:MET207 2.4 31.4 1.0
SG B:CYS200 2.4 30.7 1.0
CU2 B:CUA302 2.5 31.1 1.0
CE1 B:HIS161 3.0 29.9 1.0
CE B:MET207 3.2 31.5 1.0
CG B:HIS161 3.2 29.6 1.0
CB B:CYS200 3.3 30.7 1.0
CB B:CYS196 3.4 30.6 1.0
CG B:MET207 3.5 33.4 1.0
CB B:HIS161 3.6 30.9 1.0
O B:GLU198 4.0 31.7 1.0
NE2 B:HIS161 4.2 29.9 1.0
CA B:HIS161 4.3 28.5 1.0
CD2 B:HIS161 4.3 30.0 1.0
ND1 B:HIS204 4.5 33.5 1.0
O B:HIS102 4.6 32.5 1.0
CA B:CYS200 4.7 31.4 1.0
CA B:HIS204 4.7 30.1 1.0
O B:LEU160 4.7 30.5 1.0
CD1 B:TRP104 4.7 31.1 1.0
CA B:CYS196 4.8 29.7 1.0
CB B:MET207 4.9 32.1 1.0
O B:HIS204 4.9 31.3 1.0

Copper binding site 3 out of 6 in 9kul

Go back to Copper Binding Sites List in 9kul
Copper binding site 3 out of 6 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 Copper with other atoms in the Cu 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
B:Cu302

b:31.1
occ:1.00
 CU2 B:CUA302 0.0 31.1 1.0
ND1 B:HIS204 2.0 33.5 1.0
SG B:CYS200 2.3 30.7 1.0
SG B:CYS196 2.3 30.7 1.0
O B:GLU198 2.4 31.7 1.0
CU1 B:CUA302 2.5 31.3 1.0
CE1 B:HIS204 3.0 31.4 1.0
CG B:HIS204 3.1 29.2 1.0
CB B:CYS196 3.3 30.6 1.0
CB B:CYS200 3.3 30.7 1.0
C B:GLU198 3.5 28.6 1.0
CB B:HIS204 3.5 30.4 1.0
CA B:HIS204 3.6 30.1 1.0
N B:CYS200 3.7 29.9 1.0
O B:HIS204 3.8 31.3 1.0
CA B:CYS200 4.1 31.4 1.0
NE2 B:HIS204 4.1 30.8 1.0
N B:GLU198 4.1 31.3 1.0
C B:HIS204 4.2 31.0 1.0
CD2 B:HIS204 4.2 33.5 1.0
C B:ILE199 4.2 32.1 1.0
ND1 B:HIS161 4.2 32.2 1.0
C B:CYS196 4.2 31.6 1.0
O B:CYS196 4.2 30.8 1.0
N B:ILE199 4.3 30.4 1.0
CA B:ILE199 4.3 29.9 1.0
SD B:MET207 4.3 31.4 1.0
CA B:CYS196 4.4 29.7 1.0
CA B:GLU198 4.5 29.9 1.0
N B:SER197 4.6 30.2 1.0
CG B:MET207 4.7 33.4 1.0
N B:HIS204 4.8 31.1 1.0
CA B:HIS161 4.9 28.5 1.0

Copper binding site 4 out of 6 in 9kul

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Copper binding site 4 out of 6 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 Copper with other atoms in the Cu 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
N:Cu604

b:31.5
occ:1.00
 ND1 N:HIS240 2.0 30.6 1.0
NE2 N:HIS291 2.0 29.9 1.0
NE2 N:HIS290 2.1 32.6 1.0
O2 N:PER607 2.3 39.3 1.0
O1 N:PER607 2.7 30.1 1.0
CE1 N:HIS291 3.0 32.2 1.0
CE1 N:HIS240 3.0 29.5 1.0
CG N:HIS240 3.0 28.7 1.0
CD2 N:HIS291 3.0 29.6 1.0
CE1 N:HIS290 3.1 30.8 1.0
CD2 N:HIS290 3.1 31.2 1.0
CB N:HIS240 3.4 29.6 1.0
CA N:HIS240 3.9 30.4 1.0
ND1 N:HIS291 4.1 30.1 1.0
NE2 N:HIS240 4.1 29.2 1.0
CG N:HIS291 4.1 30.7 1.0
CD2 N:HIS240 4.1 28.2 1.0
ND1 N:HIS290 4.2 31.1 1.0
CG N:HIS290 4.2 30.9 1.0
C1A N:HEA603 4.6 28.4 1.0
NA N:HEA603 4.7 31.1 1.0
C4A N:HEA603 4.7 28.7 1.0
N N:HIS240 4.7 29.4 1.0
CG2 N:VAL243 4.9 32.2 1.0
FE N:HEA603 4.9 30.6 1.0
C2A N:HEA603 4.9 29.9 1.0
C3A N:HEA603 4.9 28.9 1.0

Copper binding site 5 out of 6 in 9kul

Go back to Copper Binding Sites List in 9kul
Copper binding site 5 out of 6 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 Copper with other atoms in the Cu 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
O:Cu305

b:35.0
occ:1.00
 CU1 O:CUA305 0.0 35.0 1.0
ND1 O:HIS161 2.1 37.2 1.0
SG O:CYS196 2.3 34.7 1.0
SG O:CYS200 2.4 35.2 1.0
SD O:MET207 2.4 35.0 1.0
CU2 O:CUA305 2.5 34.9 1.0
CE1 O:HIS161 3.0 34.7 1.0
CE O:MET207 3.2 36.1 1.0
CG O:HIS161 3.2 34.7 1.0
CB O:CYS200 3.3 34.7 1.0
CB O:CYS196 3.4 35.7 1.0
CG O:MET207 3.5 35.9 1.0
CB O:HIS161 3.6 34.9 1.0
O O:GLU198 4.0 34.7 1.0
NE2 O:HIS161 4.1 34.3 1.0
CA O:HIS161 4.2 33.5 1.0
CD2 O:HIS161 4.2 33.7 1.0
ND1 O:HIS204 4.5 36.8 1.0
CD1 O:TRP104 4.7 37.2 1.0
CA O:HIS204 4.7 35.2 1.0
O O:HIS102 4.7 36.8 1.0
CA O:CYS200 4.7 34.0 1.0
O O:LEU160 4.7 35.3 1.0
CA O:CYS196 4.8 33.2 1.0
CB O:MET207 4.9 37.7 1.0
O O:HIS204 4.9 34.1 1.0

Copper binding site 6 out of 6 in 9kul

Go back to Copper Binding Sites List in 9kul
Copper binding site 6 out of 6 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 Copper with other atoms in the Cu 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
O:Cu305

b:34.9
occ:1.00
 CU2 O:CUA305 0.0 34.9 1.0
ND1 O:HIS204 2.0 36.8 1.0
SG O:CYS200 2.3 35.2 1.0
O O:GLU198 2.3 34.7 1.0
SG O:CYS196 2.3 34.7 1.0
CU1 O:CUA305 2.5 35.0 1.0
CE1 O:HIS204 2.9 35.7 1.0
CG O:HIS204 3.1 34.5 1.0
CB O:CYS196 3.3 35.7 1.0
CB O:CYS200 3.3 34.7 1.0
C O:GLU198 3.5 32.3 1.0
CB O:HIS204 3.5 35.5 1.0
CA O:HIS204 3.6 35.2 1.0
N O:CYS200 3.8 34.8 1.0
O O:HIS204 3.8 34.1 1.0
NE2 O:HIS204 4.1 34.5 1.0
N O:GLU198 4.1 34.1 1.0
C O:HIS204 4.2 35.8 1.0
CA O:CYS200 4.2 34.0 1.0
CD2 O:HIS204 4.2 35.4 1.0
C O:CYS196 4.2 36.3 1.0
C O:ILE199 4.2 33.2 1.0
ND1 O:HIS161 4.2 37.2 1.0
O O:CYS196 4.2 32.9 1.0
N O:ILE199 4.3 34.4 1.0
CA O:ILE199 4.3 31.3 1.0
CA O:CYS196 4.4 33.2 1.0
SD O:MET207 4.4 35.0 1.0
CA O:GLU198 4.4 34.2 1.0
N O:SER197 4.7 34.7 1.0
CG O:MET207 4.7 35.9 1.0
N O:HIS204 4.8 35.2 1.0
CA O:HIS161 4.9 33.5 1.0

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: Mon Jul 14 10:00:56 2025

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