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Copper in PDB 9kum: Bovine Heart Cytochrome C Oxidase in the Xenon-Bound Fully Reduced State

Enzymatic activity of Bovine Heart Cytochrome C Oxidase in the Xenon-Bound Fully Reduced State

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

Protein crystallography data

The structure of Bovine Heart Cytochrome C Oxidase in the Xenon-Bound Fully Reduced State, PDB code: 9kum 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 (°) 182.5, 204.7, 177.8, 90, 90, 90
R / Rfree (%) 13.2 / 16.9

Other elements in 9kum:

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

Sodium (Na) 2 atoms
Zinc (Zn) 2 atoms
Magnesium (Mg) 2 atoms
Iron (Fe) 4 atoms
Xenon (Xe) 16 atoms

Copper Binding Sites:

The binding sites of Copper atom in the Bovine Heart Cytochrome C Oxidase in the Xenon-Bound Fully Reduced State (pdb code 9kum). 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 Reduced State, PDB code: 9kum:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6;

Copper binding site 1 out of 6 in 9kum

Go back to Copper Binding Sites List in 9kum
Copper binding site 1 out of 6 in the Bovine Heart Cytochrome C Oxidase in the Xenon-Bound Fully Reduced State


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 Reduced State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu603

b:33.6
occ:1.00
 NE2 A:HIS291 2.0 33.4 1.0
ND1 A:HIS240 2.0 34.2 1.0
NE2 A:HIS290 2.1 34.7 1.0
CD2 A:HIS291 2.9 30.9 1.0
CE1 A:HIS291 3.0 32.1 1.0
CG A:HIS240 3.0 30.5 1.0
CE1 A:HIS240 3.0 32.1 1.0
CE1 A:HIS290 3.0 33.5 1.0
CD2 A:HIS290 3.1 33.0 1.0
CB A:HIS240 3.3 31.8 1.0
CA A:HIS240 3.9 30.9 1.0
CG A:HIS291 4.0 31.3 1.0
ND1 A:HIS291 4.0 32.9 1.0
CD2 A:HIS240 4.1 31.6 1.0
NE2 A:HIS240 4.1 35.0 1.0
ND1 A:HIS290 4.2 33.8 1.0
CG A:HIS290 4.2 32.3 1.0
C1A A:HEA602 4.6 33.6 1.0
NA A:HEA602 4.7 32.2 1.0
C4A A:HEA602 4.7 33.3 1.0
N A:HIS240 4.7 32.5 1.0
CG2 A:VAL243 4.7 33.8 1.0
C2A A:HEA602 4.8 30.9 1.0
C3A A:HEA602 5.0 35.0 1.0

Copper binding site 2 out of 6 in 9kum

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Copper binding site 2 out of 6 in the Bovine Heart Cytochrome C Oxidase in the Xenon-Bound Fully Reduced State


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 Reduced State within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu302

b:36.6
occ:1.00
 CU1 B:CUA302 0.0 36.6 1.0
ND1 B:HIS161 2.1 37.5 1.0
SD B:MET207 2.4 36.9 1.0
SG B:CYS196 2.4 35.8 1.0
SG B:CYS200 2.4 35.1 1.0
CU2 B:CUA302 2.5 35.9 1.0
CE1 B:HIS161 2.9 36.9 1.0
CE B:MET207 3.1 37.2 1.0
CG B:HIS161 3.2 35.4 1.0
CB B:CYS200 3.3 36.4 1.0
CB B:CYS196 3.4 34.7 1.0
CG B:MET207 3.5 38.5 1.0
CB B:HIS161 3.6 36.6 1.0
O B:GLU198 4.1 37.8 1.0
NE2 B:HIS161 4.1 34.5 1.0
CA B:HIS161 4.3 35.7 1.0
CD2 B:HIS161 4.3 36.8 1.0
ND1 B:HIS204 4.5 38.4 1.0
CD1 B:TRP104 4.6 37.4 1.0
O B:HIS102 4.6 37.4 1.0
CA B:CYS200 4.7 37.1 1.0
O B:LEU160 4.8 34.8 1.0
CA B:HIS204 4.8 36.4 1.0
CA B:CYS196 4.8 34.8 1.0
CB B:MET207 4.9 39.4 1.0

Copper binding site 3 out of 6 in 9kum

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Copper binding site 3 out of 6 in the Bovine Heart Cytochrome C Oxidase in the Xenon-Bound Fully Reduced State


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 Reduced State within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu302

b:35.9
occ:1.00
 CU2 B:CUA302 0.0 35.9 1.0
ND1 B:HIS204 2.0 38.4 1.0
SG B:CYS200 2.3 35.1 1.0
SG B:CYS196 2.3 35.8 1.0
O B:GLU198 2.4 37.8 1.0
CU1 B:CUA302 2.5 36.6 1.0
CE1 B:HIS204 3.0 38.0 1.0
CG B:HIS204 3.1 36.6 1.0
CB B:CYS196 3.3 34.7 1.0
CB B:CYS200 3.3 36.4 1.0
CB B:HIS204 3.5 36.5 1.0
CA B:HIS204 3.5 36.4 1.0
C B:GLU198 3.5 33.4 1.0
N B:CYS200 3.7 36.3 1.0
O B:HIS204 3.8 37.1 1.0
NE2 B:HIS204 4.1 37.2 1.0
CA B:CYS200 4.2 37.1 1.0
C B:HIS204 4.2 37.7 1.0
CD2 B:HIS204 4.2 38.0 1.0
ND1 B:HIS161 4.2 37.5 1.0
C B:CYS196 4.2 36.6 1.0
N B:GLU198 4.2 36.4 1.0
C B:ILE199 4.3 36.4 1.0
O B:CYS196 4.3 35.6 1.0
CA B:ILE199 4.3 36.2 1.0
SD B:MET207 4.3 36.9 1.0
N B:ILE199 4.4 35.3 1.0
CA B:CYS196 4.4 34.8 1.0
CA B:GLU198 4.5 37.1 1.0
N B:SER197 4.6 35.5 1.0
CG B:MET207 4.7 38.5 1.0
N B:HIS204 4.7 36.6 1.0
CA B:HIS161 4.9 35.7 1.0

Copper binding site 4 out of 6 in 9kum

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Copper binding site 4 out of 6 in the Bovine Heart Cytochrome C Oxidase in the Xenon-Bound Fully Reduced State


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 Reduced State within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Cu604

b:34.6
occ:1.00
 ND1 N:HIS240 2.0 33.3 1.0
NE2 N:HIS291 2.0 34.5 1.0
NE2 N:HIS290 2.1 35.6 1.0
CD2 N:HIS291 2.9 32.9 1.0
CE1 N:HIS240 3.0 32.1 1.0
CE1 N:HIS291 3.0 36.5 1.0
CG N:HIS240 3.0 32.8 1.0
CD2 N:HIS290 3.1 33.0 1.0
CE1 N:HIS290 3.1 37.1 1.0
CB N:HIS240 3.3 33.2 1.0
CA N:HIS240 3.9 35.3 1.0
CG N:HIS291 4.0 33.5 1.0
ND1 N:HIS291 4.0 35.0 1.0
CD2 N:HIS240 4.1 32.2 1.0
NE2 N:HIS240 4.1 36.2 1.0
ND1 N:HIS290 4.2 35.0 1.0
CG N:HIS290 4.2 34.3 1.0
C1A N:HEA603 4.6 33.0 1.0
C4A N:HEA603 4.7 33.5 1.0
CG2 N:VAL243 4.7 35.1 1.0
NA N:HEA603 4.7 36.0 1.0
N N:HIS240 4.8 32.9 1.0
C2A N:HEA603 4.9 35.3 1.0
C3A N:HEA603 4.9 33.7 1.0

Copper binding site 5 out of 6 in 9kum

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Copper binding site 5 out of 6 in the Bovine Heart Cytochrome C Oxidase in the Xenon-Bound Fully Reduced State


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 Reduced State within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Cu306

b:38.3
occ:1.00
 CU1 O:CUA306 0.0 38.3 1.0
ND1 O:HIS161 2.1 39.5 1.0
SD O:MET207 2.4 39.1 1.0
SG O:CYS196 2.4 38.1 1.0
SG O:CYS200 2.4 36.8 1.0
CU2 O:CUA306 2.5 37.6 1.0
CE1 O:HIS161 2.9 41.0 1.0
CE O:MET207 3.1 38.5 1.0
CG O:HIS161 3.2 36.1 1.0
CB O:CYS200 3.3 37.1 1.0
CB O:CYS196 3.4 38.7 1.0
CG O:MET207 3.5 38.1 1.0
CB O:HIS161 3.6 38.3 1.0
O O:GLU198 4.0 38.3 1.0
NE2 O:HIS161 4.1 37.0 1.0
CD2 O:HIS161 4.2 38.1 1.0
CA O:HIS161 4.2 34.8 1.0
ND1 O:HIS204 4.5 38.8 1.0
CD1 O:TRP104 4.6 39.8 1.0
O O:HIS102 4.7 39.6 1.0
CA O:CYS200 4.7 37.5 1.0
CA O:HIS204 4.7 38.0 1.0
O O:LEU160 4.8 37.8 1.0
CA O:CYS196 4.8 35.9 1.0
CB O:MET207 4.9 39.0 1.0

Copper binding site 6 out of 6 in 9kum

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Copper binding site 6 out of 6 in the Bovine Heart Cytochrome C Oxidase in the Xenon-Bound Fully Reduced State


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 Reduced State within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Cu306

b:37.6
occ:1.00
 CU2 O:CUA306 0.0 37.6 1.0
ND1 O:HIS204 2.0 38.8 1.0
SG O:CYS200 2.3 36.8 1.0
SG O:CYS196 2.3 38.1 1.0
O O:GLU198 2.4 38.3 1.0
CU1 O:CUA306 2.5 38.3 1.0
CE1 O:HIS204 3.0 37.2 1.0
CG O:HIS204 3.1 39.1 1.0
CB O:CYS196 3.3 38.7 1.0
CB O:CYS200 3.4 37.1 1.0
CB O:HIS204 3.5 38.5 1.0
CA O:HIS204 3.5 38.0 1.0
C O:GLU198 3.5 34.6 1.0
N O:CYS200 3.7 39.2 1.0
O O:HIS204 3.8 38.1 1.0
NE2 O:HIS204 4.1 38.3 1.0
C O:HIS204 4.1 37.5 1.0
CD2 O:HIS204 4.2 38.2 1.0
CA O:CYS200 4.2 37.5 1.0
C O:CYS196 4.2 38.8 1.0
N O:GLU198 4.2 37.8 1.0
ND1 O:HIS161 4.2 39.5 1.0
O O:CYS196 4.3 37.0 1.0
C O:ILE199 4.3 36.1 1.0
CA O:ILE199 4.3 36.4 1.0
N O:ILE199 4.3 37.0 1.0
CA O:CYS196 4.3 35.9 1.0
SD O:MET207 4.4 39.1 1.0
CA O:GLU198 4.5 36.6 1.0
N O:SER197 4.6 37.5 1.0
CG O:MET207 4.7 38.1 1.0
N O:HIS204 4.8 37.2 1.0
CA O:HIS161 4.9 34.8 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 10:02:32 2025

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