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Copper in PDB 9m56: Bovine Heart Cytochrome C Oxidase in the Fully Reduced State

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

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

Protein crystallography data

The structure of Bovine Heart Cytochrome C Oxidase in the Fully Reduced State, PDB code: 9m56 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 / 1.60
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 181.8, 204.1, 177.8, 90, 90, 90
R / Rfree (%) 12.6 / 15.5

Other elements in 9m56:

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

Magnesium (Mg) 2 atoms
Iron (Fe) 4 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 Fully Reduced State (pdb code 9m56). 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 Fully Reduced State, PDB code: 9m56:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6;

Copper binding site 1 out of 6 in 9m56

Go back to Copper Binding Sites List in 9m56
Copper binding site 1 out of 6 in the Bovine Heart Cytochrome C Oxidase in the 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 Fully Reduced State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu603

b:30.5
occ:1.00
 ND1 A:HIS240 2.0 29.7 1.0
NE2 A:HIS291 2.0 29.1 1.0
NE2 A:HIS290 2.1 30.5 1.0
CE1 A:HIS240 2.9 29.2 1.0
CD2 A:HIS291 3.0 29.6 1.0
CG A:HIS240 3.0 29.7 1.0
CE1 A:HIS291 3.0 29.6 1.0
CE1 A:HIS290 3.1 31.1 1.0
CD2 A:HIS290 3.1 29.2 1.0
CB A:HIS240 3.3 28.3 1.0
CA A:HIS240 3.9 27.7 1.0
CG A:HIS291 4.1 28.6 1.0
NE2 A:HIS240 4.1 31.0 1.0
CD2 A:HIS240 4.1 30.6 1.0
ND1 A:HIS291 4.1 29.8 1.0
ND1 A:HIS290 4.2 29.7 1.0
CG A:HIS290 4.2 28.0 1.0
C1A A:HEA602 4.6 29.9 1.0
NA A:HEA602 4.6 31.4 1.0
C4A A:HEA602 4.7 29.0 1.0
CG2 A:VAL243 4.7 30.6 1.0
N A:HIS240 4.7 28.2 1.0
C2A A:HEA602 4.8 27.6 1.0
C3A A:HEA602 5.0 28.8 1.0
CHA A:HEA602 5.0 28.4 1.0

Copper binding site 2 out of 6 in 9m56

Go back to Copper Binding Sites List in 9m56
Copper binding site 2 out of 6 in the Bovine Heart Cytochrome C Oxidase in the 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 Fully Reduced State within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu301

b:32.3
occ:1.00
 CU1 B:CUA301 0.0 32.3 1.0
ND1 B:HIS161 2.1 32.5 1.0
SD B:MET207 2.4 32.3 1.0
SG B:CYS196 2.4 32.1 1.0
SG B:CYS200 2.4 31.5 1.0
CU2 B:CUA301 2.5 32.1 1.0
CE1 B:HIS161 3.0 32.3 1.0
CE B:MET207 3.1 33.6 1.0
CG B:HIS161 3.2 32.7 1.0
CB B:CYS200 3.3 32.5 1.0
CB B:CYS196 3.4 31.0 1.0
CG B:MET207 3.5 33.5 1.0
CB B:HIS161 3.6 30.9 1.0
O B:GLU198 4.1 33.8 1.0
NE2 B:HIS161 4.2 31.8 1.0
CD2 B:HIS161 4.3 31.4 1.0
CA B:HIS161 4.3 28.7 1.0
ND1 B:HIS204 4.5 32.8 1.0
CD1 B:TRP104 4.6 32.6 1.0
O B:HIS102 4.7 34.2 1.0
CA B:CYS200 4.7 32.8 1.0
CA B:HIS204 4.8 31.3 1.0
CA B:CYS196 4.8 32.9 1.0
O B:LEU160 4.8 31.7 1.0
CB B:MET207 4.8 32.1 1.0
N B:CYS200 5.0 31.2 1.0

Copper binding site 3 out of 6 in 9m56

Go back to Copper Binding Sites List in 9m56
Copper binding site 3 out of 6 in the Bovine Heart Cytochrome C Oxidase in the 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 Fully Reduced State within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu301

b:32.1
occ:1.00
 CU2 B:CUA301 0.0 32.1 1.0
ND1 B:HIS204 2.0 32.8 1.0
SG B:CYS200 2.3 31.5 1.0
SG B:CYS196 2.3 32.1 1.0
O B:GLU198 2.5 33.8 1.0
CU1 B:CUA301 2.5 32.3 1.0
CE1 B:HIS204 2.9 31.7 1.0
CG B:HIS204 3.1 30.7 1.0
CB B:CYS196 3.3 31.0 1.0
CB B:CYS200 3.4 32.5 1.0
CB B:HIS204 3.5 31.8 1.0
CA B:HIS204 3.5 31.3 1.0
C B:GLU198 3.6 30.9 1.0
N B:CYS200 3.7 31.2 1.0
O B:HIS204 3.8 32.1 1.0
NE2 B:HIS204 4.1 31.6 1.0
CA B:CYS200 4.1 32.8 1.0
C B:HIS204 4.2 31.8 1.0
CD2 B:HIS204 4.2 32.8 1.0
C B:CYS196 4.2 33.0 1.0
ND1 B:HIS161 4.2 32.5 1.0
N B:GLU198 4.3 31.3 1.0
C B:ILE199 4.3 31.2 1.0
O B:CYS196 4.3 32.0 1.0
CA B:ILE199 4.3 32.2 1.0
SD B:MET207 4.3 32.3 1.0
CA B:CYS196 4.4 32.9 1.0
N B:ILE199 4.4 31.2 1.0
N B:SER197 4.6 30.8 1.0
CA B:GLU198 4.6 30.0 1.0
CG B:MET207 4.7 33.5 1.0
N B:HIS204 4.8 32.5 1.0
CA B:HIS161 4.9 28.7 1.0

Copper binding site 4 out of 6 in 9m56

Go back to Copper Binding Sites List in 9m56
Copper binding site 4 out of 6 in the Bovine Heart Cytochrome C Oxidase in the 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 Fully Reduced State within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Cu603

b:32.1
occ:1.00
 NE2 N:HIS291 2.0 32.0 1.0
ND1 N:HIS240 2.0 29.8 1.0
NE2 N:HIS290 2.1 33.9 1.0
CD2 N:HIS291 2.9 31.9 1.0
CE1 N:HIS291 3.0 32.8 1.0
CE1 N:HIS240 3.0 30.2 1.0
CG N:HIS240 3.0 31.2 1.0
CD2 N:HIS290 3.0 31.4 1.0
CE1 N:HIS290 3.1 34.0 1.0
CB N:HIS240 3.3 29.1 1.0
CA N:HIS240 3.9 29.2 1.0
CG N:HIS291 4.0 30.3 1.0
ND1 N:HIS291 4.1 31.1 1.0
NE2 N:HIS240 4.1 30.7 1.0
CD2 N:HIS240 4.1 30.2 1.0
CG N:HIS290 4.2 31.9 1.0
ND1 N:HIS290 4.2 31.2 1.0
C1A N:HEA602 4.6 32.2 1.0
NA N:HEA602 4.7 36.4 1.0
N N:HIS240 4.7 30.5 1.0
CG2 N:VAL243 4.7 33.5 1.0
C4A N:HEA602 4.7 31.1 1.0
C2A N:HEA602 4.9 30.0 1.0
C3A N:HEA602 5.0 30.5 1.0

Copper binding site 5 out of 6 in 9m56

Go back to Copper Binding Sites List in 9m56
Copper binding site 5 out of 6 in the Bovine Heart Cytochrome C Oxidase in the 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 Fully Reduced State within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Cu304

b:35.9
occ:1.00
 CU1 O:CUA304 0.0 35.9 1.0
ND1 O:HIS161 2.1 37.7 1.0
SG O:CYS196 2.3 36.0 1.0
SD O:MET207 2.4 36.3 1.0
SG O:CYS200 2.4 35.3 1.0
CU2 O:CUA304 2.5 35.5 1.0
CE1 O:HIS161 2.9 36.9 1.0
CE O:MET207 3.1 37.0 1.0
CG O:HIS161 3.2 36.8 1.0
CB O:CYS200 3.3 35.0 1.0
CB O:CYS196 3.4 36.8 1.0
CG O:MET207 3.5 36.4 1.0
CB O:HIS161 3.6 34.8 1.0
NE2 O:HIS161 4.1 35.7 1.0
O O:GLU198 4.1 36.7 1.0
CD2 O:HIS161 4.2 33.0 1.0
CA O:HIS161 4.2 33.8 1.0
ND1 O:HIS204 4.5 35.6 1.0
CD1 O:TRP104 4.6 36.5 1.0
O O:HIS102 4.7 35.9 1.0
CA O:CYS200 4.7 35.9 1.0
CA O:HIS204 4.7 36.5 1.0
CA O:CYS196 4.8 35.6 1.0
O O:LEU160 4.8 36.4 1.0
CB O:MET207 4.9 37.3 1.0

Copper binding site 6 out of 6 in 9m56

Go back to Copper Binding Sites List in 9m56
Copper binding site 6 out of 6 in the Bovine Heart Cytochrome C Oxidase in the 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 Fully Reduced State within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Cu304

b:35.5
occ:1.00
 CU2 O:CUA304 0.0 35.5 1.0
ND1 O:HIS204 2.0 35.6 1.0
SG O:CYS200 2.3 35.3 1.0
SG O:CYS196 2.3 36.0 1.0
O O:GLU198 2.5 36.7 1.0
CU1 O:CUA304 2.5 35.9 1.0
CE1 O:HIS204 3.0 34.1 1.0
CG O:HIS204 3.1 34.8 1.0
CB O:CYS196 3.2 36.8 1.0
CB O:CYS200 3.4 35.0 1.0
CA O:HIS204 3.5 36.5 1.0
CB O:HIS204 3.5 35.7 1.0
C O:GLU198 3.6 33.7 1.0
N O:CYS200 3.7 34.2 1.0
O O:HIS204 3.8 35.0 1.0
NE2 O:HIS204 4.1 35.0 1.0
C O:HIS204 4.2 37.3 1.0
C O:CYS196 4.2 36.7 1.0
CD2 O:HIS204 4.2 35.3 1.0
CA O:CYS200 4.2 35.9 1.0
ND1 O:HIS161 4.2 37.7 1.0
N O:GLU198 4.3 33.9 1.0
O O:CYS196 4.3 34.4 1.0
C O:ILE199 4.3 33.2 1.0
CA O:ILE199 4.3 33.2 1.0
CA O:CYS196 4.3 35.6 1.0
SD O:MET207 4.4 36.3 1.0
N O:ILE199 4.4 34.0 1.0
N O:SER197 4.6 35.5 1.0
CA O:GLU198 4.6 34.5 1.0
CG O:MET207 4.7 36.4 1.0
N O:HIS204 4.7 36.2 1.0
CA O:HIS161 4.9 33.8 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 10:07:15 2025

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