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Copper in PDB 9ikf: Bovine Heart Cytochrome C Oxidase in the Carbon Dioxide-Bound Fully Oxidized State

Enzymatic activity of Bovine Heart Cytochrome C Oxidase in the Carbon Dioxide-Bound Fully Oxidized State

All present enzymatic activity of Bovine Heart Cytochrome C Oxidase in the Carbon Dioxide-Bound Fully Oxidized State:
7.1.1.9;

Protein crystallography data

The structure of Bovine Heart Cytochrome C Oxidase in the Carbon Dioxide-Bound Fully Oxidized State, PDB code: 9ikf 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 / 1.75
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 182.5, 204.4, 177.8, 90, 90, 90
R / Rfree (%) 13 / 16.7

Other elements in 9ikf:

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

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

Copper Binding Sites:

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

Copper binding site 1 out of 6 in 9ikf

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Copper binding site 1 out of 6 in the Bovine Heart Cytochrome C Oxidase in the Carbon Dioxide-Bound Fully Oxidized 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 Carbon Dioxide-Bound Fully Oxidized State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu603

b:31.1
occ:1.00
 NE2 A:HIS291 2.0 30.1 1.0
ND1 A:HIS240 2.1 30.5 1.0
NE2 A:HIS290 2.1 34.6 1.0
O2 A:PER606 2.3 33.8 1.0
O1 A:PER606 2.8 32.0 1.0
CE1 A:HIS291 3.0 29.1 1.0
CE1 A:HIS240 3.0 30.8 1.0
CE1 A:HIS290 3.0 32.0 1.0
CG A:HIS240 3.0 28.0 1.0
CD2 A:HIS291 3.0 28.3 1.0
CD2 A:HIS290 3.1 30.7 1.0
CB A:HIS240 3.3 30.0 1.0
CA A:HIS240 3.8 30.2 1.0
ND1 A:HIS291 4.1 29.1 1.0
CG A:HIS291 4.1 29.9 1.0
ND1 A:HIS290 4.1 31.4 1.0
CD2 A:HIS240 4.2 29.6 1.0
NE2 A:HIS240 4.2 31.4 1.0
CG A:HIS290 4.2 30.0 1.0
C1A A:HEA602 4.6 29.0 1.0
NA A:HEA602 4.7 29.1 1.0
C4A A:HEA602 4.7 29.0 1.0
N A:HIS240 4.7 28.9 1.0
C2A A:HEA602 4.9 28.2 1.0
FE A:HEA602 4.9 29.9 1.0
CG2 A:VAL243 4.9 29.7 1.0
C A:HIS240 5.0 28.4 1.0

Copper binding site 2 out of 6 in 9ikf

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Copper binding site 2 out of 6 in the Bovine Heart Cytochrome C Oxidase in the Carbon Dioxide-Bound Fully Oxidized 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 Carbon Dioxide-Bound Fully Oxidized State within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu301

b:33.7
occ:1.00
 CU1 B:CUA301 0.0 33.7 1.0
ND1 B:HIS161 2.1 34.2 1.0
SG B:CYS196 2.3 32.7 1.0
SD B:MET207 2.4 33.9 1.0
SG B:CYS200 2.4 31.9 1.0
CU2 B:CUA301 2.5 32.8 1.0
CE1 B:HIS161 3.0 34.4 1.0
CE B:MET207 3.1 33.7 1.0
CG B:HIS161 3.2 33.2 1.0
CB B:CYS200 3.3 32.1 1.0
CB B:CYS196 3.4 31.8 1.0
CG B:MET207 3.5 34.8 1.0
CB B:HIS161 3.6 32.8 1.0
O B:GLU198 4.0 33.9 1.0
NE2 B:HIS161 4.2 32.5 1.0
CA B:HIS161 4.3 31.0 1.0
CD2 B:HIS161 4.3 32.1 1.0
ND1 B:HIS204 4.5 35.2 1.0
O B:HIS102 4.7 34.8 1.0
CA B:CYS200 4.7 32.9 1.0
CA B:HIS204 4.7 33.0 1.0
O B:LEU160 4.7 32.7 1.0
CA B:CYS196 4.8 32.1 1.0
CD1 B:TRP104 4.8 32.8 1.0
CB B:MET207 4.9 35.9 1.0
O B:HIS204 4.9 34.9 1.0

Copper binding site 3 out of 6 in 9ikf

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Copper binding site 3 out of 6 in the Bovine Heart Cytochrome C Oxidase in the Carbon Dioxide-Bound Fully Oxidized 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 Carbon Dioxide-Bound Fully Oxidized State within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu301

b:32.8
occ:1.00
 CU2 B:CUA301 0.0 32.8 1.0
ND1 B:HIS204 2.0 35.2 1.0
O B:GLU198 2.3 33.9 1.0
SG B:CYS200 2.3 31.9 1.0
SG B:CYS196 2.4 32.7 1.0
CU1 B:CUA301 2.5 33.7 1.0
CE1 B:HIS204 3.0 33.6 1.0
CG B:HIS204 3.1 32.6 1.0
CB B:CYS196 3.3 31.8 1.0
CB B:CYS200 3.4 32.1 1.0
C B:GLU198 3.4 30.0 1.0
CB B:HIS204 3.5 33.4 1.0
CA B:HIS204 3.6 33.0 1.0
N B:CYS200 3.7 34.5 1.0
O B:HIS204 3.8 34.9 1.0
NE2 B:HIS204 4.1 33.4 1.0
N B:GLU198 4.2 33.3 1.0
CA B:CYS200 4.2 32.9 1.0
C B:HIS204 4.2 33.2 1.0
ND1 B:HIS161 4.2 34.2 1.0
C B:ILE199 4.2 35.0 1.0
CD2 B:HIS204 4.2 35.0 1.0
C B:CYS196 4.2 33.4 1.0
O B:CYS196 4.3 32.5 1.0
N B:ILE199 4.3 31.2 1.0
CA B:ILE199 4.3 33.9 1.0
SD B:MET207 4.3 33.9 1.0
CA B:CYS196 4.4 32.1 1.0
CA B:GLU198 4.4 32.4 1.0
N B:SER197 4.7 32.7 1.0
CG B:MET207 4.7 34.8 1.0
N B:HIS204 4.8 32.9 1.0
CA B:HIS161 4.9 31.0 1.0

Copper binding site 4 out of 6 in 9ikf

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Copper binding site 4 out of 6 in the Bovine Heart Cytochrome C Oxidase in the Carbon Dioxide-Bound Fully Oxidized 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 Carbon Dioxide-Bound Fully Oxidized State within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Cu603

b:33.2
occ:1.00
 ND1 N:HIS240 2.0 33.5 1.0
NE2 N:HIS291 2.0 33.1 1.0
NE2 N:HIS290 2.1 36.9 1.0
O2 N:PER606 2.2 35.8 1.0
O1 N:PER606 2.8 35.0 1.0
CE1 N:HIS240 3.0 30.3 1.0
CE1 N:HIS291 3.0 34.9 1.0
CG N:HIS240 3.0 30.5 1.0
CD2 N:HIS291 3.0 32.3 1.0
CD2 N:HIS290 3.1 32.4 1.0
CE1 N:HIS290 3.1 34.0 1.0
CB N:HIS240 3.3 30.9 1.0
CA N:HIS240 3.9 31.9 1.0
ND1 N:HIS291 4.1 34.0 1.0
CD2 N:HIS240 4.1 31.4 1.0
NE2 N:HIS240 4.1 33.1 1.0
CG N:HIS291 4.1 32.1 1.0
ND1 N:HIS290 4.2 33.1 1.0
CG N:HIS290 4.2 32.5 1.0
C1A N:HEA602 4.6 31.3 1.0
C4A N:HEA602 4.7 30.7 1.0
NA N:HEA602 4.7 34.0 1.0
N N:HIS240 4.7 30.0 1.0
C2A N:HEA602 4.9 32.5 1.0
FE N:HEA602 4.9 32.1 1.0
CG2 N:VAL243 4.9 33.1 1.0
C3A N:HEA602 5.0 31.9 1.0

Copper binding site 5 out of 6 in 9ikf

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Copper binding site 5 out of 6 in the Bovine Heart Cytochrome C Oxidase in the Carbon Dioxide-Bound Fully Oxidized 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 Carbon Dioxide-Bound Fully Oxidized State within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Cu305

b:37.8
occ:1.00
 CU1 O:CUA305 0.0 37.8 1.0
ND1 O:HIS161 2.1 41.3 1.0
SG O:CYS196 2.3 37.3 1.0
SG O:CYS200 2.4 37.0 1.0
SD O:MET207 2.4 38.7 1.0
CU2 O:CUA305 2.5 37.4 1.0
CE1 O:HIS161 2.9 42.5 1.0
CE O:MET207 3.1 38.3 1.0
CG O:HIS161 3.1 36.0 1.0
CB O:CYS200 3.3 37.1 1.0
CB O:CYS196 3.4 38.4 1.0
CG O:MET207 3.5 39.2 1.0
CB O:HIS161 3.6 37.1 1.0
O O:GLU198 4.0 36.9 1.0
NE2 O:HIS161 4.1 39.4 1.0
CD2 O:HIS161 4.2 37.2 1.0
CA O:HIS161 4.2 34.9 1.0
ND1 O:HIS204 4.5 39.3 1.0
O O:HIS102 4.7 40.1 1.0
CA O:HIS204 4.7 36.1 1.0
CA O:CYS200 4.7 39.1 1.0
CD1 O:TRP104 4.7 40.9 1.0
O O:LEU160 4.8 39.0 1.0
CA O:CYS196 4.8 37.2 1.0
CB O:MET207 4.9 40.1 1.0
O O:HIS204 4.9 38.8 1.0

Copper binding site 6 out of 6 in 9ikf

Go back to Copper Binding Sites List in 9ikf
Copper binding site 6 out of 6 in the Bovine Heart Cytochrome C Oxidase in the Carbon Dioxide-Bound Fully Oxidized 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 Carbon Dioxide-Bound Fully Oxidized State within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Cu305

b:37.4
occ:1.00
 CU2 O:CUA305 0.0 37.4 1.0
ND1 O:HIS204 2.1 39.3 1.0
O O:GLU198 2.3 36.9 1.0
SG O:CYS200 2.3 37.0 1.0
SG O:CYS196 2.3 37.3 1.0
CU1 O:CUA305 2.5 37.8 1.0
CE1 O:HIS204 3.0 38.3 1.0
CG O:HIS204 3.1 38.6 1.0
CB O:CYS196 3.3 38.4 1.0
CB O:CYS200 3.3 37.1 1.0
C O:GLU198 3.4 34.7 1.0
CB O:HIS204 3.5 39.8 1.0
CA O:HIS204 3.6 36.1 1.0
N O:CYS200 3.8 38.0 1.0
O O:HIS204 3.8 38.8 1.0
NE2 O:HIS204 4.1 38.1 1.0
N O:GLU198 4.1 37.4 1.0
C O:HIS204 4.1 37.4 1.0
CA O:CYS200 4.2 39.1 1.0
CD2 O:HIS204 4.2 37.5 1.0
ND1 O:HIS161 4.2 41.3 1.0
N O:ILE199 4.2 37.2 1.0
C O:ILE199 4.2 36.9 1.0
C O:CYS196 4.2 40.3 1.0
O O:CYS196 4.3 37.2 1.0
CA O:ILE199 4.3 35.6 1.0
CA O:CYS196 4.4 37.2 1.0
SD O:MET207 4.4 38.7 1.0
CA O:GLU198 4.4 36.0 1.0
N O:SER197 4.6 38.8 1.0
CG O:MET207 4.7 39.2 1.0
N O:HIS204 4.8 37.9 1.0
CA O:HIS161 4.9 34.9 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 09:57:38 2025

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