Atomistry » Copper » PDB 9jqc-9vqm » 9kuk
Atomistry »
  Copper »
    PDB 9jqc-9vqm »
      9kuk »

Copper in PDB 9kuk: Bovine Heart Cytochrome C Oxidase in the Xenon-Bound Fully Oxidized State Under Aerobic Condition

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

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

Protein crystallography data

The structure of Bovine Heart Cytochrome C Oxidase in the Xenon-Bound Fully Oxidized State Under Aerobic Condition, PDB code: 9kuk 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 / 15.6

Other elements in 9kuk:

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

Zinc (Zn) 2 atoms
Sodium (Na) 2 atoms
Xenon (Xe) 14 atoms
Iron (Fe) 4 atoms
Magnesium (Mg) 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 Aerobic Condition (pdb code 9kuk). 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 Aerobic Condition, PDB code: 9kuk:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6;

Copper binding site 1 out of 6 in 9kuk

Go back to Copper Binding Sites List in 9kuk
Copper binding site 1 out of 6 in the Bovine Heart Cytochrome C Oxidase in the Xenon-Bound Fully Oxidized State Under Aerobic 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 Aerobic Condition within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu603

b:29.3
occ:1.00
 NE2 A:HIS291 2.0 27.2 1.0
ND1 A:HIS240 2.0 28.7 1.0
NE2 A:HIS290 2.1 29.6 1.0
O2 A:PER606 2.3 37.0 1.0
O1 A:PER606 2.7 26.8 1.0
CE1 A:HIS291 3.0 26.4 1.0
CE1 A:HIS240 3.0 27.8 1.0
CD2 A:HIS291 3.0 25.7 1.0
CG A:HIS240 3.0 27.3 1.0
CE1 A:HIS290 3.0 32.1 1.0
CD2 A:HIS290 3.1 30.3 1.0
CB A:HIS240 3.3 28.6 1.0
CA A:HIS240 3.9 27.9 1.0
ND1 A:HIS291 4.1 26.7 1.0
NE2 A:HIS240 4.1 29.2 1.0
CG A:HIS291 4.1 27.1 1.0
CD2 A:HIS240 4.1 25.8 1.0
ND1 A:HIS290 4.2 28.6 1.0
CG A:HIS290 4.2 28.5 1.0
C1A A:HEA602 4.6 26.3 1.0
NA A:HEA602 4.7 27.1 1.0
C4A A:HEA602 4.7 25.2 1.0
N A:HIS240 4.7 27.6 1.0
CG2 A:VAL243 4.9 29.6 1.0
FE A:HEA602 4.9 28.1 1.0
C2A A:HEA602 4.9 25.1 1.0
C3A A:HEA602 5.0 26.5 1.0

Copper binding site 2 out of 6 in 9kuk

Go back to Copper Binding Sites List in 9kuk
Copper binding site 2 out of 6 in the Bovine Heart Cytochrome C Oxidase in the Xenon-Bound Fully Oxidized State Under Aerobic 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 Aerobic Condition within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu302

b:30.8
occ:1.00
 CU1 B:CUA302 0.0 30.8 1.0
ND1 B:HIS161 2.1 30.8 1.0
SG B:CYS196 2.3 29.9 1.0
SD B:MET207 2.4 30.7 1.0
SG B:CYS200 2.4 29.8 1.0
CU2 B:CUA302 2.5 30.1 1.0
CE1 B:HIS161 3.0 29.4 1.0
CE B:MET207 3.1 30.3 1.0
CG B:HIS161 3.2 29.4 1.0
CB B:CYS200 3.3 30.1 1.0
CB B:CYS196 3.4 30.4 1.0
CG B:MET207 3.5 31.2 1.0
CB B:HIS161 3.6 29.6 1.0
O B:GLU198 4.0 31.7 1.0
NE2 B:HIS161 4.2 28.6 1.0
CA B:HIS161 4.3 27.7 1.0
CD2 B:HIS161 4.3 29.4 1.0
ND1 B:HIS204 4.5 32.1 1.0
O B:HIS102 4.6 31.5 1.0
CA B:CYS200 4.7 30.4 1.0
CA B:HIS204 4.7 29.2 1.0
O B:LEU160 4.7 29.8 1.0
CD1 B:TRP104 4.7 30.7 1.0
CA B:CYS196 4.7 29.7 1.0
CB B:MET207 4.9 31.0 1.0
O B:HIS204 4.9 30.8 1.0

Copper binding site 3 out of 6 in 9kuk

Go back to Copper Binding Sites List in 9kuk
Copper binding site 3 out of 6 in the Bovine Heart Cytochrome C Oxidase in the Xenon-Bound Fully Oxidized State Under Aerobic 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 Aerobic Condition within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu302

b:30.1
occ:1.00
 CU2 B:CUA302 0.0 30.1 1.0
ND1 B:HIS204 2.1 32.1 1.0
SG B:CYS200 2.3 29.8 1.0
SG B:CYS196 2.3 29.9 1.0
O B:GLU198 2.3 31.7 1.0
CU1 B:CUA302 2.5 30.8 1.0
CE1 B:HIS204 3.0 30.7 1.0
CG B:HIS204 3.1 28.8 1.0
CB B:CYS196 3.3 30.4 1.0
CB B:CYS200 3.4 30.1 1.0
C B:GLU198 3.4 27.5 1.0
CB B:HIS204 3.5 30.0 1.0
CA B:HIS204 3.6 29.2 1.0
N B:CYS200 3.7 29.8 1.0
O B:HIS204 3.8 30.8 1.0
CA B:CYS200 4.1 30.4 1.0
NE2 B:HIS204 4.1 29.4 1.0
N B:GLU198 4.2 30.2 1.0
C B:HIS204 4.2 29.9 1.0
CD2 B:HIS204 4.2 31.6 1.0
C B:ILE199 4.2 31.4 1.0
ND1 B:HIS161 4.2 30.8 1.0
C B:CYS196 4.2 30.9 1.0
O B:CYS196 4.3 29.1 1.0
N B:ILE199 4.3 29.9 1.0
CA B:ILE199 4.3 29.3 1.0
SD B:MET207 4.3 30.7 1.0
CA B:CYS196 4.4 29.7 1.0
CA B:GLU198 4.4 29.7 1.0
N B:SER197 4.6 29.8 1.0
CG B:MET207 4.7 31.2 1.0
N B:HIS204 4.8 30.2 1.0
CA B:HIS161 5.0 27.7 1.0

Copper binding site 4 out of 6 in 9kuk

Go back to Copper Binding Sites List in 9kuk
Copper binding site 4 out of 6 in the Bovine Heart Cytochrome C Oxidase in the Xenon-Bound Fully Oxidized State Under Aerobic 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 Aerobic Condition within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Cu605

b:30.7
occ:1.00
 ND1 N:HIS240 2.0 29.2 1.0
NE2 N:HIS291 2.0 29.0 1.0
NE2 N:HIS290 2.1 31.3 1.0
O2 N:PER608 2.3 38.5 1.0
O1 N:PER608 2.7 29.2 1.0
CE1 N:HIS240 3.0 28.8 1.0
CE1 N:HIS291 3.0 32.4 1.0
CD2 N:HIS291 3.0 28.6 1.0
CG N:HIS240 3.0 27.9 1.0
CE1 N:HIS290 3.1 30.7 1.0
CD2 N:HIS290 3.1 31.3 1.0
CB N:HIS240 3.4 27.8 1.0
CA N:HIS240 3.9 29.0 1.0
ND1 N:HIS291 4.1 29.3 1.0
NE2 N:HIS240 4.1 29.2 1.0
CG N:HIS291 4.1 31.0 1.0
CD2 N:HIS240 4.1 27.1 1.0
ND1 N:HIS290 4.2 30.2 1.0
CG N:HIS290 4.2 29.7 1.0
C1A N:HEA604 4.6 27.7 1.0
NA N:HEA604 4.6 30.1 1.0
C4A N:HEA604 4.7 27.6 1.0
N N:HIS240 4.7 28.7 1.0
CG2 N:VAL243 4.9 31.1 1.0
FE N:HEA604 4.9 29.7 1.0
C2A N:HEA604 4.9 28.8 1.0
C3A N:HEA604 5.0 28.7 1.0

Copper binding site 5 out of 6 in 9kuk

Go back to Copper Binding Sites List in 9kuk
Copper binding site 5 out of 6 in the Bovine Heart Cytochrome C Oxidase in the Xenon-Bound Fully Oxidized State Under Aerobic 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 Aerobic Condition within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Cu304

b:34.5
occ:1.00
 CU1 O:CUA304 0.0 34.5 1.0
ND1 O:HIS161 2.1 36.3 1.0
SG O:CYS196 2.3 34.3 1.0
SG O:CYS200 2.4 34.4 1.0
SD O:MET207 2.4 34.0 1.0
CU2 O:CUA304 2.5 34.3 1.0
CE1 O:HIS161 2.9 35.0 1.0
CE O:MET207 3.1 35.7 1.0
CG O:HIS161 3.2 33.9 1.0
CB O:CYS200 3.3 33.5 1.0
CB O:CYS196 3.4 34.6 1.0
CG O:MET207 3.6 36.3 1.0
CB O:HIS161 3.6 34.7 1.0
O O:GLU198 4.0 34.4 1.0
NE2 O:HIS161 4.1 32.4 1.0
CA O:HIS161 4.2 31.8 1.0
CD2 O:HIS161 4.2 33.2 1.0
ND1 O:HIS204 4.5 35.4 1.0
O O:HIS102 4.7 35.9 1.0
CA O:HIS204 4.7 34.1 1.0
CD1 O:TRP104 4.7 36.9 1.0
CA O:CYS200 4.7 33.5 1.0
O O:LEU160 4.7 34.5 1.0
CA O:CYS196 4.8 33.0 1.0
CB O:MET207 4.9 37.9 1.0
O O:HIS204 4.9 34.1 1.0

Copper binding site 6 out of 6 in 9kuk

Go back to Copper Binding Sites List in 9kuk
Copper binding site 6 out of 6 in the Bovine Heart Cytochrome C Oxidase in the Xenon-Bound Fully Oxidized State Under Aerobic 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 Aerobic Condition within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Cu304

b:34.3
occ:1.00
 CU2 O:CUA304 0.0 34.3 1.0
ND1 O:HIS204 2.0 35.4 1.0
SG O:CYS200 2.3 34.4 1.0
O O:GLU198 2.3 34.4 1.0
SG O:CYS196 2.3 34.3 1.0
CU1 O:CUA304 2.5 34.5 1.0
CE1 O:HIS204 2.9 34.4 1.0
CG O:HIS204 3.1 34.1 1.0
CB O:CYS196 3.3 34.6 1.0
CB O:CYS200 3.3 33.5 1.0
C O:GLU198 3.5 31.4 1.0
CB O:HIS204 3.5 35.0 1.0
CA O:HIS204 3.5 34.1 1.0
N O:CYS200 3.7 34.9 1.0
O O:HIS204 3.8 34.1 1.0
NE2 O:HIS204 4.1 33.7 1.0
N O:GLU198 4.1 33.9 1.0
C O:HIS204 4.1 34.9 1.0
CA O:CYS200 4.2 33.5 1.0
CD2 O:HIS204 4.2 33.7 1.0
C O:CYS196 4.2 35.7 1.0
C O:ILE199 4.2 32.3 1.0
ND1 O:HIS161 4.2 36.3 1.0
O O:CYS196 4.2 32.9 1.0
N O:ILE199 4.3 33.5 1.0
CA O:ILE199 4.3 30.2 1.0
CA O:CYS196 4.4 33.0 1.0
SD O:MET207 4.4 34.0 1.0
CA O:GLU198 4.4 33.1 1.0
N O:SER197 4.6 34.3 1.0
CG O:MET207 4.8 36.3 1.0
N O:HIS204 4.8 34.3 1.0
CA O:HIS161 4.9 31.8 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 10:00:56 2025

Last articles

Fe in 4G2D
Fe in 4G1V
Fe in 4FYZ
Fe in 4G05
Fe in 4FWI
Fe in 4FXB
Fe in 4FXC
Fe in 4FWZ
Fe in 4FWY
Fe in 4FW0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy