Atomistry » Copper » PDB 7a8v-7ev7 » 7coh
Atomistry »
  Copper »
    PDB 7a8v-7ev7 »
      7coh »

Copper in PDB 7coh: Dimeric Form of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State

Enzymatic activity of Dimeric Form of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State

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

Protein crystallography data

The structure of Dimeric Form of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State, PDB code: 7coh was solved by K.Shinzawa-Itoh, K.Muramoto, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.00 / 1.30
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 181.998, 204.193, 177.759, 90, 90, 90
R / Rfree (%) 14.9 / 17

Other elements in 7coh:

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

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

Copper Binding Sites:

The binding sites of Copper atom in the Dimeric Form of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State (pdb code 7coh). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 6 binding sites of Copper where determined in the Dimeric Form of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State, PDB code: 7coh:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6;

Copper binding site 1 out of 6 in 7coh

Go back to Copper Binding Sites List in 7coh
Copper binding site 1 out of 6 in the Dimeric Form of Bovine Heart Cytochrome C Oxidase in the 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 Dimeric Form of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu517

b:17.9
occ:1.00
 ND1 A:HIS240 2.0 16.2 1.0
NE2 A:HIS291 2.0 17.9 1.0
NE2 A:HIS290 2.0 22.9 1.0
O2 A:PER520 2.0 26.7 1.0
O1 A:PER520 2.7 20.9 1.0
CE1 A:HIS291 2.9 17.1 1.0
CE1 A:HIS290 3.0 24.9 1.0
CG A:HIS240 3.0 16.4 1.0
CE1 A:HIS240 3.0 18.5 1.0
CD2 A:HIS291 3.0 17.4 1.0
CD2 A:HIS290 3.0 20.0 1.0
CB A:HIS240 3.3 17.3 1.0
CA A:HIS240 3.9 16.1 1.0
ND1 A:HIS291 4.0 17.9 1.0
CG A:HIS291 4.1 17.2 1.0
ND1 A:HIS290 4.1 16.9 1.0
NE2 A:HIS240 4.1 17.5 1.0
CD2 A:HIS240 4.1 16.4 1.0
CG A:HIS290 4.2 19.2 1.0
NA A:HEA516 4.5 16.9 1.0
C1A A:HEA516 4.6 16.5 1.0
C4A A:HEA516 4.7 17.0 1.0
N A:HIS240 4.7 16.0 1.0
C2A A:HEA516 4.8 17.1 1.0
FE A:HEA516 4.8 17.4 1.0
CG2 A:VAL243 4.8 19.0 1.0
C3A A:HEA516 4.9 16.8 1.0
CHA A:HEA516 5.0 16.9 1.0

Copper binding site 2 out of 6 in 7coh

Go back to Copper Binding Sites List in 7coh
Copper binding site 2 out of 6 in the Dimeric Form of Bovine Heart Cytochrome C Oxidase in the 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 Dimeric Form of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu228

b:19.8
occ:1.00
 CU1 B:CUA228 0.0 19.8 1.0
ND1 B:HIS161 2.1 25.7 1.0
SG B:CYS196 2.3 19.1 1.0
SG B:CYS200 2.4 19.8 1.0
SD B:MET207 2.4 20.5 1.0
CU2 B:CUA228 2.5 19.4 1.0
CE1 B:HIS161 3.0 23.4 1.0
CE B:MET207 3.2 25.8 1.0
CG B:HIS161 3.2 24.9 1.0
CB B:CYS200 3.3 18.3 1.0
CB B:CYS196 3.4 18.4 1.0
CG B:MET207 3.5 22.7 1.0
CB B:HIS161 3.6 22.5 1.0
O B:GLU198 4.1 19.7 1.0
NE2 B:HIS161 4.2 19.4 1.0
CA B:HIS161 4.2 21.7 1.0
CD2 B:HIS161 4.2 21.0 1.0
ND1 B:HIS204 4.4 19.0 1.0
CA B:CYS200 4.6 19.7 1.0
O B:HIS102 4.7 22.4 1.0
O B:LEU160 4.7 19.7 1.0
CA B:HIS204 4.7 18.8 1.0
CD1 B:TRP104 4.8 19.7 1.0
CA B:CYS196 4.8 19.0 1.0
CB B:MET207 4.9 22.8 1.0
O B:HIS204 4.9 20.5 1.0
N B:CYS200 5.0 19.1 1.0

Copper binding site 3 out of 6 in 7coh

Go back to Copper Binding Sites List in 7coh
Copper binding site 3 out of 6 in the Dimeric Form of Bovine Heart Cytochrome C Oxidase in the 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 Dimeric Form of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu228

b:19.4
occ:1.00
 CU2 B:CUA228 0.0 19.4 1.0
ND1 B:HIS204 2.0 19.0 1.0
SG B:CYS196 2.3 19.1 1.0
SG B:CYS200 2.3 19.8 1.0
O B:GLU198 2.5 19.7 1.0
CU1 B:CUA228 2.5 19.8 1.0
CE1 B:HIS204 2.9 19.4 1.0
CG B:HIS204 3.0 18.7 1.0
CB B:CYS196 3.3 18.4 1.0
CB B:CYS200 3.4 18.3 1.0
CB B:HIS204 3.5 18.9 1.0
C B:GLU198 3.5 19.3 1.0
CA B:HIS204 3.6 18.8 1.0
N B:CYS200 3.7 19.1 1.0
O B:HIS204 3.8 20.5 1.0
N B:GLU198 4.1 17.3 1.0
CA B:CYS200 4.1 19.7 1.0
NE2 B:HIS204 4.1 19.4 1.0
CD2 B:HIS204 4.1 19.3 1.0
C B:HIS204 4.2 19.7 1.0
C B:ILE199 4.2 18.3 1.0
ND1 B:HIS161 4.2 25.7 1.0
C B:CYS196 4.2 17.8 1.0
O B:CYS196 4.2 18.8 1.0
CA B:ILE199 4.3 18.7 1.0
N B:ILE199 4.3 18.4 1.0
SD B:MET207 4.3 20.5 1.0
CA B:CYS196 4.4 19.0 1.0
CA B:GLU198 4.5 18.4 1.0
N B:SER197 4.6 19.1 1.0
CG B:MET207 4.7 22.7 1.0
N B:HIS204 4.8 19.9 1.0
CA B:HIS161 4.9 21.7 1.0
CB B:HIS161 5.0 22.5 1.0

Copper binding site 4 out of 6 in 7coh

Go back to Copper Binding Sites List in 7coh
Copper binding site 4 out of 6 in the Dimeric Form of Bovine Heart Cytochrome C Oxidase in the 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 Dimeric Form of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Cu517

b:20.0
occ:1.00
 ND1 N:HIS240 2.0 18.2 1.0
NE2 N:HIS290 2.0 20.6 1.0
NE2 N:HIS291 2.0 19.7 1.0
O2 N:PER520 2.1 26.4 1.0
O1 N:PER520 2.7 19.9 1.0
CE1 N:HIS291 3.0 20.1 1.0
CE1 N:HIS290 3.0 20.1 1.0
CE1 N:HIS240 3.0 19.9 1.0
CG N:HIS240 3.0 19.3 1.0
CD2 N:HIS291 3.0 20.3 1.0
CD2 N:HIS290 3.1 19.2 1.0
CB N:HIS240 3.4 18.9 1.0
CA N:HIS240 3.9 18.2 1.0
ND1 N:HIS291 4.1 20.0 1.0
NE2 N:HIS240 4.1 18.3 1.0
CD2 N:HIS240 4.1 18.7 1.0
CG N:HIS291 4.1 19.4 1.0
ND1 N:HIS290 4.1 20.1 1.0
CG N:HIS290 4.2 19.7 1.0
NA N:HEA516 4.5 18.8 1.0
C1A N:HEA516 4.6 18.7 1.0
C4A N:HEA516 4.7 19.4 1.0
N N:HIS240 4.7 17.8 1.0
C2A N:HEA516 4.8 19.3 1.0
FE N:HEA516 4.8 19.7 1.0
CG2 N:VAL243 4.8 19.6 1.0
C3A N:HEA516 4.9 19.1 1.0
CHA N:HEA516 5.0 19.5 1.0
C N:HIS240 5.0 18.4 1.0

Copper binding site 5 out of 6 in 7coh

Go back to Copper Binding Sites List in 7coh
Copper binding site 5 out of 6 in the Dimeric Form of Bovine Heart Cytochrome C Oxidase in the 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 Dimeric Form of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Cu228

b:25.4
occ:1.00
 CU1 O:CUA228 0.0 25.4 1.0
ND1 O:HIS161 2.1 25.5 1.0
SG O:CYS196 2.3 24.4 1.0
SG O:CYS200 2.4 24.9 1.0
SD O:MET207 2.4 26.3 1.0
CU2 O:CUA228 2.5 24.9 1.0
CE1 O:HIS161 3.0 24.4 1.0
CG O:HIS161 3.2 22.7 1.0
CE O:MET207 3.2 26.9 1.0
CB O:CYS200 3.3 23.2 1.0
CB O:CYS196 3.4 25.4 1.0
CG O:MET207 3.5 28.0 1.0
CB O:HIS161 3.6 22.1 1.0
O O:GLU198 4.1 25.1 1.0
NE2 O:HIS161 4.1 24.7 1.0
CD2 O:HIS161 4.2 23.9 1.0
CA O:HIS161 4.2 23.0 1.0
ND1 O:HIS204 4.4 22.6 1.0
CD1 O:TRP104 4.7 26.1 1.0
CA O:CYS200 4.7 24.9 1.0
O O:HIS102 4.7 26.9 1.0
O O:LEU160 4.7 23.5 1.0
CA O:HIS204 4.7 25.8 1.0
CA O:CYS196 4.8 24.1 1.0
CB O:MET207 4.9 28.1 1.0
O O:HIS204 4.9 26.0 1.0

Copper binding site 6 out of 6 in 7coh

Go back to Copper Binding Sites List in 7coh
Copper binding site 6 out of 6 in the Dimeric Form of Bovine Heart Cytochrome C Oxidase in the 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 Dimeric Form of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Cu228

b:24.9
occ:1.00
 CU2 O:CUA228 0.0 24.9 1.0
ND1 O:HIS204 2.0 22.6 1.0
SG O:CYS196 2.3 24.4 1.0
SG O:CYS200 2.3 24.9 1.0
O O:GLU198 2.5 25.1 1.0
CU1 O:CUA228 2.5 25.4 1.0
CE1 O:HIS204 2.9 23.0 1.0
CG O:HIS204 3.1 24.6 1.0
CB O:CYS196 3.3 25.4 1.0
CB O:CYS200 3.3 23.2 1.0
C O:GLU198 3.5 24.3 1.0
CB O:HIS204 3.5 24.6 1.0
CA O:HIS204 3.6 25.8 1.0
N O:CYS200 3.7 23.8 1.0
O O:HIS204 3.8 26.0 1.0
NE2 O:HIS204 4.1 24.1 1.0
N O:GLU198 4.1 22.0 1.0
CA O:CYS200 4.1 24.9 1.0
CD2 O:HIS204 4.2 24.9 1.0
C O:HIS204 4.2 28.1 1.0
O O:CYS196 4.2 24.4 1.0
C O:ILE199 4.2 23.3 1.0
C O:CYS196 4.2 25.1 1.0
ND1 O:HIS161 4.2 25.5 1.0
CA O:ILE199 4.3 22.2 1.0
N O:ILE199 4.3 22.1 1.0
SD O:MET207 4.3 26.3 1.0
CA O:CYS196 4.3 24.1 1.0
CA O:GLU198 4.5 23.3 1.0
N O:SER197 4.7 25.0 1.0
CG O:MET207 4.7 28.0 1.0
N O:HIS204 4.8 26.2 1.0
CA O:HIS161 4.9 23.0 1.0

Reference:

K.Shinzawa-Itoh, M.Hatanaka, K.Fujita, N.Yano, Y.Ogasawara, J.Iwata, E.Yamashita, T.Tsukihara, S.Yoshikawa, K.Muramoto. The 1.3-A Resolution Structure of Bovine Cytochrome C Oxidase Suggests A Dimerization Mechanism Biochim.Biophys.Acta 2021.
ISSN: ISSN 0006-3002
DOI: 10.1016/J.BBADVA.2021.100009
Page generated: Mon Jul 14 07:55:10 2025

Last articles

Fe in 8FGG
Fe in 8FGF
Fe in 8FGE
Fe in 8FGC
Fe in 8FGD
Fe in 8FGA
Fe in 8FGB
Fe in 8FG9
Fe in 8FF7
Fe in 8FF6
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy