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

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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

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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

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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

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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

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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

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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: Sat Apr 17 15:23:02 2021

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