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Copper in PDB 5xdq: Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State with pH 7.3 at 1.77 Angstrom Resolution

Enzymatic activity of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State with pH 7.3 at 1.77 Angstrom Resolution

All present enzymatic activity of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State with pH 7.3 at 1.77 Angstrom Resolution:
1.9.3.1;

Protein crystallography data

The structure of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State with pH 7.3 at 1.77 Angstrom Resolution, PDB code: 5xdq was solved by F.J.Luo, A.Shimada, N.Hagimoto, S.Shimada, K.Shinzawa-Itoh, E.Yamashita, S.Yoshikawa, T.Tsukihara, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 134.45 / 1.77
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 183.307, 205.904, 177.526, 90.00, 90.00, 90.00
R / Rfree (%) 16.4 / 19

Other elements in 5xdq:

The structure of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State with pH 7.3 at 1.77 Angstrom Resolution also contains other interesting chemical elements:

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

Copper Binding Sites:

The binding sites of Copper atom in the Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State with pH 7.3 at 1.77 Angstrom Resolution (pdb code 5xdq). 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 Oxidized State with pH 7.3 at 1.77 Angstrom Resolution, PDB code: 5xdq:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6;

Copper binding site 1 out of 6 in 5xdq

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Copper binding site 1 out of 6 in the Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State with pH 7.3 at 1.77 Angstrom Resolution


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 Oxidized State with pH 7.3 at 1.77 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu603

b:27.2
occ:1.00
 NE2 A:HIS291 2.0 40.5 1.0
O2 A:PER607 2.0 6.5 0.1
NE2 A:HIS290 2.0 27.5 1.0
ND1 A:HIS240 2.0 29.5 1.0
O2 A:PER607 2.2 24.9 0.9
O1 A:PER607 2.7 6.5 0.1
O1 A:PER607 2.8 25.4 0.9
CD2 A:HIS291 2.9 26.4 1.0
CE1 A:HIS291 2.9 41.9 1.0
CE1 A:HIS290 3.0 26.4 1.0
CG A:HIS240 3.0 24.1 1.0
CD2 A:HIS290 3.0 24.3 1.0
CE1 A:HIS240 3.1 34.6 1.0
CB A:HIS240 3.3 23.8 1.0
CA A:HIS240 3.9 32.5 1.0
ND1 A:HIS291 4.0 28.2 1.0
CG A:HIS291 4.0 25.3 1.0
ND1 A:HIS290 4.1 24.3 1.0
CG A:HIS290 4.2 24.5 1.0
CD2 A:HIS240 4.2 24.4 1.0
NE2 A:HIS240 4.2 29.5 1.0
NA A:HEA602 4.5 31.6 1.0
C1A A:HEA602 4.6 25.0 1.0
C4A A:HEA602 4.7 25.3 1.0
N A:HIS240 4.7 25.1 1.0
FE A:HEA602 4.8 27.1 1.0
CG2 A:VAL243 4.9 23.7 1.0
C2A A:HEA602 4.9 24.3 1.0
CHA A:HEA602 5.0 23.4 1.0
C A:HIS240 5.0 24.5 1.0

Copper binding site 2 out of 6 in 5xdq

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Copper binding site 2 out of 6 in the Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State with pH 7.3 at 1.77 Angstrom Resolution


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 Oxidized State with pH 7.3 at 1.77 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu302

b:30.5
occ:1.00
 CU1 B:CUA302 0.0 30.5 1.0
ND1 B:HIS161 2.0 29.5 1.0
SG B:CYS200 2.3 29.2 1.0
SG B:CYS196 2.3 30.1 1.0
SD B:MET207 2.3 30.9 1.0
CU2 B:CUA302 2.6 29.6 1.0
CE1 B:HIS161 2.9 29.4 1.0
CE B:MET207 3.0 27.1 1.0
CG B:HIS161 3.1 26.9 1.0
CB B:CYS200 3.3 25.7 1.0
CB B:CYS196 3.4 27.2 1.0
CG B:MET207 3.5 29.7 1.0
CB B:HIS161 3.6 25.2 1.0
O B:GLU198 3.9 33.3 1.0
NE2 B:HIS161 4.1 28.4 1.0
CD2 B:HIS161 4.2 27.0 1.0
CA B:HIS161 4.2 25.9 1.0
ND1 B:HIS204 4.5 30.1 1.0
O B:HIS102 4.6 30.3 1.0
O B:LEU160 4.7 26.6 1.0
CA B:CYS200 4.7 26.0 1.0
CA B:HIS204 4.8 26.6 1.0
CA B:CYS196 4.8 28.1 1.0
CD1 B:TRP104 4.8 28.1 1.0
CB B:MET207 4.9 28.6 1.0
O B:HIS204 4.9 31.4 1.0

Copper binding site 3 out of 6 in 5xdq

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Copper binding site 3 out of 6 in the Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State with pH 7.3 at 1.77 Angstrom Resolution


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 Oxidized State with pH 7.3 at 1.77 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu302

b:29.6
occ:1.00
 CU2 B:CUA302 0.0 29.6 1.0
ND1 B:HIS204 2.0 30.1 1.0
O B:GLU198 2.0 33.3 1.0
SG B:CYS200 2.3 29.2 1.0
SG B:CYS196 2.3 30.1 1.0
CU1 B:CUA302 2.6 30.5 1.0
CE1 B:HIS204 2.8 29.3 1.0
CG B:HIS204 3.0 27.7 1.0
C B:GLU198 3.2 25.6 1.0
CB B:CYS196 3.3 27.2 1.0
CB B:CYS200 3.3 25.7 1.0
CB B:HIS204 3.5 25.8 1.0
CA B:HIS204 3.6 26.6 1.0
N B:CYS200 3.7 25.9 1.0
O B:HIS204 3.8 31.4 1.0
NE2 B:HIS204 4.0 28.1 1.0
N B:ILE199 4.0 26.9 1.0
N B:GLU198 4.1 26.9 1.0
CD2 B:HIS204 4.1 28.7 1.0
C B:ILE199 4.1 26.8 1.0
C B:HIS204 4.1 28.3 1.0
CA B:ILE199 4.1 27.0 1.0
CA B:CYS200 4.2 26.0 1.0
C B:CYS196 4.2 26.2 1.0
ND1 B:HIS161 4.2 29.5 1.0
O B:CYS196 4.2 27.2 1.0
CA B:GLU198 4.3 26.8 1.0
SD B:MET207 4.4 30.9 1.0
CA B:CYS196 4.4 28.1 1.0
N B:SER197 4.7 26.9 1.0
CG B:MET207 4.8 29.7 1.0
N B:HIS204 4.8 28.1 1.0
O B:ILE199 4.9 26.5 1.0
CA B:HIS161 5.0 25.9 1.0

Copper binding site 4 out of 6 in 5xdq

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Copper binding site 4 out of 6 in the Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State with pH 7.3 at 1.77 Angstrom Resolution


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 Oxidized State with pH 7.3 at 1.77 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Cu603

b:31.6
occ:1.00
 NE2 N:HIS291 1.9 28.1 1.0
NE2 N:HIS290 2.0 31.9 1.0
ND1 N:HIS240 2.0 28.4 1.0
O2 N:PER608 2.1 16.1 0.1
O2 N:PER608 2.3 31.7 0.9
O1 N:PER608 2.8 28.4 0.9
O1 N:PER608 2.8 15.0 0.1
CE1 N:HIS291 2.9 26.5 1.0
CD2 N:HIS291 2.9 27.0 1.0
CE1 N:HIS290 2.9 29.3 1.0
CG N:HIS240 3.0 28.6 1.0
CE1 N:HIS240 3.0 27.1 1.0
CD2 N:HIS290 3.0 28.4 1.0
CB N:HIS240 3.3 26.1 1.0
CA N:HIS240 3.9 28.0 1.0
ND1 N:HIS291 4.0 30.1 1.0
CG N:HIS291 4.0 28.3 1.0
ND1 N:HIS290 4.1 29.1 1.0
CD2 N:HIS240 4.2 27.2 1.0
NE2 N:HIS240 4.2 29.1 1.0
CG N:HIS290 4.2 28.0 1.0
NA N:HEA602 4.5 31.2 1.0
C1A N:HEA602 4.6 29.6 1.0
N N:HIS240 4.7 27.0 1.0
C4A N:HEA602 4.7 29.6 1.0
FE N:HEA602 4.8 31.2 1.0
CG2 N:VAL243 4.9 26.7 1.0
C2A N:HEA602 4.9 30.5 1.0
CHA N:HEA602 5.0 26.9 1.0

Copper binding site 5 out of 6 in 5xdq

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Copper binding site 5 out of 6 in the Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State with pH 7.3 at 1.77 Angstrom Resolution


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 Oxidized State with pH 7.3 at 1.77 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Cu302

b:39.4
occ:1.00
 CU1 O:CUA302 0.0 39.4 1.0
ND1 O:HIS161 2.0 39.0 1.0
SG O:CYS196 2.3 40.0 1.0
SG O:CYS200 2.3 37.8 1.0
SD O:MET207 2.3 41.3 1.0
CU2 O:CUA302 2.7 39.0 1.0
CE1 O:HIS161 2.8 38.4 1.0
CE O:MET207 3.1 36.9 1.0
CG O:HIS161 3.1 35.6 1.0
CB O:CYS200 3.3 33.2 1.0
CB O:CYS196 3.4 38.0 1.0
CG O:MET207 3.5 40.1 1.0
CB O:HIS161 3.6 34.4 1.0
O O:GLU198 3.9 39.7 1.0
NE2 O:HIS161 4.0 37.1 1.0
CD2 O:HIS161 4.2 36.3 1.0
CA O:HIS161 4.3 35.7 1.0
ND1 O:HIS204 4.6 39.4 1.0
O O:HIS102 4.6 40.9 1.0
O O:LEU160 4.7 36.8 1.0
CD1 O:TRP104 4.7 40.1 1.0
CA O:CYS200 4.7 38.0 1.0
CA O:HIS204 4.8 37.0 1.0
CA O:CYS196 4.8 37.4 1.0
CB O:MET207 4.9 42.0 1.0
O O:HIS204 4.9 41.2 1.0

Copper binding site 6 out of 6 in 5xdq

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Copper binding site 6 out of 6 in the Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State with pH 7.3 at 1.77 Angstrom Resolution


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 Oxidized State with pH 7.3 at 1.77 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Cu302

b:39.0
occ:1.00
 CU2 O:CUA302 0.0 39.0 1.0
O O:GLU198 2.0 39.7 1.0
ND1 O:HIS204 2.0 39.4 1.0
SG O:CYS200 2.3 37.8 1.0
SG O:CYS196 2.3 40.0 1.0
CU1 O:CUA302 2.7 39.4 1.0
CE1 O:HIS204 2.9 38.1 1.0
CG O:HIS204 3.0 38.5 1.0
C O:GLU198 3.2 34.6 1.0
CB O:CYS200 3.3 33.2 1.0
CB O:CYS196 3.4 38.0 1.0
CB O:HIS204 3.5 36.0 1.0
N O:CYS200 3.6 38.0 1.0
CA O:HIS204 3.6 37.0 1.0
O O:HIS204 3.8 41.2 1.0
NE2 O:HIS204 4.0 39.8 1.0
N O:ILE199 4.0 36.4 1.0
N O:GLU198 4.0 35.2 1.0
C O:ILE199 4.0 34.8 1.0
CA O:ILE199 4.1 35.2 1.0
CA O:CYS200 4.1 38.0 1.0
CD2 O:HIS204 4.1 36.9 1.0
C O:HIS204 4.1 36.9 1.0
CA O:GLU198 4.2 34.1 1.0
ND1 O:HIS161 4.2 39.0 1.0
C O:CYS196 4.3 36.6 1.0
O O:CYS196 4.3 36.0 1.0
SD O:MET207 4.4 41.3 1.0
CA O:CYS196 4.5 37.4 1.0
N O:SER197 4.7 34.7 1.0
CG O:MET207 4.8 40.1 1.0
N O:HIS204 4.8 37.0 1.0
O O:ILE199 4.9 32.3 1.0
CA O:HIS161 5.0 35.7 1.0

Reference:

F.Luo, K.Shinzawa-Itoh, K.Hagimoto, A.Shimada, S.Shimada, E.Yamashita, S.Yoshikawa, T.Tsukihara. Structure of Bovine Cytochrome C Oxidase Crystallized at A Neutral pH Using A Fluorinated Detergent. Acta Crystallogr F Struct V. 73 416 2017BIOL Commun.
ISSN: ESSN 2053-230X
PubMed: 28695851
DOI: 10.1107/S2053230X17008834
Page generated: Mon Jul 14 05:33:58 2025

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