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Copper in PDB 7d5x: Bovine Heart Cytochrome C Oxidase in A Catalytic Intermediate, IO10, at 1.74 Angstrom Resolution

Enzymatic activity of Bovine Heart Cytochrome C Oxidase in A Catalytic Intermediate, IO10, at 1.74 Angstrom Resolution

All present enzymatic activity of Bovine Heart Cytochrome C Oxidase in A Catalytic Intermediate, IO10, at 1.74 Angstrom Resolution:
7.1.1.9;

Protein crystallography data

The structure of Bovine Heart Cytochrome C Oxidase in A Catalytic Intermediate, IO10, at 1.74 Angstrom Resolution, PDB code: 7d5x was solved by T.Tsukihara, A.Shimada, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.70 / 1.74
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 181.767, 203.304, 177.566, 90, 90, 90
R / Rfree (%) 15.6 / 18.4

Other elements in 7d5x:

The structure of Bovine Heart Cytochrome C Oxidase in A Catalytic Intermediate, IO10, at 1.74 Angstrom Resolution also contains other interesting chemical elements:

Zinc (Zn) 2 atoms
Sodium (Na) 4 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 A Catalytic Intermediate, IO10, at 1.74 Angstrom Resolution (pdb code 7d5x). 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 A Catalytic Intermediate, IO10, at 1.74 Angstrom Resolution, PDB code: 7d5x:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6;

Copper binding site 1 out of 6 in 7d5x

Go back to Copper Binding Sites List in 7d5x
Copper binding site 1 out of 6 in the Bovine Heart Cytochrome C Oxidase in A Catalytic Intermediate, IO10, at 1.74 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 A Catalytic Intermediate, IO10, at 1.74 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu603

b:22.6
occ:1.00
 NE2 A:HIS291 2.0 22.9 1.0
ND1 A:HIS240 2.0 19.5 1.0
NE2 A:HIS290 2.1 21.2 1.0
O2 A:OXY607 2.6 30.0 0.2
CD2 A:HIS291 2.9 21.3 1.0
CE1 A:HIS291 2.9 19.6 1.0
CG A:HIS240 3.0 21.6 1.0
CE1 A:HIS240 3.0 22.4 1.0
CE1 A:HIS290 3.0 22.9 1.0
CD2 A:HIS290 3.1 21.6 1.0
O1 A:OXY607 3.3 14.7 0.2
CB A:HIS240 3.3 20.5 1.0
CA A:HIS240 3.9 18.6 1.0
CG A:HIS291 4.0 19.1 1.0
ND1 A:HIS291 4.0 20.4 1.0
NE2 A:HIS240 4.1 19.7 1.0
CD2 A:HIS240 4.1 19.3 1.0
ND1 A:HIS290 4.1 20.8 1.0
CG A:HIS290 4.2 20.7 1.0
NA A:HEA602 4.5 21.8 1.0
C1A A:HEA602 4.5 20.9 1.0
CG2 A:VAL243 4.7 23.4 1.0
N A:HIS240 4.7 22.1 1.0
C4A A:HEA602 4.7 21.5 1.0
C2A A:HEA602 4.8 20.8 1.0
CHA A:HEA602 4.9 20.9 1.0
C3A A:HEA602 5.0 24.1 1.0
CG2 A:VAL287 5.0 21.8 1.0

Copper binding site 2 out of 6 in 7d5x

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Copper binding site 2 out of 6 in the Bovine Heart Cytochrome C Oxidase in A Catalytic Intermediate, IO10, at 1.74 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 A Catalytic Intermediate, IO10, at 1.74 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu302

b:24.4
occ:1.00
 CU1 B:CUA302 0.0 24.4 1.0
ND1 B:HIS161 2.1 24.8 1.0
SG B:CYS196 2.3 26.5 1.0
SG B:CYS200 2.4 24.4 1.0
SD B:MET207 2.4 27.5 1.0
CU2 B:CUA302 2.5 24.2 1.0
CE1 B:HIS161 3.0 24.9 1.0
CG B:HIS161 3.2 22.1 1.0
CE B:MET207 3.2 26.7 1.0
CB B:CYS200 3.3 22.9 1.0
CB B:CYS196 3.4 25.0 1.0
CG B:MET207 3.4 25.2 1.0
CB B:HIS161 3.6 21.4 1.0
NE2 B:HIS161 4.1 22.9 1.0
CA B:HIS161 4.2 23.3 1.0
O B:GLU198 4.3 25.8 1.0
CD2 B:HIS161 4.3 22.4 1.0
ND1 B:HIS204 4.4 23.6 1.0
CD1 B:TRP104 4.6 23.9 1.0
O B:HIS102 4.7 26.0 1.0
CA B:CYS200 4.7 27.3 1.0
CA B:HIS204 4.7 22.9 1.0
O B:LEU160 4.8 25.2 1.0
CA B:CYS196 4.8 24.4 1.0
CB B:MET207 4.8 25.2 1.0

Copper binding site 3 out of 6 in 7d5x

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Copper binding site 3 out of 6 in the Bovine Heart Cytochrome C Oxidase in A Catalytic Intermediate, IO10, at 1.74 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 A Catalytic Intermediate, IO10, at 1.74 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu302

b:24.2
occ:1.00
 CU2 B:CUA302 0.0 24.2 1.0
ND1 B:HIS204 2.0 23.6 1.0
SG B:CYS200 2.3 24.4 1.0
SG B:CYS196 2.3 26.5 1.0
CU1 B:CUA302 2.5 24.4 1.0
O B:GLU198 2.7 25.8 1.0
CE1 B:HIS204 2.9 23.1 1.0
CG B:HIS204 3.0 25.3 1.0
CB B:CYS196 3.2 25.0 1.0
CB B:CYS200 3.3 22.9 1.0
CB B:HIS204 3.5 21.8 1.0
CA B:HIS204 3.5 22.9 1.0
N B:CYS200 3.7 24.9 1.0
C B:GLU198 3.7 24.2 1.0
O B:HIS204 3.8 26.3 1.0
NE2 B:HIS204 4.0 24.9 1.0
CD2 B:HIS204 4.1 23.6 1.0
CA B:CYS200 4.1 27.3 1.0
C B:HIS204 4.1 28.0 1.0
ND1 B:HIS161 4.2 24.8 1.0
C B:CYS196 4.2 27.7 1.0
N B:GLU198 4.2 23.6 1.0
O B:CYS196 4.2 24.5 1.0
C B:ILE199 4.2 25.4 1.0
CA B:ILE199 4.3 25.2 1.0
SD B:MET207 4.3 27.5 1.0
CA B:CYS196 4.4 24.4 1.0
N B:ILE199 4.5 23.2 1.0
CG B:MET207 4.5 25.2 1.0
N B:SER197 4.6 25.1 1.0
CA B:GLU198 4.6 26.8 1.0
N B:HIS204 4.7 25.3 1.0
CA B:HIS161 4.9 23.3 1.0
CB B:HIS161 5.0 21.4 1.0

Copper binding site 4 out of 6 in 7d5x

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Copper binding site 4 out of 6 in the Bovine Heart Cytochrome C Oxidase in A Catalytic Intermediate, IO10, at 1.74 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 A Catalytic Intermediate, IO10, at 1.74 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Cu603

b:24.1
occ:1.00
 NE2 N:HIS291 2.0 21.9 1.0
ND1 N:HIS240 2.1 21.8 1.0
NE2 N:HIS290 2.1 26.0 1.0
O2 N:OXY609 2.6 25.1 0.2
CD2 N:HIS291 2.9 23.6 1.0
CE1 N:HIS291 2.9 23.1 1.0
CG N:HIS240 3.0 21.3 1.0
CD2 N:HIS290 3.0 24.8 1.0
CE1 N:HIS240 3.1 21.4 1.0
CE1 N:HIS290 3.1 26.4 1.0
CB N:HIS240 3.3 22.5 1.0
O1 N:OXY609 3.3 16.3 0.2
CA N:HIS240 3.9 20.7 1.0
ND1 N:HIS291 4.0 23.4 1.0
CG N:HIS291 4.0 23.0 1.0
NE2 N:HIS240 4.1 22.2 1.0
CD2 N:HIS240 4.1 21.7 1.0
ND1 N:HIS290 4.2 21.6 1.0
CG N:HIS290 4.2 22.0 1.0
C1A N:HEA602 4.5 26.2 1.0
NA N:HEA602 4.5 24.1 1.0
CG2 N:VAL243 4.7 23.6 1.0
N N:HIS240 4.7 22.2 1.0
C4A N:HEA602 4.8 21.2 1.0
C2A N:HEA602 4.8 23.2 1.0
CHA N:HEA602 4.9 22.5 1.0
C3A N:HEA602 4.9 24.7 1.0

Copper binding site 5 out of 6 in 7d5x

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Copper binding site 5 out of 6 in the Bovine Heart Cytochrome C Oxidase in A Catalytic Intermediate, IO10, at 1.74 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 A Catalytic Intermediate, IO10, at 1.74 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Cu301

b:27.8
occ:1.00
 CU1 O:CUA301 0.0 27.8 1.0
ND1 O:HIS161 2.1 32.9 1.0
SG O:CYS200 2.3 29.1 1.0
SD O:MET207 2.3 31.9 1.0
SG O:CYS196 2.3 29.7 1.0
CU2 O:CUA301 2.5 27.6 1.0
CE1 O:HIS161 2.9 29.2 1.0
CE O:MET207 3.1 31.6 1.0
CG O:HIS161 3.2 28.5 1.0
CB O:CYS200 3.3 26.8 1.0
CG O:MET207 3.4 27.6 1.0
CB O:CYS196 3.4 29.4 1.0
CB O:HIS161 3.7 27.5 1.0
NE2 O:HIS161 4.1 28.9 1.0
CA O:HIS161 4.3 28.1 1.0
CD2 O:HIS161 4.3 26.6 1.0
O O:GLU198 4.3 30.0 1.0
CD1 O:TRP104 4.4 28.9 1.0
ND1 O:HIS204 4.5 28.0 1.0
O O:HIS102 4.7 31.2 1.0
CA O:HIS204 4.7 29.3 1.0
CA O:CYS200 4.7 27.1 1.0
O O:LEU160 4.8 28.8 1.0
CB O:MET207 4.8 28.4 1.0
CA O:CYS196 4.8 28.8 1.0
O O:HIS204 5.0 28.6 1.0

Copper binding site 6 out of 6 in 7d5x

Go back to Copper Binding Sites List in 7d5x
Copper binding site 6 out of 6 in the Bovine Heart Cytochrome C Oxidase in A Catalytic Intermediate, IO10, at 1.74 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 A Catalytic Intermediate, IO10, at 1.74 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Cu301

b:27.6
occ:1.00
 CU2 O:CUA301 0.0 27.6 1.0
ND1 O:HIS204 2.0 28.0 1.0
SG O:CYS200 2.3 29.1 1.0
SG O:CYS196 2.3 29.7 1.0
CU1 O:CUA301 2.5 27.8 1.0
O O:GLU198 2.6 30.0 1.0
CE1 O:HIS204 2.8 25.6 1.0
CG O:HIS204 3.1 31.9 1.0
CB O:CYS196 3.3 29.4 1.0
CB O:CYS200 3.4 26.8 1.0
CA O:HIS204 3.5 29.3 1.0
CB O:HIS204 3.6 28.2 1.0
C O:GLU198 3.7 25.4 1.0
N O:CYS200 3.7 27.9 1.0
O O:HIS204 3.8 28.6 1.0
NE2 O:HIS204 4.0 27.2 1.0
CD2 O:HIS204 4.1 27.9 1.0
C O:HIS204 4.2 32.4 1.0
CA O:CYS200 4.2 27.1 1.0
C O:CYS196 4.2 28.8 1.0
O O:CYS196 4.2 27.8 1.0
N O:GLU198 4.2 27.1 1.0
CA O:ILE199 4.2 25.2 1.0
C O:ILE199 4.2 30.9 1.0
ND1 O:HIS161 4.2 32.9 1.0
CA O:CYS196 4.4 28.8 1.0
SD O:MET207 4.4 31.9 1.0
N O:ILE199 4.4 25.2 1.0
N O:SER197 4.5 29.4 1.0
CA O:GLU198 4.6 28.5 1.0
CG O:MET207 4.6 27.6 1.0
N O:HIS204 4.7 30.0 1.0
CA O:HIS161 4.9 28.1 1.0

Reference:

A.Shimada, F.Hara, K.Shinzawa-Itoh, N.Kanehisa, E.Yamashita, K.Muramoto, T.Tsukihara, S.Yoshikawa. Critical Roles of the Cub Site in Efficient Proton Pumping As Revealed By Crystal Structures of Mammalian Cytochrome C Oxidase Catalytic Intermediates J.Biol.Chem. 2021.
ISSN: ESSN 1083-351X
Page generated: Mon Jul 14 07:57:15 2025

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