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Copper in PDB 7d5w: Bovine Heart Cytochrome C Oxidase in A Catalytic Intermediate of O at 1.84 Angstrom Resolution

Enzymatic activity of Bovine Heart Cytochrome C Oxidase in A Catalytic Intermediate of O at 1.84 Angstrom Resolution

All present enzymatic activity of Bovine Heart Cytochrome C Oxidase in A Catalytic Intermediate of O at 1.84 Angstrom Resolution:
7.1.1.9;

Protein crystallography data

The structure of Bovine Heart Cytochrome C Oxidase in A Catalytic Intermediate of O at 1.84 Angstrom Resolution, PDB code: 7d5w 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) 39.92 / 1.84
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 181.435, 203.092, 177.794, 90, 90, 90
R / Rfree (%) 15.4 / 18.4

Other elements in 7d5w:

The structure of Bovine Heart Cytochrome C Oxidase in A Catalytic Intermediate of O at 1.84 Angstrom Resolution also contains other interesting chemical elements:

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

Copper Binding Sites:

The binding sites of Copper atom in the Bovine Heart Cytochrome C Oxidase in A Catalytic Intermediate of O at 1.84 Angstrom Resolution (pdb code 7d5w). 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 of O at 1.84 Angstrom Resolution, PDB code: 7d5w:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6;

Copper binding site 1 out of 6 in 7d5w

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Copper binding site 1 out of 6 in the Bovine Heart Cytochrome C Oxidase in A Catalytic Intermediate of O at 1.84 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 of O at 1.84 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu603

b:23.3
occ:1.00
 NE2 A:HIS291 2.0 22.5 1.0
NE2 A:HIS290 2.0 22.0 1.0
ND1 A:HIS240 2.1 20.3 1.0
O2 A:PER609 2.2 20.6 0.4
O1 A:PER609 2.7 24.8 0.4
O A:HOH909 2.7 27.0 0.4
CE1 A:HIS291 2.9 23.9 1.0
CE1 A:HIS290 3.0 21.6 1.0
CD2 A:HIS291 3.0 22.1 1.0
CG A:HIS240 3.1 24.5 1.0
CD2 A:HIS290 3.1 18.8 1.0
CE1 A:HIS240 3.1 23.6 1.0
O A:HOH721 3.2 15.1 0.5
CB A:HIS240 3.3 20.7 1.0
CA A:HIS240 3.9 21.6 1.0
ND1 A:HIS291 4.0 18.4 1.0
CG A:HIS291 4.1 18.2 1.0
ND1 A:HIS290 4.1 20.9 1.0
CG A:HIS290 4.2 18.5 1.0
CD2 A:HIS240 4.2 19.7 1.0
NE2 A:HIS240 4.2 19.7 1.0
NA A:HEA602 4.4 21.9 1.0
C1A A:HEA602 4.4 22.7 1.0
C4A A:HEA602 4.6 22.8 1.0
N A:HIS240 4.7 21.8 1.0
C2A A:HEA602 4.7 21.3 1.0
CHA A:HEA602 4.8 17.2 1.0
FE A:HEA602 4.8 21.5 1.0
CG2 A:VAL243 4.8 20.6 1.0
C3A A:HEA602 4.9 26.5 1.0
ND A:HEA602 5.0 22.3 1.0

Copper binding site 2 out of 6 in 7d5w

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Copper binding site 2 out of 6 in the Bovine Heart Cytochrome C Oxidase in A Catalytic Intermediate of O at 1.84 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 of O at 1.84 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu301

b:23.2
occ:1.00
 CU1 B:CUA301 0.0 23.2 1.0
ND1 B:HIS161 2.1 23.9 1.0
SG B:CYS196 2.3 24.9 1.0
SG B:CYS200 2.3 22.0 1.0
SD B:MET207 2.4 25.8 1.0
CU2 B:CUA301 2.5 23.0 1.0
CE1 B:HIS161 2.9 21.6 1.0
CG B:HIS161 3.2 28.0 1.0
CE B:MET207 3.2 22.2 1.0
CB B:CYS200 3.2 23.5 1.0
CB B:CYS196 3.4 26.6 1.0
CG B:MET207 3.5 22.0 1.0
CB B:HIS161 3.6 21.1 1.0
NE2 B:HIS161 4.1 22.9 1.0
O B:GLU198 4.1 24.7 1.0
CA B:HIS161 4.2 19.8 1.0
CD2 B:HIS161 4.2 23.2 1.0
ND1 B:HIS204 4.4 23.3 1.0
CA B:CYS200 4.7 25.6 1.0
O B:HIS102 4.7 24.7 1.0
CA B:HIS204 4.7 21.0 1.0
CD1 B:TRP104 4.7 22.8 1.0
O B:LEU160 4.7 23.7 1.0
CA B:CYS196 4.8 21.1 1.0
CB B:MET207 4.9 27.5 1.0
O B:HIS204 4.9 26.2 1.0
N B:CYS200 5.0 23.2 1.0

Copper binding site 3 out of 6 in 7d5w

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Copper binding site 3 out of 6 in the Bovine Heart Cytochrome C Oxidase in A Catalytic Intermediate of O at 1.84 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 of O at 1.84 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu301

b:23.0
occ:1.00
 CU2 B:CUA301 0.0 23.0 1.0
ND1 B:HIS204 2.0 23.3 1.0
SG B:CYS200 2.3 22.0 1.0
SG B:CYS196 2.3 24.9 1.0
CU1 B:CUA301 2.5 23.2 1.0
O B:GLU198 2.6 24.7 1.0
CE1 B:HIS204 2.9 23.8 1.0
CG B:HIS204 3.1 23.3 1.0
CB B:CYS196 3.3 26.6 1.0
CB B:CYS200 3.3 23.5 1.0
CB B:HIS204 3.5 20.1 1.0
C B:GLU198 3.6 21.2 1.0
CA B:HIS204 3.6 21.0 1.0
N B:CYS200 3.7 23.2 1.0
O B:HIS204 3.9 26.2 1.0
NE2 B:HIS204 4.0 22.9 1.0
ND1 B:HIS161 4.1 23.9 1.0
CA B:CYS200 4.1 25.6 1.0
N B:GLU198 4.1 22.4 1.0
C B:ILE199 4.2 23.1 1.0
CD2 B:HIS204 4.2 24.1 1.0
C B:CYS196 4.2 20.4 1.0
C B:HIS204 4.2 26.4 1.0
CA B:ILE199 4.2 23.9 1.0
O B:CYS196 4.2 25.0 1.0
N B:ILE199 4.3 18.3 1.0
SD B:MET207 4.3 25.8 1.0
CA B:CYS196 4.4 21.1 1.0
CA B:GLU198 4.5 25.1 1.0
CG B:MET207 4.6 22.0 1.0
N B:SER197 4.6 21.2 1.0
N B:HIS204 4.8 25.0 1.0
CA B:HIS161 4.9 19.8 1.0
CE1 B:HIS161 5.0 21.6 1.0

Copper binding site 4 out of 6 in 7d5w

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Copper binding site 4 out of 6 in the Bovine Heart Cytochrome C Oxidase in A Catalytic Intermediate of O at 1.84 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 of O at 1.84 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Cu604

b:24.1
occ:1.00
 NE2 N:HIS291 2.0 23.6 1.0
NE2 N:HIS290 2.1 22.9 1.0
ND1 N:HIS240 2.1 20.3 1.0
O2 N:PER611 2.2 20.6 0.4
O N:HOH908 2.7 28.5 0.4
O1 N:PER611 2.8 31.0 0.4
CE1 N:HIS291 2.9 21.5 1.0
CD2 N:HIS291 3.0 24.9 1.0
CD2 N:HIS290 3.0 24.9 1.0
CG N:HIS240 3.0 26.5 1.0
CE1 N:HIS290 3.1 26.9 1.0
CE1 N:HIS240 3.1 22.4 1.0
O N:HOH725 3.3 15.9 0.5
CB N:HIS240 3.3 20.3 1.0
CA N:HIS240 3.9 21.6 1.0
ND1 N:HIS291 4.0 23.8 1.0
CG N:HIS291 4.1 21.1 1.0
ND1 N:HIS290 4.2 21.5 1.0
CG N:HIS290 4.2 20.3 1.0
CD2 N:HIS240 4.2 21.6 1.0
NE2 N:HIS240 4.2 22.5 1.0
NA N:HEA603 4.4 21.4 1.0
C1A N:HEA603 4.4 24.8 1.0
C4A N:HEA603 4.6 21.5 1.0
N N:HIS240 4.7 22.6 1.0
C2A N:HEA603 4.8 23.4 1.0
CHA N:HEA603 4.8 18.1 1.0
FE N:HEA603 4.8 23.3 1.0
CG2 N:VAL243 4.9 21.1 1.0
C3A N:HEA603 4.9 25.1 1.0
ND N:HEA603 5.0 22.3 1.0

Copper binding site 5 out of 6 in 7d5w

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Copper binding site 5 out of 6 in the Bovine Heart Cytochrome C Oxidase in A Catalytic Intermediate of O at 1.84 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 of O at 1.84 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Cu301

b:27.0
occ:1.00
 CU1 O:CUA301 0.0 27.0 1.0
ND1 O:HIS161 2.0 30.2 1.0
SG O:CYS196 2.3 29.7 1.0
SG O:CYS200 2.3 28.4 1.0
SD O:MET207 2.4 31.4 1.0
CU2 O:CUA301 2.5 27.0 1.0
CE1 O:HIS161 2.9 27.6 1.0
CG O:HIS161 3.2 30.9 1.0
CE O:MET207 3.2 28.2 1.0
CB O:CYS200 3.3 28.8 1.0
CB O:CYS196 3.4 32.1 1.0
CG O:MET207 3.5 27.0 1.0
CB O:HIS161 3.6 26.6 1.0
NE2 O:HIS161 4.0 28.1 1.0
O O:GLU198 4.2 27.5 1.0
CD2 O:HIS161 4.2 28.9 1.0
CA O:HIS161 4.2 25.7 1.0
ND1 O:HIS204 4.4 27.9 1.0
CD1 O:TRP104 4.6 28.4 1.0
O O:HIS102 4.7 30.2 1.0
CA O:CYS200 4.7 27.4 1.0
O O:LEU160 4.7 27.6 1.0
CA O:HIS204 4.7 32.7 1.0
CA O:CYS196 4.8 30.1 1.0
CB O:MET207 4.9 31.6 1.0
O O:HIS204 5.0 28.5 1.0

Copper binding site 6 out of 6 in 7d5w

Go back to Copper Binding Sites List in 7d5w
Copper binding site 6 out of 6 in the Bovine Heart Cytochrome C Oxidase in A Catalytic Intermediate of O at 1.84 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 of O at 1.84 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Cu301

b:27.0
occ:1.00
 CU2 O:CUA301 0.0 27.0 1.0
ND1 O:HIS204 2.0 27.9 1.0
SG O:CYS200 2.2 28.4 1.0
SG O:CYS196 2.3 29.7 1.0
CU1 O:CUA301 2.5 27.0 1.0
O O:GLU198 2.6 27.5 1.0
CE1 O:HIS204 2.9 27.0 1.0
CG O:HIS204 3.1 26.4 1.0
CB O:CYS196 3.3 32.1 1.0
CB O:CYS200 3.3 28.8 1.0
CB O:HIS204 3.5 29.7 1.0
CA O:HIS204 3.6 32.7 1.0
C O:GLU198 3.6 27.9 1.0
N O:CYS200 3.7 31.4 1.0
O O:HIS204 3.9 28.5 1.0
NE2 O:HIS204 4.0 27.5 1.0
CA O:CYS200 4.1 27.4 1.0
ND1 O:HIS161 4.1 30.2 1.0
CD2 O:HIS204 4.1 27.1 1.0
N O:GLU198 4.2 27.0 1.0
C O:HIS204 4.2 32.9 1.0
C O:ILE199 4.2 30.5 1.0
C O:CYS196 4.2 33.8 1.0
CA O:ILE199 4.2 23.4 1.0
O O:CYS196 4.3 27.7 1.0
N O:ILE199 4.3 24.7 1.0
SD O:MET207 4.4 31.4 1.0
CA O:CYS196 4.4 30.1 1.0
CA O:GLU198 4.5 28.9 1.0
CG O:MET207 4.7 27.0 1.0
N O:SER197 4.7 30.0 1.0
N O:HIS204 4.8 33.4 1.0
CE1 O:HIS161 4.9 27.6 1.0
CA O:HIS161 4.9 25.7 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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