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Copper in PDB 1occ: Structure of Bovine Heart Cytochrome C Oxidase at the Fully Oxidized State

Enzymatic activity of Structure of Bovine Heart Cytochrome C Oxidase at the Fully Oxidized State

All present enzymatic activity of Structure of Bovine Heart Cytochrome C Oxidase at the Fully Oxidized State:
1.9.3.1;

Protein crystallography data

The structure of Structure of Bovine Heart Cytochrome C Oxidase at the Fully Oxidized State, PDB code: 1occ was solved by T.Tsukihara, H.Aoyama, E.Yamashita, T.Tomizaki, H.Yamaguchi, K.Shinzawa-Itoh, R.Nakashima, R.Yaono, S.Yoshikawa, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 10.00 / 2.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 189.100, 210.500, 178.600, 90.00, 90.00, 90.00
R / Rfree (%) 20.1 / 25.2

Other elements in 1occ:

The structure of Structure of Bovine Heart Cytochrome C Oxidase at the Fully Oxidized State also contains other interesting chemical elements:

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

Copper Binding Sites:

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

Copper binding site 1 out of 6 in 1occ

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

b:15.3
occ:1.00
 ND1 A:HIS240 1.9 26.2 1.0
NE2 A:HIS291 2.2 7.0 1.0
NE2 A:HIS290 2.2 7.0 1.0
CE1 A:HIS240 2.6 27.2 1.0
CD2 A:HIS291 3.0 18.9 1.0
CG A:HIS240 3.1 18.8 1.0
CE1 A:HIS290 3.1 7.0 1.0
CE1 A:HIS291 3.2 23.1 1.0
CD2 A:HIS290 3.2 17.6 1.0
CB A:HIS240 3.6 11.4 1.0
NE2 A:HIS240 3.9 7.0 1.0
CD2 A:HIS240 4.1 15.7 1.0
CG A:HIS291 4.2 20.1 1.0
CA A:HIS240 4.2 13.6 1.0
ND1 A:HIS291 4.2 23.8 1.0
ND1 A:HIS290 4.2 7.9 1.0
CG A:HIS290 4.3 14.5 1.0
NA A:HEA516 4.4 14.8 1.0
C1A A:HEA516 4.5 7.0 1.0
C4A A:HEA516 4.7 14.3 1.0
FE A:HEA516 4.7 8.0 1.0
C2A A:HEA516 4.9 7.0 1.0
C3A A:HEA516 4.9 7.0 1.0
CHA A:HEA516 4.9 8.6 1.0

Copper binding site 2 out of 6 in 1occ

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Copper binding site 2 out of 6 in the Structure of Bovine Heart Cytochrome C Oxidase at 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 Structure of Bovine Heart Cytochrome C Oxidase at the Fully Oxidized State within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu228

b:25.9
occ:1.00
 ND1 B:HIS161 1.9 7.0 1.0
SG B:CYS196 2.3 10.8 1.0
SG B:CYS200 2.3 10.4 1.0
CU B:CU229 2.4 13.4 1.0
SD B:MET207 2.5 14.2 1.0
CE1 B:HIS161 2.6 7.0 1.0
CG B:HIS161 3.1 7.0 1.0
CE B:MET207 3.2 10.6 1.0
CB B:CYS200 3.3 11.0 1.0
CB B:CYS196 3.5 17.1 1.0
CB B:HIS161 3.7 7.0 1.0
CG B:MET207 3.7 10.4 1.0
O B:GLU198 3.8 20.2 1.0
NE2 B:HIS161 3.9 7.0 1.0
CD2 B:HIS161 4.1 7.0 1.0
CA B:HIS161 4.1 7.0 1.0
ND1 B:HIS204 4.2 16.2 1.0
O B:LEU160 4.6 7.0 1.0
CA B:CYS200 4.7 10.1 1.0
O B:HIS204 4.8 17.7 1.0
CA B:CYS196 4.8 8.4 1.0
N B:CYS200 4.9 16.8 1.0
CA B:HIS204 5.0 9.2 1.0
CD1 B:TRP104 5.0 16.1 1.0

Copper binding site 3 out of 6 in 1occ

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Copper binding site 3 out of 6 in the Structure of Bovine Heart Cytochrome C Oxidase at 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 Structure of Bovine Heart Cytochrome C Oxidase at the Fully Oxidized State within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu229

b:13.4
occ:1.00
 ND1 B:HIS204 1.9 16.2 1.0
O B:GLU198 2.2 20.2 1.0
SG B:CYS200 2.2 10.4 1.0
SG B:CYS196 2.3 10.8 1.0
CU B:CU228 2.4 25.9 1.0
CE1 B:HIS204 2.8 19.0 1.0
CG B:HIS204 3.0 9.0 1.0
CB B:CYS200 3.3 11.0 1.0
C B:GLU198 3.4 11.5 1.0
CB B:CYS196 3.4 17.1 1.0
CB B:HIS204 3.5 12.8 1.0
N B:CYS200 3.6 16.8 1.0
CA B:HIS204 3.6 9.2 1.0
O B:HIS204 3.6 17.7 1.0
NE2 B:HIS204 3.9 10.2 1.0
C B:HIS204 4.0 10.3 1.0
ND1 B:HIS161 4.1 7.0 1.0
CD2 B:HIS204 4.1 11.1 1.0
CA B:CYS200 4.1 10.1 1.0
SD B:MET207 4.1 14.2 1.0
C B:ILE199 4.1 12.8 1.0
CA B:ILE199 4.3 11.1 1.0
N B:ILE199 4.3 13.2 1.0
N B:GLU198 4.3 16.7 1.0
CA B:GLU198 4.4 8.4 1.0
O B:CYS196 4.5 15.9 1.0
CG B:MET207 4.5 10.4 1.0
C B:CYS196 4.6 14.1 1.0
CE1 B:HIS161 4.7 7.0 1.0
CA B:CYS196 4.7 8.4 1.0
N B:HIS204 4.9 15.7 1.0
C B:CYS200 4.9 7.5 1.0
O B:ILE199 4.9 8.4 1.0

Copper binding site 4 out of 6 in 1occ

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Copper binding site 4 out of 6 in the Structure of Bovine Heart Cytochrome C Oxidase at 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 Structure of Bovine Heart Cytochrome C Oxidase at the Fully Oxidized State within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Cu517

b:15.3
occ:1.00
 ND1 N:HIS240 1.9 26.2 1.0
NE2 N:HIS291 2.2 7.0 1.0
NE2 N:HIS290 2.2 7.0 1.0
CE1 N:HIS240 2.6 27.2 1.0
CD2 N:HIS291 3.0 18.9 1.0
CG N:HIS240 3.1 18.8 1.0
CE1 N:HIS290 3.1 7.0 1.0
CE1 N:HIS291 3.2 23.1 1.0
CD2 N:HIS290 3.2 17.6 1.0
CB N:HIS240 3.6 11.4 1.0
NE2 N:HIS240 3.9 7.0 1.0
CD2 N:HIS240 4.1 15.7 1.0
CG N:HIS291 4.2 20.1 1.0
CA N:HIS240 4.2 13.6 1.0
ND1 N:HIS291 4.2 23.8 1.0
ND1 N:HIS290 4.2 7.9 1.0
CG N:HIS290 4.3 14.5 1.0
NA N:HEA516 4.4 14.8 1.0
C1A N:HEA516 4.5 7.0 1.0
C4A N:HEA516 4.7 14.3 1.0
FE N:HEA516 4.7 8.0 1.0
C2A N:HEA516 4.9 7.0 1.0
C3A N:HEA516 4.9 7.0 1.0
CHA N:HEA516 4.9 8.6 1.0

Copper binding site 5 out of 6 in 1occ

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Copper binding site 5 out of 6 in the Structure of Bovine Heart Cytochrome C Oxidase at 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 Structure of Bovine Heart Cytochrome C Oxidase at the Fully Oxidized State within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Cu228

b:25.9
occ:1.00
 ND1 O:HIS161 1.9 7.0 1.0
SG O:CYS196 2.3 10.8 1.0
SG O:CYS200 2.3 10.4 1.0
CU O:CU229 2.4 13.4 1.0
SD O:MET207 2.5 14.2 1.0
CE1 O:HIS161 2.6 7.0 1.0
CG O:HIS161 3.1 7.0 1.0
CE O:MET207 3.2 10.6 1.0
CB O:CYS200 3.3 11.0 1.0
CB O:CYS196 3.5 17.1 1.0
CB O:HIS161 3.7 7.0 1.0
CG O:MET207 3.7 10.4 1.0
O O:GLU198 3.8 20.2 1.0
NE2 O:HIS161 3.9 7.0 1.0
CD2 O:HIS161 4.1 7.0 1.0
CA O:HIS161 4.1 7.0 1.0
ND1 O:HIS204 4.2 16.2 1.0
O O:LEU160 4.6 7.0 1.0
CA O:CYS200 4.7 10.1 1.0
O O:HIS204 4.8 17.7 1.0
CA O:CYS196 4.8 8.4 1.0
N O:CYS200 4.9 16.8 1.0
CA O:HIS204 5.0 9.2 1.0
CD1 O:TRP104 5.0 16.1 1.0

Copper binding site 6 out of 6 in 1occ

Go back to Copper Binding Sites List in 1occ
Copper binding site 6 out of 6 in the Structure of Bovine Heart Cytochrome C Oxidase at 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 Structure of Bovine Heart Cytochrome C Oxidase at the Fully Oxidized State within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Cu229

b:13.4
occ:1.00
 ND1 O:HIS204 1.9 16.2 1.0
O O:GLU198 2.2 20.2 1.0
SG O:CYS200 2.2 10.4 1.0
SG O:CYS196 2.3 10.8 1.0
CU O:CU228 2.4 25.9 1.0
CE1 O:HIS204 2.8 19.0 1.0
CG O:HIS204 3.0 9.0 1.0
CB O:CYS200 3.3 11.0 1.0
C O:GLU198 3.4 11.5 1.0
CB O:CYS196 3.4 17.1 1.0
CB O:HIS204 3.5 12.8 1.0
N O:CYS200 3.6 16.8 1.0
CA O:HIS204 3.6 9.2 1.0
O O:HIS204 3.6 17.7 1.0
NE2 O:HIS204 3.9 10.2 1.0
C O:HIS204 4.0 10.3 1.0
ND1 O:HIS161 4.1 7.0 1.0
CD2 O:HIS204 4.1 11.1 1.0
CA O:CYS200 4.1 10.1 1.0
SD O:MET207 4.1 14.2 1.0
C O:ILE199 4.1 12.8 1.0
CA O:ILE199 4.3 11.1 1.0
N O:ILE199 4.3 13.2 1.0
N O:GLU198 4.3 16.7 1.0
CA O:GLU198 4.4 8.4 1.0
O O:CYS196 4.5 15.9 1.0
CG O:MET207 4.5 10.4 1.0
C O:CYS196 4.6 14.1 1.0
CE1 O:HIS161 4.7 7.0 1.0
CA O:CYS196 4.7 8.4 1.0
N O:HIS204 4.9 15.7 1.0
C O:CYS200 4.9 7.5 1.0
O O:ILE199 4.9 8.4 1.0

Reference:

T.Tsukihara, H.Aoyama, E.Yamashita, T.Tomizaki, H.Yamaguchi, K.Shinzawa-Itoh, R.Nakashima, R.Yaono, S.Yoshikawa. The Whole Structure of the 13-Subunit Oxidized Cytochrome C Oxidase at 2.8 A. Science V. 272 1136 1996.
ISSN: ISSN 0036-8075
PubMed: 8638158
Page generated: Sun Dec 13 11:01:00 2020

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