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Copper in PDB 2occ: Bovine Heart Cytochrome C Oxidase at the Fully Oxidized State

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

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

Protein crystallography data

The structure of Bovine Heart Cytochrome C Oxidase at the Fully Oxidized State, PDB code: 2occ was solved by T.Tsukihara, M.Yao, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 15.00 / 2.30
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 (%) 20.9 / 24.4

Other elements in 2occ:

The structure of Bovine Heart Cytochrome C Oxidase at 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 Bovine Heart Cytochrome C Oxidase at the Fully Oxidized State (pdb code 2occ). 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 at the Fully Oxidized State, PDB code: 2occ:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6;

Copper binding site 1 out of 6 in 2occ

Go back to Copper Binding Sites List in 2occ
Copper binding site 1 out of 6 in the 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 Bovine Heart Cytochrome C Oxidase at the Fully Oxidized State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu517

b:16.3
occ:1.00
 NE2 A:HIS290 1.9 12.6 1.0
NE2 A:HIS291 1.9 29.2 1.0
O2 A:PER520 2.1 15.3 1.0
ND1 A:HIS240 2.2 25.9 1.0
CE1 A:HIS291 2.8 25.4 1.0
O1 A:PER520 2.8 10.3 1.0
CE1 A:HIS290 2.9 22.4 1.0
CD2 A:HIS290 3.0 21.2 1.0
CD2 A:HIS291 3.1 26.0 1.0
CG A:HIS240 3.1 18.4 1.0
CE1 A:HIS240 3.2 22.7 1.0
CB A:HIS240 3.4 17.1 1.0
CA A:HIS240 3.9 17.0 1.0
ND1 A:HIS291 4.0 25.0 1.0
ND1 A:HIS290 4.1 17.1 1.0
CG A:HIS290 4.1 23.1 1.0
CG A:HIS291 4.1 27.2 1.0
CD2 A:HIS240 4.3 24.0 1.0
NE2 A:HIS240 4.3 28.7 1.0
NA A:HEA516 4.6 24.2 1.0
C1A A:HEA516 4.6 13.3 1.0
C4A A:HEA516 4.7 17.9 1.0
N A:HIS240 4.8 12.3 1.0
C2A A:HEA516 4.8 21.2 1.0
CG2 A:VAL243 4.8 15.2 1.0
C3A A:HEA516 4.8 17.3 1.0
FE A:HEA516 4.9 20.1 1.0

Copper binding site 2 out of 6 in 2occ

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

b:22.0
occ:1.00
 ND1 B:HIS161 1.9 10.9 1.0
SG B:CYS196 2.2 17.2 1.0
SG B:CYS200 2.3 15.5 1.0
CU B:CU229 2.4 24.3 1.0
CE1 B:HIS161 2.5 7.0 1.0
SD B:MET207 2.7 22.4 1.0
CE B:MET207 2.9 21.4 1.0
CG B:HIS161 3.2 7.0 1.0
CB B:CYS200 3.3 19.8 1.0
CB B:CYS196 3.4 26.2 1.0
CG B:MET207 3.7 25.8 1.0
NE2 B:HIS161 3.8 7.2 1.0
CB B:HIS161 3.9 17.1 1.0
O B:GLU198 4.0 32.3 1.0
CD2 B:HIS161 4.1 8.0 1.0
CA B:HIS161 4.2 14.6 1.0
ND1 B:HIS204 4.3 28.3 1.0
O B:LEU160 4.6 21.0 1.0
CA B:CYS196 4.7 23.2 1.0
CA B:CYS200 4.7 20.4 1.0
CA B:HIS204 4.9 21.4 1.0
O B:HIS102 4.9 13.5 1.0
O B:HIS204 4.9 20.1 1.0
N B:CYS200 5.0 20.8 1.0
CD1 B:TRP104 5.0 25.0 1.0

Copper binding site 3 out of 6 in 2occ

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

b:24.3
occ:1.00
 ND1 B:HIS204 1.9 28.3 1.0
SG B:CYS200 2.2 15.5 1.0
SG B:CYS196 2.3 17.2 1.0
O B:GLU198 2.4 32.3 1.0
CU B:CU228 2.4 22.0 1.0
CE1 B:HIS204 2.7 24.6 1.0
CG B:HIS204 3.1 19.1 1.0
CB B:CYS196 3.1 26.2 1.0
CB B:CYS200 3.5 19.8 1.0
C B:GLU198 3.6 22.7 1.0
CB B:HIS204 3.6 22.5 1.0
CA B:HIS204 3.7 21.4 1.0
O B:HIS204 3.7 20.1 1.0
N B:CYS200 3.7 20.8 1.0
NE2 B:HIS204 4.0 21.0 1.0
ND1 B:HIS161 4.1 10.9 1.0
C B:HIS204 4.1 19.6 1.0
CD2 B:HIS204 4.1 20.5 1.0
C B:ILE199 4.1 20.4 1.0
CA B:CYS200 4.2 20.4 1.0
CA B:ILE199 4.2 21.5 1.0
O B:CYS196 4.2 21.5 1.0
N B:GLU198 4.3 18.5 1.0
N B:ILE199 4.3 23.8 1.0
C B:CYS196 4.3 25.0 1.0
CA B:CYS196 4.3 23.2 1.0
SD B:MET207 4.4 22.4 1.0
CA B:GLU198 4.6 18.4 1.0
CE1 B:HIS161 4.6 7.0 1.0
CG B:MET207 4.7 25.8 1.0
N B:HIS204 4.9 27.4 1.0
N B:SER197 4.9 24.8 1.0
O B:ILE199 5.0 22.2 1.0
CE B:MET207 5.0 21.4 1.0

Copper binding site 4 out of 6 in 2occ

Go back to Copper Binding Sites List in 2occ
Copper binding site 4 out of 6 in the 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 Bovine Heart Cytochrome C Oxidase at the Fully Oxidized State within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Cu517

b:29.1
occ:1.00
 NE2 N:HIS290 2.0 18.9 1.0
NE2 N:HIS291 2.0 36.0 1.0
O2 N:PER520 2.0 21.1 1.0
ND1 N:HIS240 2.2 33.4 1.0
O1 N:PER520 2.7 22.6 1.0
CE1 N:HIS291 2.8 30.9 1.0
CE1 N:HIS290 2.9 27.4 1.0
CD2 N:HIS290 3.0 23.1 1.0
CG N:HIS240 3.1 29.1 1.0
CD2 N:HIS291 3.1 28.4 1.0
CE1 N:HIS240 3.2 30.2 1.0
CB N:HIS240 3.4 27.6 1.0
CA N:HIS240 3.9 28.6 1.0
ND1 N:HIS291 4.0 28.2 1.0
ND1 N:HIS290 4.1 22.6 1.0
CG N:HIS290 4.2 23.2 1.0
CG N:HIS291 4.2 26.9 1.0
CD2 N:HIS240 4.3 32.0 1.0
NE2 N:HIS240 4.3 31.3 1.0
NA N:HEA516 4.6 23.9 1.0
C1A N:HEA516 4.6 22.5 1.0
C4A N:HEA516 4.7 25.2 1.0
N N:HIS240 4.7 27.0 1.0
CG2 N:VAL243 4.7 21.4 1.0
C2A N:HEA516 4.8 25.6 1.0
C3A N:HEA516 4.8 21.6 1.0
FE N:HEA516 4.9 26.8 1.0

Copper binding site 5 out of 6 in 2occ

Go back to Copper Binding Sites List in 2occ
Copper binding site 5 out of 6 in the 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 Bovine Heart Cytochrome C Oxidase at the Fully Oxidized State within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Cu228

b:36.3
occ:1.00
 ND1 O:HIS161 2.0 26.7 1.0
SG O:CYS196 2.2 30.6 1.0
CU O:CU229 2.2 35.5 1.0
SG O:CYS200 2.2 26.3 1.0
CE1 O:HIS161 2.6 22.1 1.0
SD O:MET207 2.7 41.2 1.0
CE O:MET207 3.1 31.5 1.0
CG O:HIS161 3.3 24.6 1.0
CB O:CYS200 3.3 31.4 1.0
CB O:CYS196 3.4 35.0 1.0
O O:GLU198 3.8 39.9 1.0
CG O:MET207 3.8 37.1 1.0
NE2 O:HIS161 3.9 22.7 1.0
CB O:HIS161 3.9 26.4 1.0
ND1 O:HIS204 4.2 34.7 1.0
CD2 O:HIS161 4.2 24.9 1.0
CA O:HIS161 4.2 25.4 1.0
O O:LEU160 4.5 28.2 1.0
CA O:CYS200 4.6 33.1 1.0
CA O:CYS196 4.7 36.4 1.0
N O:CYS200 4.8 38.0 1.0
O O:HIS204 4.8 34.1 1.0
CA O:HIS204 4.8 36.5 1.0
CE1 O:HIS204 5.0 32.5 1.0

Copper binding site 6 out of 6 in 2occ

Go back to Copper Binding Sites List in 2occ
Copper binding site 6 out of 6 in the 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 Bovine Heart Cytochrome C Oxidase at the Fully Oxidized State within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Cu229

b:35.5
occ:1.00
 ND1 O:HIS204 2.0 34.7 1.0
SG O:CYS200 2.2 26.3 1.0
CU O:CU228 2.2 36.3 1.0
SG O:CYS196 2.2 30.6 1.0
O O:GLU198 2.4 39.9 1.0
CE1 O:HIS204 2.8 32.5 1.0
CG O:HIS204 3.2 34.5 1.0
CB O:CYS196 3.2 35.0 1.0
CB O:CYS200 3.4 31.4 1.0
C O:GLU198 3.6 31.8 1.0
N O:CYS200 3.6 38.0 1.0
CB O:HIS204 3.7 36.6 1.0
CA O:HIS204 3.7 36.5 1.0
O O:HIS204 3.7 34.1 1.0
ND1 O:HIS161 3.9 26.7 1.0
NE2 O:HIS204 4.1 33.1 1.0
C O:HIS204 4.1 34.7 1.0
CA O:CYS200 4.2 33.1 1.0
C O:ILE199 4.2 34.9 1.0
CD2 O:HIS204 4.2 30.8 1.0
CA O:ILE199 4.3 30.7 1.0
O O:CYS196 4.3 39.4 1.0
SD O:MET207 4.3 41.2 1.0
N O:GLU198 4.3 33.7 1.0
N O:ILE199 4.3 30.4 1.0
C O:CYS196 4.4 39.1 1.0
CA O:CYS196 4.4 36.4 1.0
CE1 O:HIS161 4.5 22.1 1.0
CA O:GLU198 4.6 30.5 1.0
CG O:MET207 4.7 37.1 1.0
CE O:MET207 4.9 31.5 1.0
N O:HIS204 4.9 41.2 1.0

Reference:

S.Yoshikawa, K.Shinzawa-Itoh, R.Nakashima, R.Yaono, E.Yamashita, N.Inoue, M.Yao, M.J.Fei, C.P.Libeu, T.Mizushima, H.Yamaguchi, T.Tomizaki, T.Tsukihara. Redox-Coupled Crystal Structural Changes in Bovine Heart Cytochrome C Oxidase. Science V. 280 1723 1998.
ISSN: ISSN 0036-8075
PubMed: 9624044
DOI: 10.1126/SCIENCE.280.5370.1723
Page generated: Tue Jul 30 23:50:41 2024

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