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Copper in PDB 2dyr: 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: 2dyr was solved by K.Shinzawa-Itoh, H.Aoyama, K.Muramoto, T.Kurauchi, T.Mizushima, E.Yamashita, T.Tsukihara, S.Yoshikawa, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.00 / 1.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 182.590, 205.140, 178.250, 90.00, 90.00, 90.00
R / Rfree (%) 20.2 / 22.7

Other elements in 2dyr:

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 2dyr). 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: 2dyr:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6;

Copper binding site 1 out of 6 in 2dyr

Go back to Copper Binding Sites List in 2dyr
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:20.0
occ:1.00
 NE2 A:HIS291 1.9 23.7 1.0
ND1 A:HIS240 2.0 21.8 1.0
NE2 A:HIS290 2.0 20.2 1.0
CD2 A:HIS291 2.9 21.1 1.0
CE1 A:HIS291 3.0 22.1 1.0
CE1 A:HIS290 3.0 16.9 1.0
CE1 A:HIS240 3.0 20.2 1.0
CG A:HIS240 3.0 21.3 1.0
CD2 A:HIS290 3.1 18.4 1.0
CB A:HIS240 3.4 17.6 1.0
CA A:HIS240 3.9 17.9 1.0
ND1 A:HIS291 4.1 20.3 1.0
CG A:HIS291 4.1 22.5 1.0
NE2 A:HIS240 4.1 22.7 1.0
ND1 A:HIS290 4.1 18.6 1.0
CD2 A:HIS240 4.1 21.9 1.0
CG A:HIS290 4.2 19.1 1.0
NA A:HEA516 4.5 19.0 1.0
C1A A:HEA516 4.6 16.5 1.0
C4A A:HEA516 4.7 17.9 1.0
N A:HIS240 4.8 17.8 1.0
CG2 A:VAL243 4.8 17.3 1.0
C2A A:HEA516 4.9 17.6 1.0
CHA A:HEA516 4.9 17.2 1.0
C3A A:HEA516 4.9 17.8 1.0
FE A:HEA516 5.0 17.8 1.0

Copper binding site 2 out of 6 in 2dyr

Go back to Copper Binding Sites List in 2dyr
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:22.8
occ:1.00
 CU1 B:CUA228 0.0 22.8 1.0
ND1 B:HIS161 2.0 18.3 1.0
SG B:CYS196 2.3 19.7 1.0
SG B:CYS200 2.3 17.6 1.0
CU2 B:CUA228 2.5 19.4 1.0
SD B:MET207 2.6 20.6 1.0
CE1 B:HIS161 2.9 17.0 1.0
CG B:HIS161 3.2 16.0 1.0
CE B:MET207 3.2 16.3 1.0
CB B:CYS200 3.3 21.3 1.0
CB B:CYS196 3.4 16.9 1.0
CG B:MET207 3.6 18.3 1.0
CB B:HIS161 3.7 19.0 1.0
NE2 B:HIS161 4.1 15.7 1.0
O B:GLU198 4.1 24.1 1.0
CA B:HIS161 4.2 17.7 1.0
CD2 B:HIS161 4.2 17.9 1.0
ND1 B:HIS204 4.5 22.2 1.0
O B:HIS102 4.7 19.6 1.0
CA B:CYS200 4.7 21.8 1.0
O B:LEU160 4.7 20.0 1.0
CA B:HIS204 4.7 18.9 1.0
CD1 B:TRP104 4.7 17.7 1.0
CA B:CYS196 4.8 18.7 1.0
N B:CYS200 4.9 22.4 1.0
O B:HIS204 4.9 18.4 1.0
CB B:MET207 4.9 18.1 1.0

Copper binding site 3 out of 6 in 2dyr

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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:Cu228

b:19.4
occ:1.00
 CU2 B:CUA228 0.0 19.4 1.0
ND1 B:HIS204 2.0 22.2 1.0
SG B:CYS200 2.2 17.6 1.0
SG B:CYS196 2.3 19.7 1.0
O B:GLU198 2.4 24.1 1.0
CU1 B:CUA228 2.5 22.8 1.0
CE1 B:HIS204 3.0 21.4 1.0
CG B:HIS204 3.1 20.0 1.0
CB B:CYS196 3.3 16.9 1.0
CB B:CYS200 3.4 21.3 1.0
CB B:HIS204 3.4 17.4 1.0
CA B:HIS204 3.5 18.9 1.0
C B:GLU198 3.5 23.1 1.0
N B:CYS200 3.6 22.4 1.0
O B:HIS204 3.8 18.4 1.0
C B:HIS204 4.1 19.4 1.0
NE2 B:HIS204 4.1 20.2 1.0
CA B:CYS200 4.1 21.8 1.0
N B:GLU198 4.2 20.3 1.0
C B:ILE199 4.2 22.0 1.0
CD2 B:HIS204 4.2 19.3 1.0
ND1 B:HIS161 4.2 18.3 1.0
O B:CYS196 4.2 18.3 1.0
CA B:ILE199 4.2 20.1 1.0
C B:CYS196 4.3 21.8 1.0
N B:ILE199 4.3 21.6 1.0
CA B:CYS196 4.4 18.7 1.0
SD B:MET207 4.5 20.6 1.0
CA B:GLU198 4.5 20.3 1.0
CG B:MET207 4.7 18.3 1.0
N B:SER197 4.8 21.1 1.0
N B:HIS204 4.8 22.3 1.0
CA B:HIS161 5.0 17.7 1.0

Copper binding site 4 out of 6 in 2dyr

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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:21.4
occ:1.00
 ND1 N:HIS240 2.0 20.5 1.0
NE2 N:HIS291 2.0 24.0 1.0
NE2 N:HIS290 2.0 19.0 1.0
CD2 N:HIS291 3.0 23.4 1.0
CE1 N:HIS240 3.0 20.5 1.0
CE1 N:HIS290 3.0 20.9 1.0
CG N:HIS240 3.0 20.7 1.0
CE1 N:HIS291 3.0 23.8 1.0
CD2 N:HIS290 3.1 19.2 1.0
CB N:HIS240 3.3 16.1 1.0
CA N:HIS240 3.9 18.9 1.0
NE2 N:HIS240 4.1 24.2 1.0
CG N:HIS291 4.1 23.9 1.0
CD2 N:HIS240 4.1 21.9 1.0
ND1 N:HIS291 4.1 24.1 1.0
ND1 N:HIS290 4.2 18.9 1.0
CG N:HIS290 4.2 21.1 1.0
NA N:HEA516 4.5 20.3 1.0
C1A N:HEA516 4.6 19.1 1.0
C4A N:HEA516 4.7 19.5 1.0
CG2 N:VAL243 4.8 18.3 1.0
N N:HIS240 4.8 18.7 1.0
C2A N:HEA516 4.9 18.8 1.0
C3A N:HEA516 4.9 18.8 1.0
CHA N:HEA516 4.9 17.8 1.0
FE N:HEA516 5.0 20.6 1.0

Copper binding site 5 out of 6 in 2dyr

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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:26.4
occ:1.00
 CU1 O:CUA228 0.0 26.4 1.0
ND1 O:HIS161 2.0 26.0 1.0
SG O:CYS196 2.3 22.6 1.0
SG O:CYS200 2.3 23.5 1.0
CU2 O:CUA228 2.4 27.1 1.0
SD O:MET207 2.7 25.8 1.0
CE1 O:HIS161 2.9 23.2 1.0
CE O:MET207 3.1 19.4 1.0
CG O:HIS161 3.2 21.6 1.0
CB O:CYS200 3.3 27.4 1.0
CB O:CYS196 3.4 24.2 1.0
CG O:MET207 3.6 26.3 1.0
CB O:HIS161 3.7 25.7 1.0
O O:GLU198 4.0 27.2 1.0
NE2 O:HIS161 4.1 21.5 1.0
CA O:HIS161 4.2 23.7 1.0
CD2 O:HIS161 4.3 20.5 1.0
ND1 O:HIS204 4.3 26.8 1.0
CA O:CYS200 4.7 25.3 1.0
CA O:HIS204 4.7 23.5 1.0
O O:LEU160 4.7 24.1 1.0
CD1 O:TRP104 4.7 23.4 1.0
CA O:CYS196 4.7 24.4 1.0
O O:HIS102 4.8 24.6 1.0
O O:HIS204 4.9 25.6 1.0
N O:CYS200 4.9 28.2 1.0

Copper binding site 6 out of 6 in 2dyr

Go back to Copper Binding Sites List in 2dyr
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:Cu228

b:27.1
occ:1.00
 CU2 O:CUA228 0.0 27.1 1.0
ND1 O:HIS204 2.0 26.8 1.0
SG O:CYS200 2.3 23.5 1.0
SG O:CYS196 2.3 22.6 1.0
CU1 O:CUA228 2.4 26.4 1.0
O O:GLU198 2.4 27.2 1.0
CE1 O:HIS204 2.9 23.1 1.0
CG O:HIS204 3.1 24.1 1.0
CB O:CYS196 3.3 24.2 1.0
CB O:CYS200 3.4 27.4 1.0
C O:GLU198 3.5 24.5 1.0
CB O:HIS204 3.6 24.6 1.0
N O:CYS200 3.6 28.2 1.0
CA O:HIS204 3.6 23.5 1.0
O O:HIS204 3.8 25.6 1.0
ND1 O:HIS161 4.0 26.0 1.0
NE2 O:HIS204 4.1 23.2 1.0
CA O:CYS200 4.1 25.3 1.0
N O:GLU198 4.1 23.6 1.0
C O:HIS204 4.2 23.2 1.0
C O:ILE199 4.2 29.2 1.0
CD2 O:HIS204 4.2 24.0 1.0
O O:CYS196 4.3 25.9 1.0
CA O:ILE199 4.3 24.8 1.0
N O:ILE199 4.3 23.6 1.0
C O:CYS196 4.3 27.7 1.0
CA O:CYS196 4.4 24.4 1.0
CA O:GLU198 4.5 23.3 1.0
SD O:MET207 4.5 25.8 1.0
CG O:MET207 4.8 26.3 1.0
N O:SER197 4.8 27.8 1.0
CE1 O:HIS161 4.8 23.2 1.0
N O:HIS204 4.9 26.1 1.0
CA O:HIS161 4.9 23.7 1.0
CG O:HIS161 5.0 21.6 1.0

Reference:

K.Shinzawa-Itoh, H.Aoyama, K.Muramoto, H.Terada, T.Kurauchi, Y.Tadehara, A.Yamasaki, T.Sugimura, S.Kurono, K.Tsujimoto, T.Mizushima, E.Yamashita, T.Tsukihara, S.Yoshikawa. Structures and Physiological Roles of 13 Integral Lipids of Bovine Heart Cytochrome C Oxidase Embo J. V. 26 1713 2007.
ISSN: ISSN 0261-4189
PubMed: 17332748
DOI: 10.1038/SJ.EMBOJ.7601618
Page generated: Tue Jul 30 23:24:53 2024

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