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Copper in PDB 2zxw: Bovine Heart Cytochrome C Oxidase at the Fully Oxidized State (1-S X- Ray Exposure Dataset)

Enzymatic activity of Bovine Heart Cytochrome C Oxidase at the Fully Oxidized State (1-S X- Ray Exposure Dataset)

All present enzymatic activity of Bovine Heart Cytochrome C Oxidase at the Fully Oxidized State (1-S X- Ray Exposure Dataset):
1.9.3.1;

Protein crystallography data

The structure of Bovine Heart Cytochrome C Oxidase at the Fully Oxidized State (1-S X- Ray Exposure Dataset), PDB code: 2zxw was solved by H.Aoyama, K.Muramoto, K.Shinzawa-Itoh, K.Hirata, E.Yamashita, T.Tsukihara, T.Ogura, S.Yoshikawa, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.00 / 2.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 184.156, 207.621, 178.247, 90.00, 90.00, 90.00
R / Rfree (%) 18.5 / 23.3

Other elements in 2zxw:

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

Copper binding site 1 out of 6 in 2zxw

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Copper binding site 1 out of 6 in the Bovine Heart Cytochrome C Oxidase at the Fully Oxidized State (1-S X- Ray Exposure Dataset)


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 (1-S X- Ray Exposure Dataset) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu517

b:17.2
occ:1.00
O2 A:PER520 2.1 10.5 1.0
ND1 A:HIS240 2.1 21.3 1.0
NE2 A:HIS291 2.1 15.2 1.0
NE2 A:HIS290 2.2 12.7 1.0
O1 A:PER520 2.8 8.5 1.0
CD2 A:HIS291 3.0 13.6 1.0
CG A:HIS240 3.0 16.7 1.0
CD2 A:HIS290 3.0 12.9 1.0
CE1 A:HIS240 3.1 20.9 1.0
CE1 A:HIS291 3.2 20.9 1.0
CE1 A:HIS290 3.2 16.5 1.0
CB A:HIS240 3.3 15.3 1.0
CA A:HIS240 3.9 14.4 1.0
CD2 A:HIS240 4.2 19.0 1.0
CG A:HIS291 4.2 15.5 1.0
NE2 A:HIS240 4.2 19.0 1.0
CG A:HIS290 4.2 15.6 1.0
ND1 A:HIS291 4.3 15.6 1.0
ND1 A:HIS290 4.3 14.6 1.0
NA A:HEA516 4.4 17.1 1.0
C4A A:HEA516 4.6 16.5 1.0
C1A A:HEA516 4.6 15.0 1.0
N A:HIS240 4.7 13.9 1.0
CG2 A:VAL243 4.7 11.4 1.0
C3A A:HEA516 4.8 12.6 1.0
C2A A:HEA516 4.9 14.7 1.0
FE A:HEA516 4.9 15.0 1.0
C A:HIS240 5.0 15.6 1.0

Copper binding site 2 out of 6 in 2zxw

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Copper binding site 2 out of 6 in the Bovine Heart Cytochrome C Oxidase at the Fully Oxidized State (1-S X- Ray Exposure Dataset)


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 (1-S X- Ray Exposure Dataset) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu228

b:18.3
occ:1.00
CU1 B:CUA228 0.0 18.3 1.0
ND1 B:HIS161 2.0 14.2 1.0
SG B:CYS200 2.3 15.7 1.0
SG B:CYS196 2.3 16.4 1.0
SD B:MET207 2.5 18.3 1.0
CU2 B:CUA228 2.5 17.4 1.0
CE1 B:HIS161 2.9 12.6 1.0
CG B:HIS161 3.0 11.8 1.0
CE B:MET207 3.2 7.4 1.0
CB B:CYS200 3.2 17.0 1.0
CB B:CYS196 3.4 14.1 1.0
CB B:HIS161 3.4 12.4 1.0
O B:GLU198 3.7 18.9 1.0
CG B:MET207 3.8 12.6 1.0
NE2 B:HIS161 4.1 9.6 1.0
CA B:HIS161 4.1 12.2 1.0
CD2 B:HIS161 4.1 10.5 1.0
O B:LEU160 4.5 11.2 1.0
ND1 B:HIS204 4.5 19.6 1.0
CA B:CYS200 4.7 16.9 1.0
CA B:HIS204 4.7 15.9 1.0
CA B:CYS196 4.7 15.5 1.0
O B:HIS102 4.8 13.6 1.0
CD1 B:TRP104 4.8 17.6 1.0
O B:HIS204 4.9 13.0 1.0
N B:CYS200 5.0 15.5 1.0
CZ2 B:TRP106 5.0 16.8 1.0

Copper binding site 3 out of 6 in 2zxw

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Copper binding site 3 out of 6 in the Bovine Heart Cytochrome C Oxidase at the Fully Oxidized State (1-S X- Ray Exposure Dataset)


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 (1-S X- Ray Exposure Dataset) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu228

b:17.4
occ:1.00
CU2 B:CUA228 0.0 17.4 1.0
ND1 B:HIS204 2.0 19.6 1.0
O B:GLU198 2.1 18.9 1.0
SG B:CYS200 2.2 15.7 1.0
SG B:CYS196 2.3 16.4 1.0
CU1 B:CUA228 2.5 18.3 1.0
CE1 B:HIS204 2.9 15.8 1.0
CG B:HIS204 3.0 17.5 1.0
C B:GLU198 3.3 17.9 1.0
CB B:CYS196 3.3 14.1 1.0
CB B:HIS204 3.4 15.7 1.0
CB B:CYS200 3.4 17.0 1.0
CA B:HIS204 3.4 15.9 1.0
O B:HIS204 3.6 13.0 1.0
N B:CYS200 3.7 15.5 1.0
C B:HIS204 4.0 14.3 1.0
NE2 B:HIS204 4.1 18.3 1.0
CD2 B:HIS204 4.1 15.7 1.0
C B:ILE199 4.1 15.2 1.0
N B:GLU198 4.1 18.5 1.0
N B:ILE199 4.2 16.7 1.0
CA B:CYS200 4.2 16.9 1.0
CA B:ILE199 4.2 15.6 1.0
O B:CYS196 4.2 15.5 1.0
C B:CYS196 4.2 15.7 1.0
SD B:MET207 4.2 18.3 1.0
ND1 B:HIS161 4.3 14.2 1.0
CA B:GLU198 4.4 18.4 1.0
CA B:CYS196 4.4 15.5 1.0
N B:HIS204 4.7 18.8 1.0
N B:SER197 4.7 16.3 1.0
CG B:MET207 4.7 12.6 1.0
O B:ILE199 5.0 13.9 1.0
CA B:HIS161 5.0 12.2 1.0

Copper binding site 4 out of 6 in 2zxw

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Copper binding site 4 out of 6 in the Bovine Heart Cytochrome C Oxidase at the Fully Oxidized State (1-S X- Ray Exposure Dataset)


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 (1-S X- Ray Exposure Dataset) within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Cu517

b:18.6
occ:1.00
NE2 N:HIS291 2.0 17.8 1.0
ND1 N:HIS240 2.1 21.1 1.0
NE2 N:HIS290 2.1 15.0 1.0
O2 N:PER520 2.2 13.6 1.0
O1 N:PER520 2.7 13.6 1.0
CE1 N:HIS291 2.9 18.4 1.0
CE1 N:HIS240 3.0 24.1 1.0
CE1 N:HIS290 3.1 22.2 1.0
CG N:HIS240 3.1 20.8 1.0
CD2 N:HIS291 3.1 15.3 1.0
CD2 N:HIS290 3.2 21.0 1.0
CB N:HIS240 3.4 18.8 1.0
CA N:HIS240 4.0 19.2 1.0
ND1 N:HIS291 4.1 17.5 1.0
NE2 N:HIS240 4.2 26.4 1.0
CG N:HIS291 4.2 18.4 1.0
CD2 N:HIS240 4.2 23.5 1.0
ND1 N:HIS290 4.2 18.4 1.0
CG N:HIS290 4.3 22.8 1.0
NA N:HEA516 4.4 21.4 1.0
C1A N:HEA516 4.5 21.1 1.0
C4A N:HEA516 4.6 18.5 1.0
CG2 N:VAL243 4.7 18.2 1.0
N N:HIS240 4.8 19.4 1.0
FE N:HEA516 4.8 20.4 1.0
C2A N:HEA516 4.9 17.3 1.0
C3A N:HEA516 4.9 19.9 1.0
CHA N:HEA516 4.9 22.2 1.0

Copper binding site 5 out of 6 in 2zxw

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Copper binding site 5 out of 6 in the Bovine Heart Cytochrome C Oxidase at the Fully Oxidized State (1-S X- Ray Exposure Dataset)


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 (1-S X- Ray Exposure Dataset) within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Cu228

b:26.8
occ:1.00
CU1 O:CUA228 0.0 26.8 1.0
ND1 O:HIS161 2.0 22.2 1.0
SG O:CYS196 2.3 20.4 1.0
SG O:CYS200 2.3 26.3 1.0
SD O:MET207 2.4 29.3 1.0
CU2 O:CUA228 2.5 25.2 1.0
CE1 O:HIS161 2.8 18.7 1.0
CG O:HIS161 3.1 18.4 1.0
CE O:MET207 3.2 18.5 1.0
CB O:CYS200 3.3 24.1 1.0
CB O:CYS196 3.4 22.4 1.0
CB O:HIS161 3.6 21.2 1.0
CG O:MET207 3.7 24.5 1.0
O O:GLU198 3.9 26.1 1.0
NE2 O:HIS161 4.0 20.0 1.0
CD2 O:HIS161 4.2 16.3 1.0
CA O:HIS161 4.3 21.8 1.0
ND1 O:HIS204 4.4 25.7 1.0
CA O:HIS204 4.7 25.9 1.0
CD1 O:TRP104 4.7 24.7 1.0
CA O:CYS200 4.7 24.8 1.0
O O:HIS102 4.7 20.4 1.0
O O:LEU160 4.7 19.8 1.0
CA O:CYS196 4.7 23.4 1.0
O O:HIS204 4.8 23.5 1.0

Copper binding site 6 out of 6 in 2zxw

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Copper binding site 6 out of 6 in the Bovine Heart Cytochrome C Oxidase at the Fully Oxidized State (1-S X- Ray Exposure Dataset)


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 (1-S X- Ray Exposure Dataset) within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Cu228

b:25.2
occ:1.00
CU2 O:CUA228 0.0 25.2 1.0
ND1 O:HIS204 2.0 25.7 1.0
O O:GLU198 2.1 26.1 1.0
SG O:CYS200 2.2 26.3 1.0
SG O:CYS196 2.3 20.4 1.0
CU1 O:CUA228 2.5 26.8 1.0
CG O:HIS204 2.9 26.3 1.0
CE1 O:HIS204 3.0 23.5 1.0
CB O:HIS204 3.2 26.6 1.0
CB O:CYS200 3.2 24.1 1.0
C O:GLU198 3.4 24.3 1.0
CA O:HIS204 3.4 25.9 1.0
CB O:CYS196 3.5 22.4 1.0
N O:CYS200 3.5 24.8 1.0
O O:HIS204 3.8 23.5 1.0
CA O:CYS200 4.0 24.8 1.0
CD2 O:HIS204 4.0 25.3 1.0
NE2 O:HIS204 4.0 20.9 1.0
C O:HIS204 4.0 24.9 1.0
ND1 O:HIS161 4.1 22.2 1.0
C O:ILE199 4.1 24.2 1.0
N O:GLU198 4.2 24.6 1.0
CA O:ILE199 4.2 23.6 1.0
N O:ILE199 4.2 22.6 1.0
O O:CYS196 4.3 22.9 1.0
SD O:MET207 4.3 29.3 1.0
CA O:GLU198 4.4 24.1 1.0
C O:CYS196 4.4 23.4 1.0
CA O:CYS196 4.6 23.4 1.0
N O:HIS204 4.7 27.1 1.0
CG O:MET207 4.8 24.5 1.0
CE1 O:HIS161 4.8 18.7 1.0
C O:CYS200 4.9 24.4 1.0
N O:SER197 5.0 23.1 1.0

Reference:

H.Aoyama, K.Muramoto, K.Shinzawa-Itoh, K.Hirata, E.Yamashita, T.Tsukihara, T.Ogura, S.Yoshikawa. A Peroxide Bridge Between Fe and Cu Ions in the O2 Reduction Site of Fully Oxidized Cytochrome C Oxidase Could Suppress the Proton Pump Proc.Natl.Acad.Sci.Usa V. 106 2165 2009.
ISSN: ISSN 0027-8424
PubMed: 19164527
DOI: 10.1073/PNAS.0806391106
Page generated: Sun Dec 13 11:08:38 2020

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