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Copper in PDB 3abl: Bovine Heart Cytochrome C Oxidase at the Fully Oxidized State (15-S X-Ray Exposure Dataset)

Enzymatic activity of Bovine Heart Cytochrome C Oxidase at the Fully Oxidized State (15-S X-Ray Exposure Dataset)

All present enzymatic activity of Bovine Heart Cytochrome C Oxidase at the Fully Oxidized State (15-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 (15-S X-Ray Exposure Dataset), PDB code: 3abl was solved by H.Aoyama, K.Muramoto, K.Shinzawa-Itoh, 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 / 2.10
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 184.137, 207.514, 178.173, 90.00, 90.00, 90.00
R / Rfree (%) 17.6 / 21

Copper Binding Sites:

The binding sites of Copper atom in the Bovine Heart Cytochrome C Oxidase at the Fully Oxidized State (15-S X-Ray Exposure Dataset) (pdb code 3abl). 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 (15-S X-Ray Exposure Dataset), PDB code: 3abl:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6;

Copper binding site 1 out of 6 in 3abl

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Copper binding site 1 out of 6 in the Bovine Heart Cytochrome C Oxidase at the Fully Oxidized State (15-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 (15-S X-Ray Exposure Dataset) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu517

b:24.5
occ:1.00
NE2 A:HIS291 1.9 27.3 1.0
NE2 A:HIS290 2.0 24.4 1.0
ND1 A:HIS240 2.0 25.5 1.0
O2 A:PER520 2.2 19.0 1.0
O1 A:PER520 2.8 16.2 1.0
CE1 A:HIS291 2.9 24.6 1.0
CD2 A:HIS291 3.0 20.8 1.0
CG A:HIS240 3.0 25.6 1.0
CD2 A:HIS290 3.0 20.1 1.0
CE1 A:HIS290 3.0 23.5 1.0
CE1 A:HIS240 3.1 23.1 1.0
CB A:HIS240 3.3 20.4 1.0
CA A:HIS240 3.9 20.9 1.0
ND1 A:HIS291 4.0 20.1 1.0
CG A:HIS291 4.1 25.3 1.0
CD2 A:HIS240 4.1 21.7 1.0
ND1 A:HIS290 4.1 20.6 1.0
NE2 A:HIS240 4.2 28.2 1.0
CG A:HIS290 4.2 22.3 1.0
NA A:HEA516 4.5 21.3 1.0
C1A A:HEA516 4.6 18.6 1.0
C4A A:HEA516 4.7 19.4 1.0
N A:HIS240 4.7 18.3 1.0
C2A A:HEA516 4.8 19.9 1.0
FE A:HEA516 4.9 22.9 1.0
CG2 A:VAL243 4.9 25.1 1.0
C3A A:HEA516 4.9 20.4 1.0
C A:HIS240 5.0 21.1 1.0

Copper binding site 2 out of 6 in 3abl

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Copper binding site 2 out of 6 in the Bovine Heart Cytochrome C Oxidase at the Fully Oxidized State (15-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 (15-S X-Ray Exposure Dataset) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu228

b:26.4
occ:1.00
CU1 B:CUA228 0.0 26.4 1.0
ND1 B:HIS161 2.0 18.2 1.0
SG B:CYS200 2.3 23.2 1.0
SG B:CYS196 2.3 24.7 1.0
SD B:MET207 2.4 25.1 1.0
CU2 B:CUA228 2.5 23.8 1.0
CE1 B:HIS161 2.8 19.8 1.0
CE B:MET207 2.9 19.5 1.0
CG B:HIS161 3.2 20.6 1.0
CB B:CYS200 3.3 22.4 1.0
CB B:CYS196 3.4 24.1 1.0
CG B:MET207 3.5 20.7 1.0
CB B:HIS161 3.7 22.9 1.0
O B:GLU198 3.9 24.8 1.0
NE2 B:HIS161 4.1 20.6 1.0
CA B:HIS161 4.1 21.4 1.0
CD2 B:HIS161 4.2 22.7 1.0
ND1 B:HIS204 4.4 25.7 1.0
CA B:HIS204 4.6 23.3 1.0
O B:LEU160 4.6 21.0 1.0
CA B:CYS196 4.7 24.1 1.0
CA B:CYS200 4.8 20.2 1.0
O B:HIS102 4.8 21.2 1.0
CD1 B:TRP104 4.8 22.8 1.0
O B:HIS204 4.8 23.4 1.0
CB B:MET207 5.0 24.8 1.0

Copper binding site 3 out of 6 in 3abl

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Copper binding site 3 out of 6 in the Bovine Heart Cytochrome C Oxidase at the Fully Oxidized State (15-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 (15-S X-Ray Exposure Dataset) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu228

b:23.8
occ:1.00
CU2 B:CUA228 0.0 23.8 1.0
ND1 B:HIS204 2.0 25.7 1.0
O B:GLU198 2.2 24.8 1.0
SG B:CYS200 2.3 23.2 1.0
SG B:CYS196 2.3 24.7 1.0
CU1 B:CUA228 2.5 26.4 1.0
CE1 B:HIS204 2.9 28.9 1.0
CG B:HIS204 3.1 20.9 1.0
C B:GLU198 3.4 21.6 1.0
CB B:CYS200 3.4 22.4 1.0
CB B:CYS196 3.5 24.1 1.0
CB B:HIS204 3.5 19.4 1.0
CA B:HIS204 3.5 23.3 1.0
N B:CYS200 3.8 22.3 1.0
O B:HIS204 3.8 23.4 1.0
NE2 B:HIS204 4.0 30.0 1.0
ND1 B:HIS161 4.1 18.2 1.0
C B:HIS204 4.1 21.5 1.0
C B:ILE199 4.1 21.8 1.0
CD2 B:HIS204 4.1 19.8 1.0
N B:GLU198 4.2 21.4 1.0
CA B:CYS200 4.2 20.2 1.0
N B:ILE199 4.2 21.9 1.0
CA B:ILE199 4.3 21.6 1.0
C B:CYS196 4.3 24.0 1.0
O B:CYS196 4.3 22.2 1.0
SD B:MET207 4.4 25.1 1.0
CA B:GLU198 4.4 21.9 1.0
CA B:CYS196 4.5 24.1 1.0
N B:SER197 4.7 20.0 1.0
CG B:MET207 4.7 20.7 1.0
N B:HIS204 4.8 22.2 1.0
CA B:HIS161 4.8 21.4 1.0
O B:ILE199 4.8 23.9 1.0
CE1 B:HIS161 4.9 19.8 1.0
O B:LEU160 5.0 21.0 1.0

Copper binding site 4 out of 6 in 3abl

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Copper binding site 4 out of 6 in the Bovine Heart Cytochrome C Oxidase at the Fully Oxidized State (15-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 (15-S X-Ray Exposure Dataset) within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Cu517

b:30.2
occ:1.00
NE2 N:HIS290 2.0 24.7 1.0
ND1 N:HIS240 2.0 30.9 1.0
NE2 N:HIS291 2.0 33.0 1.0
O2 N:PER520 2.1 27.6 1.0
O1 N:PER520 2.8 21.0 1.0
CE1 N:HIS290 2.9 24.7 1.0
CE1 N:HIS291 3.0 32.5 1.0
CG N:HIS240 3.0 34.3 1.0
CD2 N:HIS290 3.0 19.2 1.0
CD2 N:HIS291 3.0 30.0 1.0
CE1 N:HIS240 3.1 26.0 1.0
CB N:HIS240 3.3 28.0 1.0
CA N:HIS240 3.9 30.4 1.0
ND1 N:HIS290 4.1 26.5 1.0
ND1 N:HIS291 4.1 29.2 1.0
CG N:HIS290 4.1 29.8 1.0
NE2 N:HIS240 4.2 29.8 1.0
CD2 N:HIS240 4.2 24.7 1.0
CG N:HIS291 4.2 29.4 1.0
NA N:HEA516 4.5 28.8 1.0
C1A N:HEA516 4.6 25.0 1.0
C4A N:HEA516 4.7 29.1 1.0
N N:HIS240 4.8 28.6 1.0
CG2 N:VAL243 4.8 28.6 1.0
C2A N:HEA516 4.8 27.6 1.0
FE N:HEA516 4.8 29.2 1.0
C3A N:HEA516 4.9 27.5 1.0
CHA N:HEA516 4.9 25.7 1.0

Copper binding site 5 out of 6 in 3abl

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Copper binding site 5 out of 6 in the Bovine Heart Cytochrome C Oxidase at the Fully Oxidized State (15-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 (15-S X-Ray Exposure Dataset) within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Cu228

b:32.5
occ:1.00
CU1 O:CUA228 0.0 32.5 1.0
ND1 O:HIS161 2.0 24.2 1.0
SG O:CYS200 2.3 31.1 1.0
SG O:CYS196 2.3 34.1 1.0
SD O:MET207 2.4 36.3 1.0
CU2 O:CUA228 2.6 31.9 1.0
CE1 O:HIS161 2.8 25.8 1.0
CE O:MET207 3.0 23.0 1.0
CG O:HIS161 3.2 28.9 1.0
CB O:CYS200 3.3 32.6 1.0
CB O:CYS196 3.5 33.8 1.0
CG O:MET207 3.5 27.6 1.0
CB O:HIS161 3.6 29.7 1.0
O O:GLU198 3.9 28.2 1.0
NE2 O:HIS161 4.0 29.2 1.0
CA O:HIS161 4.2 31.0 1.0
CD2 O:HIS161 4.2 29.2 1.0
ND1 O:HIS204 4.5 33.6 1.0
CD1 O:TRP104 4.6 35.1 1.0
CA O:CYS200 4.7 30.8 1.0
O O:LEU160 4.7 28.8 1.0
O O:HIS102 4.7 27.1 1.0
CA O:HIS204 4.7 31.6 1.0
CA O:CYS196 4.8 33.9 1.0
CB O:MET207 4.9 29.8 1.0

Copper binding site 6 out of 6 in 3abl

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Copper binding site 6 out of 6 in the Bovine Heart Cytochrome C Oxidase at the Fully Oxidized State (15-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 (15-S X-Ray Exposure Dataset) within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Cu228

b:31.9
occ:1.00
CU2 O:CUA228 0.0 31.9 1.0
ND1 O:HIS204 2.0 33.6 1.0
O O:GLU198 2.2 28.2 1.0
SG O:CYS200 2.2 31.1 1.0
SG O:CYS196 2.3 34.1 1.0
CU1 O:CUA228 2.6 32.5 1.0
CE1 O:HIS204 2.9 37.8 1.0
CG O:HIS204 3.1 34.8 1.0
CB O:CYS200 3.3 32.6 1.0
C O:GLU198 3.4 26.9 1.0
CB O:CYS196 3.5 33.8 1.0
CB O:HIS204 3.5 32.4 1.0
CA O:HIS204 3.6 31.6 1.0
N O:CYS200 3.7 32.3 1.0
O O:HIS204 4.0 28.9 1.0
NE2 O:HIS204 4.0 33.4 1.0
N O:GLU198 4.1 27.3 1.0
C O:ILE199 4.1 30.7 1.0
ND1 O:HIS161 4.1 24.2 1.0
CA O:CYS200 4.2 30.8 1.0
CD2 O:HIS204 4.2 32.7 1.0
N O:ILE199 4.2 28.5 1.0
C O:CYS196 4.2 33.0 1.0
O O:CYS196 4.3 31.0 1.0
CA O:ILE199 4.3 28.9 1.0
C O:HIS204 4.3 30.4 1.0
CA O:GLU198 4.3 27.4 1.0
SD O:MET207 4.4 36.3 1.0
CA O:CYS196 4.5 33.9 1.0
CG O:MET207 4.7 27.6 1.0
N O:SER197 4.7 32.2 1.0
N O:HIS204 4.8 33.2 1.0
CA O:HIS161 4.9 31.0 1.0
CE1 O:HIS161 4.9 25.8 1.0
O O:ILE199 4.9 30.6 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: Thu Sep 3 17:04:33 2020
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