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Copper in PDB 3abm: Bovine Heart Cytochrome C Oxidase at the Fully Oxidized State (200-S X-Ray Exposure Dataset)

Enzymatic activity of Bovine Heart Cytochrome C Oxidase at the Fully Oxidized State (200-S X-Ray Exposure Dataset)

All present enzymatic activity of Bovine Heart Cytochrome C Oxidase at the Fully Oxidized State (200-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 (200-S X-Ray Exposure Dataset), PDB code: 3abm 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 / 1.95
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 183.697, 206.991, 178.251, 90.00, 90.00, 90.00
R / Rfree (%) 18.1 / 21.4

Other elements in 3abm:

The structure of Bovine Heart Cytochrome C Oxidase at the Fully Oxidized State (200-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 (200-S X-Ray Exposure Dataset) (pdb code 3abm). 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 (200-S X-Ray Exposure Dataset), PDB code: 3abm:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6;

Copper binding site 1 out of 6 in 3abm

Go back to Copper Binding Sites List in 3abm
Copper binding site 1 out of 6 in the Bovine Heart Cytochrome C Oxidase at the Fully Oxidized State (200-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 (200-S X-Ray Exposure Dataset) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu517

b:29.1
occ:1.00
 NE2 A:HIS291 2.0 30.6 1.0
ND1 A:HIS240 2.1 30.7 1.0
NE2 A:HIS290 2.1 24.4 1.0
O2 A:PER520 2.2 32.9 1.0
O1 A:PER520 2.8 25.6 1.0
CD2 A:HIS291 2.9 25.8 1.0
CE1 A:HIS291 3.0 25.2 1.0
CD2 A:HIS290 3.0 24.2 1.0
CE1 A:HIS240 3.1 27.7 1.0
CG A:HIS240 3.1 29.1 1.0
CE1 A:HIS290 3.2 27.5 1.0
CB A:HIS240 3.4 27.9 1.0
CA A:HIS240 3.9 25.5 1.0
CG A:HIS291 4.1 27.6 1.0
ND1 A:HIS291 4.1 23.9 1.0
NE2 A:HIS240 4.2 29.9 1.0
CD2 A:HIS240 4.2 27.7 1.0
CG A:HIS290 4.2 29.9 1.0
ND1 A:HIS290 4.2 27.5 1.0
NA A:HEA516 4.5 22.3 1.0
C1A A:HEA516 4.6 23.8 1.0
C4A A:HEA516 4.7 20.9 1.0
N A:HIS240 4.8 25.3 1.0
C2A A:HEA516 4.8 21.2 1.0
CG2 A:VAL243 4.9 27.0 1.0
FE A:HEA516 4.9 27.1 1.0
CHA A:HEA516 4.9 23.4 1.0
ND A:HEA516 5.0 26.8 1.0

Copper binding site 2 out of 6 in 3abm

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Copper binding site 2 out of 6 in the Bovine Heart Cytochrome C Oxidase at the Fully Oxidized State (200-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 (200-S X-Ray Exposure Dataset) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu228

b:30.0
occ:1.00
 CU1 B:CUA228 0.0 30.0 1.0
ND1 B:HIS161 2.0 26.8 1.0
SG B:CYS196 2.3 27.4 1.0
SG B:CYS200 2.4 26.4 1.0
SD B:MET207 2.4 28.1 1.0
CU2 B:CUA228 2.5 27.4 1.0
CE1 B:HIS161 2.9 20.0 1.0
CE B:MET207 3.1 22.4 1.0
CG B:HIS161 3.1 26.1 1.0
CB B:CYS196 3.4 23.0 1.0
CB B:CYS200 3.4 31.1 1.0
CG B:MET207 3.5 24.9 1.0
CB B:HIS161 3.6 24.7 1.0
O B:GLU198 4.0 29.4 1.0
NE2 B:HIS161 4.1 23.9 1.0
CD2 B:HIS161 4.2 20.6 1.0
CA B:HIS161 4.2 24.4 1.0
ND1 B:HIS204 4.5 30.2 1.0
O B:LEU160 4.6 27.1 1.0
CD1 B:TRP104 4.7 21.3 1.0
CA B:HIS204 4.7 28.1 1.0
O B:HIS102 4.7 28.4 1.0
CA B:CYS196 4.8 24.6 1.0
CA B:CYS200 4.8 28.2 1.0
O B:HIS204 4.9 28.3 1.0
CB B:MET207 4.9 27.5 1.0

Copper binding site 3 out of 6 in 3abm

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Copper binding site 3 out of 6 in the Bovine Heart Cytochrome C Oxidase at the Fully Oxidized State (200-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 (200-S X-Ray Exposure Dataset) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu228

b:27.4
occ:1.00
 CU2 B:CUA228 0.0 27.4 1.0
ND1 B:HIS204 2.0 30.2 1.0
O B:GLU198 2.2 29.4 1.0
SG B:CYS200 2.2 26.4 1.0
SG B:CYS196 2.3 27.4 1.0
CU1 B:CUA228 2.5 30.0 1.0
CE1 B:HIS204 2.9 29.4 1.0
CG B:HIS204 3.1 27.4 1.0
CB B:CYS196 3.3 23.0 1.0
C B:GLU198 3.4 27.3 1.0
CB B:HIS204 3.6 26.6 1.0
CB B:CYS200 3.6 31.1 1.0
CA B:HIS204 3.6 28.1 1.0
N B:CYS200 3.8 28.7 1.0
O B:HIS204 3.8 28.3 1.0
NE2 B:HIS204 4.1 27.9 1.0
N B:GLU198 4.1 25.0 1.0
ND1 B:HIS161 4.2 26.8 1.0
C B:HIS204 4.2 26.8 1.0
C B:ILE199 4.2 27.2 1.0
CD2 B:HIS204 4.2 27.5 1.0
C B:CYS196 4.2 26.2 1.0
N B:ILE199 4.2 29.3 1.0
CA B:ILE199 4.3 25.0 1.0
O B:CYS196 4.3 23.7 1.0
CA B:CYS200 4.3 28.2 1.0
SD B:MET207 4.4 28.1 1.0
CA B:CYS196 4.4 24.6 1.0
CA B:GLU198 4.4 27.0 1.0
N B:SER197 4.6 25.5 1.0
CG B:MET207 4.7 24.9 1.0
CA B:HIS161 4.9 24.4 1.0
N B:HIS204 4.9 27.0 1.0
CE1 B:HIS161 5.0 20.0 1.0

Copper binding site 4 out of 6 in 3abm

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Copper binding site 4 out of 6 in the Bovine Heart Cytochrome C Oxidase at the Fully Oxidized State (200-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 (200-S X-Ray Exposure Dataset) within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Cu517

b:32.4
occ:1.00
 NE2 N:HIS290 2.0 30.5 1.0
NE2 N:HIS291 2.0 34.4 1.0
ND1 N:HIS240 2.1 30.6 1.0
O2 N:PER520 2.1 35.0 1.0
O1 N:PER520 2.6 31.0 1.0
CE1 N:HIS290 3.0 32.3 1.0
CG N:HIS240 3.0 32.4 1.0
CE1 N:HIS291 3.0 29.3 1.0
CD2 N:HIS291 3.0 28.7 1.0
CD2 N:HIS290 3.1 28.9 1.0
CE1 N:HIS240 3.1 29.4 1.0
CB N:HIS240 3.3 34.1 1.0
CA N:HIS240 3.8 33.1 1.0
ND1 N:HIS290 4.1 31.2 1.0
ND1 N:HIS291 4.1 26.4 1.0
CG N:HIS291 4.1 34.4 1.0
CD2 N:HIS240 4.2 26.4 1.0
CG N:HIS290 4.2 32.0 1.0
NE2 N:HIS240 4.2 33.0 1.0
NA N:HEA516 4.5 31.2 1.0
C1A N:HEA516 4.6 28.9 1.0
N N:HIS240 4.7 31.7 1.0
C4A N:HEA516 4.7 28.3 1.0
CG2 N:VAL243 4.7 33.3 1.0
FE N:HEA516 4.9 33.7 1.0
CHA N:HEA516 4.9 30.2 1.0
C2A N:HEA516 4.9 27.6 1.0
ND N:HEA516 4.9 33.8 1.0

Copper binding site 5 out of 6 in 3abm

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Copper binding site 5 out of 6 in the Bovine Heart Cytochrome C Oxidase at the Fully Oxidized State (200-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 (200-S X-Ray Exposure Dataset) within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Cu228

b:37.8
occ:1.00
 CU1 O:CUA228 0.0 37.8 1.0
ND1 O:HIS161 2.0 32.9 1.0
SG O:CYS200 2.3 35.2 1.0
SG O:CYS196 2.3 36.3 1.0
SD O:MET207 2.4 37.5 1.0
CE1 O:HIS161 2.5 31.8 1.0
CU2 O:CUA228 2.6 36.9 1.0
CE O:MET207 3.1 30.6 1.0
CG O:HIS161 3.3 31.2 1.0
CB O:CYS200 3.4 33.7 1.0
CB O:CYS196 3.5 32.4 1.0
CG O:MET207 3.6 33.8 1.0
NE2 O:HIS161 3.8 29.8 1.0
CB O:HIS161 3.9 33.8 1.0
O O:GLU198 4.0 35.6 1.0
CD2 O:HIS161 4.1 30.1 1.0
CA O:HIS161 4.3 34.6 1.0
ND1 O:HIS204 4.5 36.6 1.0
CD1 O:TRP104 4.6 36.1 1.0
O O:LEU160 4.7 30.4 1.0
CA O:HIS204 4.8 34.4 1.0
CA O:CYS200 4.8 33.1 1.0
O O:HIS102 4.8 36.6 1.0
O O:HIS204 4.8 34.6 1.0
CA O:CYS196 4.8 33.6 1.0
CB O:MET207 4.9 33.5 1.0

Copper binding site 6 out of 6 in 3abm

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Copper binding site 6 out of 6 in the Bovine Heart Cytochrome C Oxidase at the Fully Oxidized State (200-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 (200-S X-Ray Exposure Dataset) within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Cu228

b:36.9
occ:1.00
 CU2 O:CUA228 0.0 36.9 1.0
ND1 O:HIS204 2.0 36.6 1.0
O O:GLU198 2.1 35.6 1.0
SG O:CYS200 2.3 35.2 1.0
SG O:CYS196 2.3 36.3 1.0
CU1 O:CUA228 2.6 37.8 1.0
CE1 O:HIS204 2.9 38.1 1.0
CG O:HIS204 3.1 35.2 1.0
CB O:CYS196 3.4 32.4 1.0
C O:GLU198 3.4 30.9 1.0
CB O:CYS200 3.5 33.7 1.0
CB O:HIS204 3.6 35.1 1.0
CA O:HIS204 3.7 34.4 1.0
O O:HIS204 3.7 34.6 1.0
N O:CYS200 3.8 33.0 1.0
NE2 O:HIS204 4.1 28.4 1.0
ND1 O:HIS161 4.1 32.9 1.0
N O:GLU198 4.1 30.0 1.0
C O:HIS204 4.2 33.4 1.0
CD2 O:HIS204 4.2 31.2 1.0
C O:ILE199 4.2 32.1 1.0
C O:CYS196 4.2 34.0 1.0
O O:CYS196 4.2 31.5 1.0
CA O:CYS200 4.3 33.1 1.0
N O:ILE199 4.3 30.8 1.0
CA O:ILE199 4.3 31.6 1.0
SD O:MET207 4.4 37.5 1.0
CA O:GLU198 4.4 31.0 1.0
CA O:CYS196 4.5 33.6 1.0
N O:SER197 4.6 31.7 1.0
CE1 O:HIS161 4.7 31.8 1.0
CG O:MET207 4.8 33.8 1.0
N O:HIS204 4.9 36.0 1.0
O O:ILE199 5.0 31.3 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: Wed Jul 31 00:35:20 2024

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