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Copper in PDB 3abk: Bovine Heart Cytochrome C Oxidase at the No-Bound Fully Reduced State (50K)

Enzymatic activity of Bovine Heart Cytochrome C Oxidase at the No-Bound Fully Reduced State (50K)

All present enzymatic activity of Bovine Heart Cytochrome C Oxidase at the No-Bound Fully Reduced State (50K):
1.9.3.1;

Protein crystallography data

The structure of Bovine Heart Cytochrome C Oxidase at the No-Bound Fully Reduced State (50K), PDB code: 3abk was solved by K.Ohta, K.Muramoto, K.Shinzawa-Itoh, E.Yamashita, S.Yoshikawa, T.Tsukihara, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.00 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 182.247, 207.944, 177.997, 90.00, 90.00, 90.00
R / Rfree (%) 18.3 / 21.9

Other elements in 3abk:

The structure of Bovine Heart Cytochrome C Oxidase at the No-Bound Fully Reduced State (50K) 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 No-Bound Fully Reduced State (50K) (pdb code 3abk). 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 No-Bound Fully Reduced State (50K), PDB code: 3abk:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6;

Copper binding site 1 out of 6 in 3abk

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Copper binding site 1 out of 6 in the Bovine Heart Cytochrome C Oxidase at the No-Bound Fully Reduced State (50K)


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 No-Bound Fully Reduced State (50K) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu517

b:29.1
occ:1.00
 NE2 A:HIS291 1.9 27.2 1.0
NE2 A:HIS290 2.0 27.3 1.0
ND1 A:HIS240 2.0 27.1 1.0
N A:NO520 2.4 32.2 1.0
O A:NO520 2.4 36.3 1.0
CD2 A:HIS291 2.9 27.9 1.0
CE1 A:HIS291 3.0 23.9 1.0
CE1 A:HIS290 3.0 25.7 1.0
CE1 A:HIS240 3.0 23.3 1.0
CG A:HIS240 3.0 25.6 1.0
CD2 A:HIS290 3.0 27.3 1.0
CB A:HIS240 3.4 22.8 1.0
CA A:HIS240 4.0 23.2 1.0
CG A:HIS291 4.0 27.2 1.0
ND1 A:HIS291 4.0 28.2 1.0
ND1 A:HIS290 4.1 23.8 1.0
NE2 A:HIS240 4.1 28.6 1.0
CD2 A:HIS240 4.1 24.0 1.0
CG A:HIS290 4.2 27.5 1.0
NA A:HEA516 4.4 23.1 1.0
C1A A:HEA516 4.5 25.7 1.0
C4A A:HEA516 4.6 24.4 1.0
CG2 A:VAL243 4.7 27.6 1.0
C2A A:HEA516 4.8 26.5 1.0
C3A A:HEA516 4.8 22.1 1.0
CHA A:HEA516 4.9 22.9 1.0
N A:HIS240 4.9 22.9 1.0
FE A:HEA516 4.9 27.4 1.0

Copper binding site 2 out of 6 in 3abk

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Copper binding site 2 out of 6 in the Bovine Heart Cytochrome C Oxidase at the No-Bound Fully Reduced State (50K)


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 No-Bound Fully Reduced State (50K) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu228

b:28.4
occ:1.00
 CU1 B:CUA228 0.0 28.4 1.0
ND1 B:HIS161 2.0 24.5 1.0
SG B:CYS196 2.3 25.6 1.0
SD B:MET207 2.4 27.1 1.0
SG B:CYS200 2.4 27.2 1.0
CU2 B:CUA228 2.5 27.6 1.0
CE1 B:HIS161 2.9 22.3 1.0
CE B:MET207 3.1 24.9 1.0
CG B:HIS161 3.1 24.1 1.0
CG B:MET207 3.4 24.7 1.0
CB B:CYS200 3.4 26.9 1.0
CB B:CYS196 3.4 27.9 1.0
CB B:HIS161 3.6 27.2 1.0
O B:GLU198 4.1 28.4 1.0
NE2 B:HIS161 4.1 23.2 1.0
CA B:HIS161 4.2 24.4 1.0
CD2 B:HIS161 4.2 24.5 1.0
ND1 B:HIS204 4.5 27.4 1.0
CD1 B:TRP104 4.5 25.9 1.0
O B:HIS102 4.7 25.6 1.0
O B:LEU160 4.8 26.2 1.0
CA B:HIS204 4.8 26.0 1.0
CB B:MET207 4.8 27.8 1.0
CA B:CYS196 4.8 24.9 1.0
CA B:CYS200 4.9 23.5 1.0

Copper binding site 3 out of 6 in 3abk

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Copper binding site 3 out of 6 in the Bovine Heart Cytochrome C Oxidase at the No-Bound Fully Reduced State (50K)


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 No-Bound Fully Reduced State (50K) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu228

b:27.6
occ:1.00
 CU2 B:CUA228 0.0 27.6 1.0
ND1 B:HIS204 2.0 27.4 1.0
SG B:CYS200 2.3 27.2 1.0
SG B:CYS196 2.3 25.6 1.0
O B:GLU198 2.4 28.4 1.0
CU1 B:CUA228 2.5 28.4 1.0
CE1 B:HIS204 2.9 28.1 1.0
CG B:HIS204 3.1 27.1 1.0
CB B:CYS196 3.3 27.9 1.0
CB B:CYS200 3.5 26.9 1.0
C B:GLU198 3.6 24.9 1.0
CB B:HIS204 3.6 24.2 1.0
CA B:HIS204 3.6 26.0 1.0
N B:CYS200 3.8 25.6 1.0
O B:HIS204 3.8 26.7 1.0
NE2 B:HIS204 4.0 25.5 1.0
ND1 B:HIS161 4.2 24.5 1.0
CD2 B:HIS204 4.2 24.9 1.0
N B:GLU198 4.2 23.2 1.0
CA B:ILE199 4.2 25.1 1.0
C B:ILE199 4.2 27.1 1.0
C B:HIS204 4.2 25.3 1.0
C B:CYS196 4.3 27.8 1.0
O B:CYS196 4.3 25.8 1.0
CA B:CYS200 4.3 23.5 1.0
N B:ILE199 4.3 27.2 1.0
SD B:MET207 4.4 27.1 1.0
CA B:CYS196 4.4 24.9 1.0
CG B:MET207 4.5 24.7 1.0
CA B:GLU198 4.6 25.5 1.0
N B:SER197 4.7 28.9 1.0
CA B:HIS161 4.8 24.4 1.0
N B:HIS204 4.8 27.0 1.0

Copper binding site 4 out of 6 in 3abk

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Copper binding site 4 out of 6 in the Bovine Heart Cytochrome C Oxidase at the No-Bound Fully Reduced State (50K)


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 No-Bound Fully Reduced State (50K) within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Cu517

b:35.7
occ:1.00
 NE2 N:HIS291 1.9 36.4 1.0
ND1 N:HIS240 2.0 33.4 1.0
NE2 N:HIS290 2.0 30.3 1.0
O N:NO520 2.4 42.9 1.0
N N:NO520 2.4 39.5 1.0
CE1 N:HIS290 2.9 33.1 1.0
CE1 N:HIS291 2.9 33.8 1.0
CD2 N:HIS291 2.9 36.1 1.0
CE1 N:HIS240 3.0 31.2 1.0
CG N:HIS240 3.0 35.1 1.0
CD2 N:HIS290 3.1 27.0 1.0
CB N:HIS240 3.4 30.9 1.0
ND1 N:HIS291 4.0 32.8 1.0
ND1 N:HIS290 4.1 28.4 1.0
CA N:HIS240 4.1 29.8 1.0
CG N:HIS291 4.1 36.9 1.0
NE2 N:HIS240 4.1 32.8 1.0
CD2 N:HIS240 4.1 36.1 1.0
CG N:HIS290 4.2 32.1 1.0
NA N:HEA516 4.4 33.0 1.0
C1A N:HEA516 4.4 31.7 1.0
C4A N:HEA516 4.6 27.6 1.0
C2A N:HEA516 4.7 30.5 1.0
CG2 N:VAL243 4.8 27.5 1.0
C3A N:HEA516 4.8 29.7 1.0
CHA N:HEA516 4.9 32.9 1.0
FE N:HEA516 4.9 34.6 1.0
N N:HIS240 5.0 30.5 1.0
CG2 N:VAL287 5.0 33.6 1.0
ND N:HEA516 5.0 30.2 1.0

Copper binding site 5 out of 6 in 3abk

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Copper binding site 5 out of 6 in the Bovine Heart Cytochrome C Oxidase at the No-Bound Fully Reduced State (50K)


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 No-Bound Fully Reduced State (50K) within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Cu228

b:36.1
occ:1.00
 CU1 O:CUA228 0.0 36.1 1.0
ND1 O:HIS161 2.1 33.4 1.0
SG O:CYS196 2.3 35.1 1.0
SG O:CYS200 2.3 31.9 1.0
SD O:MET207 2.4 36.4 1.0
CU2 O:CUA228 2.6 34.9 1.0
CE1 O:HIS161 3.0 32.2 1.0
CE O:MET207 3.2 31.4 1.0
CG O:HIS161 3.2 30.7 1.0
CB O:CYS200 3.4 34.4 1.0
CB O:CYS196 3.4 34.5 1.0
CG O:MET207 3.5 36.7 1.0
CB O:HIS161 3.6 30.6 1.0
O O:GLU198 4.0 39.1 1.0
NE2 O:HIS161 4.2 28.7 1.0
CA O:HIS161 4.2 30.6 1.0
CD2 O:HIS161 4.3 29.1 1.0
ND1 O:HIS204 4.5 35.0 1.0
CD1 O:TRP104 4.5 34.2 1.0
O O:HIS102 4.7 34.9 1.0
CA O:HIS204 4.7 39.1 1.0
CA O:CYS200 4.8 34.6 1.0
O O:LEU160 4.8 31.6 1.0
CA O:CYS196 4.8 35.1 1.0
CB O:MET207 4.9 32.5 1.0
N O:CYS200 4.9 36.5 1.0
O O:HIS204 5.0 40.6 1.0

Copper binding site 6 out of 6 in 3abk

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Copper binding site 6 out of 6 in the Bovine Heart Cytochrome C Oxidase at the No-Bound Fully Reduced State (50K)


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 No-Bound Fully Reduced State (50K) within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Cu228

b:34.9
occ:1.00
 CU2 O:CUA228 0.0 34.9 1.0
ND1 O:HIS204 2.0 35.0 1.0
SG O:CYS200 2.2 31.9 1.0
O O:GLU198 2.3 39.1 1.0
SG O:CYS196 2.3 35.1 1.0
CU1 O:CUA228 2.6 36.1 1.0
CE1 O:HIS204 2.8 37.5 1.0
CG O:HIS204 3.1 39.5 1.0
CB O:CYS196 3.4 34.5 1.0
CB O:CYS200 3.5 34.4 1.0
CA O:HIS204 3.5 39.1 1.0
C O:GLU198 3.5 34.2 1.0
CB O:HIS204 3.5 36.9 1.0
N O:CYS200 3.6 36.5 1.0
O O:HIS204 3.9 40.6 1.0
NE2 O:HIS204 4.0 38.6 1.0
CD2 O:HIS204 4.1 34.5 1.0
C O:ILE199 4.2 36.1 1.0
C O:HIS204 4.2 38.5 1.0
CA O:CYS200 4.2 34.6 1.0
CA O:ILE199 4.2 33.4 1.0
C O:CYS196 4.2 35.6 1.0
ND1 O:HIS161 4.2 33.4 1.0
N O:GLU198 4.2 31.7 1.0
O O:CYS196 4.3 33.2 1.0
N O:ILE199 4.3 33.1 1.0
CA O:CYS196 4.4 35.1 1.0
SD O:MET207 4.5 36.4 1.0
CA O:GLU198 4.6 33.5 1.0
N O:SER197 4.6 35.4 1.0
N O:HIS204 4.7 38.5 1.0
CG O:MET207 4.8 36.7 1.0
CA O:HIS161 4.9 30.6 1.0

Reference:

K.Ohta, K.Muramoto, K.Shinzawa-Itoh, E.Yamashita, S.Yoshikawa, T.Tsukihara. X-Ray Structure of the No-Bound Cu(B) in Bovine Cytochrome C Oxidase Acta Crystallogr.,Sect.F V. 66 251 2010.
ISSN: ESSN 1744-3091
PubMed: 20208153
DOI: 10.1107/S1744309109055109
Page generated: Wed Jul 31 00:33:40 2024

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