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Copper in PDB 2eil: Cadmium Ion Binding Structure of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State

Enzymatic activity of Cadmium Ion Binding Structure of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State

All present enzymatic activity of Cadmium Ion Binding Structure of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State:
1.9.3.1;

Protein crystallography data

The structure of Cadmium Ion Binding Structure of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State, PDB code: 2eil was solved by K.Muramoto, K.Hirata, K.Shinzawa-Itoh, S.Yoko-O, E.Yamashita, H.Aoyama, 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 / 2.10
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 183.379, 205.898, 178.182, 90.00, 90.00, 90.00
R / Rfree (%) 19.9 / 23.1

Other elements in 2eil:

The structure of Cadmium Ion Binding Structure of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms
Zinc (Zn) 2 atoms
Cadmium (Cd) 3 atoms
Iron (Fe) 4 atoms
Sodium (Na) 2 atoms

Copper Binding Sites:

The binding sites of Copper atom in the Cadmium Ion Binding Structure of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State (pdb code 2eil). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 6 binding sites of Copper where determined in the Cadmium Ion Binding Structure of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State, PDB code: 2eil:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6;

Copper binding site 1 out of 6 in 2eil

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Copper binding site 1 out of 6 in the Cadmium Ion Binding Structure of Bovine Heart Cytochrome C Oxidase in 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 Cadmium Ion Binding Structure of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu517

b:22.5
occ:1.00
 NE2 A:HIS291 1.9 28.4 1.0
ND1 A:HIS240 2.0 28.8 1.0
NE2 A:HIS290 2.0 19.5 1.0
CE1 A:HIS291 2.9 26.5 1.0
CE1 A:HIS240 3.0 24.5 1.0
CD2 A:HIS291 3.0 24.9 1.0
CE1 A:HIS290 3.0 18.0 1.0
CG A:HIS240 3.1 25.1 1.0
CD2 A:HIS290 3.1 15.3 1.0
CB A:HIS240 3.4 19.5 1.0
CA A:HIS240 3.9 19.0 1.0
ND1 A:HIS291 4.1 24.0 1.0
CG A:HIS291 4.1 25.5 1.0
NE2 A:HIS240 4.1 28.1 1.0
CD2 A:HIS240 4.2 25.4 1.0
ND1 A:HIS290 4.2 16.1 1.0
CG A:HIS290 4.3 17.9 1.0
NA A:HEA516 4.5 20.6 1.0
C1A A:HEA516 4.6 17.1 1.0
CG2 A:VAL243 4.7 15.6 1.0
N A:HIS240 4.8 17.0 1.0
C4A A:HEA516 4.8 20.5 1.0
FE A:HEA516 4.8 19.6 1.0
C2A A:HEA516 4.9 19.5 1.0
CHA A:HEA516 4.9 18.0 1.0
C3A A:HEA516 5.0 18.5 1.0

Copper binding site 2 out of 6 in 2eil

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Copper binding site 2 out of 6 in the Cadmium Ion Binding Structure of Bovine Heart Cytochrome C Oxidase in 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 Cadmium Ion Binding Structure of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu228

b:24.0
occ:1.00
 CU1 B:CUA228 0.0 24.0 1.0
ND1 B:HIS161 2.0 17.9 1.0
SG B:CYS196 2.3 20.3 1.0
SG B:CYS200 2.3 20.9 1.0
CU2 B:CUA228 2.6 23.1 1.0
SD B:MET207 2.7 24.6 1.0
CE1 B:HIS161 2.9 16.1 1.0
CE B:MET207 3.0 11.4 1.0
CG B:HIS161 3.2 16.0 1.0
CB B:CYS200 3.3 22.2 1.0
CB B:CYS196 3.4 19.4 1.0
CG B:MET207 3.6 20.9 1.0
CB B:HIS161 3.7 21.4 1.0
O B:GLU198 4.1 30.1 1.0
NE2 B:HIS161 4.1 15.5 1.0
CA B:HIS161 4.2 18.7 1.0
CD2 B:HIS161 4.3 15.3 1.0
ND1 B:HIS204 4.4 24.6 1.0
O B:LEU160 4.6 21.4 1.0
CA B:CYS200 4.7 25.0 1.0
O B:HIS102 4.7 19.6 1.0
CD1 B:TRP104 4.7 23.6 1.0
CA B:CYS196 4.7 22.1 1.0
CA B:HIS204 4.8 24.9 1.0
N B:CYS200 4.9 24.7 1.0
O B:HIS204 5.0 20.5 1.0

Copper binding site 3 out of 6 in 2eil

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Copper binding site 3 out of 6 in the Cadmium Ion Binding Structure of Bovine Heart Cytochrome C Oxidase in 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 Cadmium Ion Binding Structure of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu228

b:23.1
occ:1.00
 CU2 B:CUA228 0.0 23.1 1.0
ND1 B:HIS204 1.9 24.6 1.0
SG B:CYS200 2.2 20.9 1.0
SG B:CYS196 2.3 20.3 1.0
O B:GLU198 2.4 30.1 1.0
CU1 B:CUA228 2.6 24.0 1.0
CE1 B:HIS204 2.8 19.2 1.0
CG B:HIS204 3.0 22.4 1.0
CB B:CYS196 3.3 19.4 1.0
CB B:CYS200 3.5 22.2 1.0
CB B:HIS204 3.5 22.4 1.0
C B:GLU198 3.5 24.6 1.0
CA B:HIS204 3.5 24.9 1.0
N B:CYS200 3.6 24.7 1.0
O B:HIS204 3.7 20.5 1.0
NE2 B:HIS204 4.0 24.4 1.0
C B:HIS204 4.1 22.2 1.0
O B:CYS196 4.1 21.1 1.0
CD2 B:HIS204 4.1 22.4 1.0
N B:GLU198 4.1 23.3 1.0
C B:ILE199 4.2 23.2 1.0
CA B:CYS200 4.2 25.0 1.0
C B:CYS196 4.2 24.6 1.0
CA B:ILE199 4.2 20.6 1.0
ND1 B:HIS161 4.2 17.9 1.0
N B:ILE199 4.3 24.8 1.0
CA B:CYS196 4.3 22.1 1.0
CA B:GLU198 4.5 22.0 1.0
SD B:MET207 4.5 24.6 1.0
CG B:MET207 4.7 20.9 1.0
N B:SER197 4.8 22.9 1.0
N B:HIS204 4.8 28.2 1.0
CA B:HIS161 5.0 18.7 1.0

Copper binding site 4 out of 6 in 2eil

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Copper binding site 4 out of 6 in the Cadmium Ion Binding Structure of Bovine Heart Cytochrome C Oxidase in 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 Cadmium Ion Binding Structure of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Cu517

b:27.1
occ:1.00
 NE2 N:HIS291 2.0 29.1 1.0
ND1 N:HIS240 2.0 25.4 1.0
NE2 N:HIS290 2.0 19.8 1.0
CE1 N:HIS291 2.9 30.7 1.0
CE1 N:HIS290 2.9 25.0 1.0
CE1 N:HIS240 2.9 24.0 1.0
CD2 N:HIS291 3.0 29.4 1.0
CG N:HIS240 3.1 27.3 1.0
CD2 N:HIS290 3.1 21.7 1.0
CB N:HIS240 3.4 26.4 1.0
CA N:HIS240 3.9 26.2 1.0
ND1 N:HIS291 4.1 28.9 1.0
NE2 N:HIS240 4.1 27.9 1.0
CG N:HIS291 4.1 28.4 1.0
ND1 N:HIS290 4.1 21.3 1.0
CD2 N:HIS240 4.2 27.6 1.0
CG N:HIS290 4.2 23.5 1.0
NA N:HEA516 4.5 25.4 1.0
C1A N:HEA516 4.7 24.1 1.0
N N:HIS240 4.7 24.0 1.0
CG2 N:VAL243 4.7 21.5 1.0
C4A N:HEA516 4.8 26.3 1.0
FE N:HEA516 4.9 24.1 1.0
C2A N:HEA516 4.9 24.5 1.0
CHA N:HEA516 4.9 22.8 1.0
ND N:HEA516 5.0 24.3 1.0
C3A N:HEA516 5.0 20.5 1.0

Copper binding site 5 out of 6 in 2eil

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Copper binding site 5 out of 6 in the Cadmium Ion Binding Structure of Bovine Heart Cytochrome C Oxidase in 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 Cadmium Ion Binding Structure of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Cu228

b:32.8
occ:1.00
 CU1 O:CUA228 0.0 32.8 1.0
ND1 O:HIS161 2.0 32.8 1.0
SG O:CYS196 2.3 27.3 1.0
SG O:CYS200 2.3 29.7 1.0
CU2 O:CUA228 2.4 32.3 1.0
SD O:MET207 2.7 34.0 1.0
CE1 O:HIS161 2.8 29.1 1.0
CE O:MET207 3.1 22.2 1.0
CG O:HIS161 3.2 28.6 1.0
CB O:CYS196 3.3 34.8 1.0
CB O:CYS200 3.3 33.1 1.0
CG O:MET207 3.7 33.2 1.0
CB O:HIS161 3.7 30.1 1.0
NE2 O:HIS161 4.0 27.8 1.0
O O:GLU198 4.1 32.2 1.0
CD2 O:HIS161 4.2 27.0 1.0
CA O:HIS161 4.2 28.8 1.0
ND1 O:HIS204 4.3 32.9 1.0
CD1 O:TRP104 4.7 34.4 1.0
CA O:CYS200 4.7 33.0 1.0
CA O:HIS204 4.7 30.8 1.0
CA O:CYS196 4.7 33.3 1.0
O O:LEU160 4.7 28.6 1.0
O O:HIS102 4.8 26.6 1.0
O O:HIS204 4.9 29.0 1.0
N O:CYS200 4.9 34.3 1.0

Copper binding site 6 out of 6 in 2eil

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Copper binding site 6 out of 6 in the Cadmium Ion Binding Structure of Bovine Heart Cytochrome C Oxidase in 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 Cadmium Ion Binding Structure of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Cu228

b:32.3
occ:1.00
 CU2 O:CUA228 0.0 32.3 1.0
ND1 O:HIS204 2.1 32.9 1.0
SG O:CYS196 2.2 27.3 1.0
SG O:CYS200 2.3 29.7 1.0
CU1 O:CUA228 2.4 32.8 1.0
O O:GLU198 2.4 32.2 1.0
CE1 O:HIS204 2.9 29.0 1.0
CG O:HIS204 3.2 29.8 1.0
CB O:CYS196 3.2 34.8 1.0
CB O:CYS200 3.4 33.1 1.0
C O:GLU198 3.5 25.9 1.0
N O:CYS200 3.6 34.3 1.0
CA O:HIS204 3.6 30.8 1.0
CB O:HIS204 3.7 30.0 1.0
O O:HIS204 3.9 29.0 1.0
ND1 O:HIS161 3.9 32.8 1.0
NE2 O:HIS204 4.1 28.5 1.0
CA O:CYS200 4.1 33.0 1.0
N O:GLU198 4.1 29.9 1.0
O O:CYS196 4.2 30.0 1.0
C O:ILE199 4.2 32.3 1.0
C O:HIS204 4.2 27.0 1.0
CD2 O:HIS204 4.2 26.4 1.0
C O:CYS196 4.3 32.9 1.0
CA O:ILE199 4.3 28.4 1.0
N O:ILE199 4.3 27.3 1.0
CA O:CYS196 4.4 33.3 1.0
CA O:GLU198 4.5 26.3 1.0
SD O:MET207 4.5 34.0 1.0
CE1 O:HIS161 4.7 29.1 1.0
CG O:MET207 4.8 33.2 1.0
N O:SER197 4.8 31.5 1.0
N O:HIS204 4.9 31.4 1.0
CA O:HIS161 4.9 28.8 1.0
CG O:HIS161 5.0 28.6 1.0

Reference:

K.Muramoto, K.Hirata, K.Shinzawa-Itoh, S.Yoko-O, E.Yamashita, H.Aoyama, T.Tsukihara, S.Yoshikawa. A Histidine Residue Acting As A Controlling Site For Dioxygen Reduction and Proton Pumping By Cytochrome C Oxidase Proc.Natl.Acad.Sci.Usa V. 104 7881 2007.
ISSN: ISSN 0027-8424
PubMed: 17470809
DOI: 10.1073/PNAS.0610031104
Page generated: Tue Jul 30 23:26:58 2024

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