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

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

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

Protein crystallography data

The structure of Cadmium Ion Binding Structure of Bovine Heart Cytochrome C Oxidase in the Fully Reduced State, PDB code: 2eik 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 (°) 183.321, 206.525, 178.159, 90.00, 90.00, 90.00
R / Rfree (%) 19.9 / 22.8

Other elements in 2eik:

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

Magnesium (Mg) 2 atoms
Zinc (Zn) 2 atoms
Cadmium (Cd) 6 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 Reduced State (pdb code 2eik). 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 Reduced State, PDB code: 2eik:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6;

Copper binding site 1 out of 6 in 2eik

Go back to Copper Binding Sites List in 2eik
Copper binding site 1 out of 6 in the Cadmium Ion Binding Structure of Bovine Heart Cytochrome C Oxidase in the Fully Reduced 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 Reduced State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu517

b:19.9
occ:1.00
NE2 A:HIS291 2.0 23.8 1.0
NE2 A:HIS290 2.0 17.8 1.0
ND1 A:HIS240 2.0 21.8 1.0
CD2 A:HIS291 2.9 20.5 1.0
CE1 A:HIS290 2.9 17.0 1.0
CE1 A:HIS240 3.0 15.3 1.0
CG A:HIS240 3.0 15.7 1.0
CE1 A:HIS291 3.0 22.0 1.0
CD2 A:HIS290 3.1 16.1 1.0
CB A:HIS240 3.4 13.8 1.0
CA A:HIS240 3.9 15.9 1.0
CG A:HIS291 4.1 21.2 1.0
ND1 A:HIS290 4.1 17.8 1.0
ND1 A:HIS291 4.1 20.5 1.0
NE2 A:HIS240 4.1 23.2 1.0
CD2 A:HIS240 4.1 17.7 1.0
CG A:HIS290 4.2 14.5 1.0
NA A:HEA516 4.6 18.9 1.0
C1A A:HEA516 4.6 16.5 1.0
CG2 A:VAL243 4.7 15.4 1.0
N A:HIS240 4.7 12.8 1.0
C4A A:HEA516 4.8 18.8 1.0
C2A A:HEA516 4.9 16.6 1.0
CHA A:HEA516 5.0 15.9 1.0
C3A A:HEA516 5.0 18.8 1.0

Copper binding site 2 out of 6 in 2eik

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

b:21.7
occ:1.00
CU1 B:CUA228 0.0 21.7 1.0
ND1 B:HIS161 2.0 15.9 1.0
SG B:CYS196 2.3 19.6 1.0
SG B:CYS200 2.3 19.5 1.0
CU2 B:CUA228 2.6 20.9 1.0
SD B:MET207 2.6 24.6 1.0
CE1 B:HIS161 2.9 11.6 1.0
CE B:MET207 2.9 14.7 1.0
CG B:HIS161 3.2 15.0 1.0
CB B:CYS200 3.3 22.6 1.0
CB B:CYS196 3.4 18.8 1.0
CB B:HIS161 3.7 20.0 1.0
CG B:MET207 3.7 19.6 1.0
NE2 B:HIS161 4.1 13.1 1.0
O B:GLU198 4.2 28.0 1.0
CA B:HIS161 4.2 19.5 1.0
CD2 B:HIS161 4.2 13.3 1.0
ND1 B:HIS204 4.5 22.9 1.0
CD1 B:TRP104 4.6 20.1 1.0
O B:HIS102 4.7 16.7 1.0
CA B:CYS200 4.7 20.0 1.0
O B:LEU160 4.7 20.2 1.0
CA B:CYS196 4.8 20.2 1.0
CA B:HIS204 4.8 19.5 1.0
N B:CYS200 4.9 23.3 1.0
CZ2 B:TRP106 5.0 17.5 1.0

Copper binding site 3 out of 6 in 2eik

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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 Reduced 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 Reduced State within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu228

b:20.9
occ:1.00
CU2 B:CUA228 0.0 20.9 1.0
ND1 B:HIS204 2.0 22.9 1.0
SG B:CYS200 2.2 19.5 1.0
SG B:CYS196 2.3 19.6 1.0
O B:GLU198 2.5 28.0 1.0
CU1 B:CUA228 2.6 21.7 1.0
CE1 B:HIS204 2.8 16.6 1.0
CG B:HIS204 3.1 19.8 1.0
CB B:CYS196 3.2 18.8 1.0
CB B:CYS200 3.4 22.6 1.0
CA B:HIS204 3.5 19.5 1.0
CB B:HIS204 3.5 18.7 1.0
C B:GLU198 3.6 22.6 1.0
N B:CYS200 3.6 23.3 1.0
O B:HIS204 3.7 16.8 1.0
NE2 B:HIS204 4.0 20.0 1.0
C B:HIS204 4.1 17.7 1.0
CD2 B:HIS204 4.1 20.2 1.0
CA B:CYS200 4.1 20.0 1.0
O B:CYS196 4.1 20.5 1.0
N B:GLU198 4.2 21.4 1.0
C B:ILE199 4.2 22.6 1.0
ND1 B:HIS161 4.2 15.9 1.0
C B:CYS196 4.2 23.9 1.0
CA B:ILE199 4.2 21.0 1.0
N B:ILE199 4.3 22.4 1.0
CA B:CYS196 4.3 20.2 1.0
CA B:GLU198 4.6 19.9 1.0
SD B:MET207 4.6 24.6 1.0
N B:SER197 4.7 22.6 1.0
N B:HIS204 4.8 22.9 1.0
CG B:MET207 4.8 19.6 1.0
CA B:HIS161 5.0 19.5 1.0

Copper binding site 4 out of 6 in 2eik

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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 Reduced 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 Reduced State within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Cu517

b:23.6
occ:1.00
NE2 N:HIS291 1.9 24.3 1.0
ND1 N:HIS240 2.0 21.3 1.0
NE2 N:HIS290 2.0 17.6 1.0
CE1 N:HIS290 2.9 21.2 1.0
CE1 N:HIS291 2.9 24.2 1.0
CD2 N:HIS291 3.0 25.1 1.0
CE1 N:HIS240 3.0 21.9 1.0
CG N:HIS240 3.0 23.5 1.0
CD2 N:HIS290 3.2 19.7 1.0
CB N:HIS240 3.3 23.0 1.0
CA N:HIS240 3.8 23.6 1.0
ND1 N:HIS291 4.1 21.4 1.0
CG N:HIS291 4.1 21.7 1.0
ND1 N:HIS290 4.1 18.2 1.0
NE2 N:HIS240 4.1 25.5 1.0
CD2 N:HIS240 4.1 23.9 1.0
CG N:HIS290 4.2 21.4 1.0
NA N:HEA516 4.6 21.9 1.0
C1A N:HEA516 4.6 21.7 1.0
CG2 N:VAL243 4.6 18.4 1.0
N N:HIS240 4.7 21.9 1.0
C4A N:HEA516 4.8 22.9 1.0
C2A N:HEA516 4.9 20.6 1.0
CHA N:HEA516 4.9 18.4 1.0
C N:HIS240 5.0 23.2 1.0
C3A N:HEA516 5.0 19.4 1.0

Copper binding site 5 out of 6 in 2eik

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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 Reduced 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 Reduced State within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Cu228

b:29.4
occ:1.00
CU1 O:CUA228 0.0 29.4 1.0
ND1 O:HIS161 2.0 29.1 1.0
SG O:CYS196 2.3 27.1 1.0
SG O:CYS200 2.3 25.6 1.0
CU2 O:CUA228 2.3 26.9 1.0
SD O:MET207 2.7 30.2 1.0
CE1 O:HIS161 2.8 28.1 1.0
CE O:MET207 3.1 24.8 1.0
CG O:HIS161 3.2 26.9 1.0
CB O:CYS200 3.3 28.9 1.0
CB O:CYS196 3.3 28.7 1.0
CG O:MET207 3.6 30.3 1.0
CB O:HIS161 3.7 25.9 1.0
NE2 O:HIS161 4.0 25.6 1.0
O O:GLU198 4.1 28.2 1.0
CD2 O:HIS161 4.2 26.9 1.0
CA O:HIS161 4.2 25.4 1.0
ND1 O:HIS204 4.3 28.6 1.0
CD1 O:TRP104 4.6 26.9 1.0
CA O:CYS200 4.6 28.6 1.0
CA O:CYS196 4.7 26.6 1.0
CA O:HIS204 4.7 28.4 1.0
O O:LEU160 4.8 23.9 1.0
O O:HIS102 4.8 24.6 1.0
N O:CYS200 4.8 31.0 1.0
O O:HIS204 4.9 30.4 1.0
CB O:MET207 5.0 29.6 1.0

Copper binding site 6 out of 6 in 2eik

Go back to Copper Binding Sites List in 2eik
Copper binding site 6 out of 6 in the Cadmium Ion Binding Structure of Bovine Heart Cytochrome C Oxidase in the Fully Reduced 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 Reduced State within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Cu228

b:26.9
occ:1.00
CU2 O:CUA228 0.0 26.9 1.0
ND1 O:HIS204 2.0 28.6 1.0
SG O:CYS196 2.2 27.1 1.0
SG O:CYS200 2.3 25.6 1.0
CU1 O:CUA228 2.3 29.4 1.0
O O:GLU198 2.4 28.2 1.0
CE1 O:HIS204 2.9 24.6 1.0
CG O:HIS204 3.2 27.3 1.0
CB O:CYS196 3.2 28.7 1.0
CB O:CYS200 3.4 28.9 1.0
N O:CYS200 3.5 31.0 1.0
C O:GLU198 3.6 22.4 1.0
CA O:HIS204 3.6 28.4 1.0
CB O:HIS204 3.7 28.3 1.0
O O:HIS204 3.9 30.4 1.0
ND1 O:HIS161 4.0 29.1 1.0
NE2 O:HIS204 4.1 25.7 1.0
CA O:CYS200 4.1 28.6 1.0
O O:CYS196 4.2 27.3 1.0
N O:GLU198 4.2 25.3 1.0
C O:HIS204 4.2 26.9 1.0
CD2 O:HIS204 4.2 23.4 1.0
C O:ILE199 4.2 27.9 1.0
C O:CYS196 4.2 27.7 1.0
CA O:ILE199 4.3 24.3 1.0
N O:ILE199 4.3 23.4 1.0
CA O:CYS196 4.4 26.6 1.0
CA O:GLU198 4.5 23.8 1.0
SD O:MET207 4.6 30.2 1.0
CE1 O:HIS161 4.7 28.1 1.0
N O:SER197 4.7 26.5 1.0
CG O:MET207 4.7 30.3 1.0
N O:HIS204 4.8 28.2 1.0
CA O:HIS161 4.8 25.4 1.0
CG O:HIS161 4.9 26.9 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: Sun Dec 13 11:04:27 2020

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