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

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

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

Protein crystallography data

The structure of Zinc Ion Binding Structure of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State, PDB code: 2ein 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 / 2.70
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 187.810, 203.581, 177.927, 90.00, 90.00, 90.00
R / Rfree (%) 20.8 / 25.8

Other elements in 2ein:

The structure of Zinc 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) 14 atoms
Iron (Fe) 4 atoms
Sodium (Na) 2 atoms

Copper Binding Sites:

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

Copper binding site 1 out of 6 in 2ein

Go back to Copper Binding Sites List in 2ein
Copper binding site 1 out of 6 in the Zinc 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 Zinc 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:41.4
occ:1.00
 ND1 A:HIS240 1.9 48.0 1.0
NE2 A:HIS291 2.0 57.0 1.0
NE2 A:HIS290 2.0 45.5 1.0
CE1 A:HIS240 2.8 45.9 1.0
CE1 A:HIS290 2.9 49.1 1.0
CE1 A:HIS291 3.0 60.3 1.0
CD2 A:HIS291 3.0 55.8 1.0
CG A:HIS240 3.1 39.0 1.0
CD2 A:HIS290 3.2 46.1 1.0
CB A:HIS240 3.5 34.0 1.0
CA A:HIS240 3.8 31.6 1.0
NE2 A:HIS240 4.0 43.6 1.0
ND1 A:HIS290 4.1 47.8 1.0
CD2 A:HIS240 4.1 41.6 1.0
ND1 A:HIS291 4.1 51.3 1.0
CG A:HIS291 4.2 47.9 1.0
CG A:HIS290 4.2 47.0 1.0
NA A:HEA516 4.4 50.4 1.0
C1A A:HEA516 4.4 45.4 1.0
CG2 A:VAL243 4.6 31.4 1.0
FE A:HEA516 4.6 34.0 1.0
C2A A:HEA516 4.7 41.3 1.0
C4A A:HEA516 4.8 48.6 1.0
N A:HIS240 4.8 29.4 1.0
CHA A:HEA516 4.8 45.6 1.0
O A:HIS240 4.8 36.8 1.0
C3A A:HEA516 4.9 43.7 1.0
C A:HIS240 4.9 36.2 1.0
CG1 A:VAL243 4.9 36.4 1.0
ND A:HEA516 4.9 41.8 1.0

Copper binding site 2 out of 6 in 2ein

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Copper binding site 2 out of 6 in the Zinc 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 Zinc 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:44.6
occ:1.00
 CU1 B:CUA228 0.0 44.6 1.0
ND1 B:HIS161 2.1 25.7 1.0
SG B:CYS196 2.3 32.5 1.0
SG B:CYS200 2.4 27.7 1.0
CU2 B:CUA228 2.5 41.9 1.0
SD B:MET207 2.8 44.8 1.0
CE1 B:HIS161 3.1 21.8 1.0
CB B:CYS200 3.1 36.8 1.0
CG B:HIS161 3.1 19.7 1.0
CE B:MET207 3.2 32.0 1.0
CB B:CYS196 3.4 31.7 1.0
CB B:HIS161 3.4 24.3 1.0
CG B:MET207 3.9 37.7 1.0
O B:GLU198 4.0 49.4 1.0
CA B:HIS161 4.0 27.0 1.0
CD2 B:HIS161 4.2 24.4 1.0
NE2 B:HIS161 4.2 23.6 1.0
ND1 B:HIS204 4.5 48.1 1.0
CA B:CYS200 4.5 43.1 1.0
O B:LEU160 4.6 39.5 1.0
CA B:CYS196 4.7 38.2 1.0
N B:CYS200 4.8 45.8 1.0
CA B:HIS204 4.9 44.1 1.0
CD1 B:TRP104 5.0 47.1 1.0

Copper binding site 3 out of 6 in 2ein

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Copper binding site 3 out of 6 in the Zinc 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 Zinc 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:41.9
occ:1.00
 CU2 B:CUA228 0.0 41.9 1.0
ND1 B:HIS204 2.0 48.1 1.0
SG B:CYS200 2.2 27.7 1.0
SG B:CYS196 2.3 32.5 1.0
O B:GLU198 2.4 49.4 1.0
CU1 B:CUA228 2.5 44.6 1.0
CE1 B:HIS204 2.9 44.4 1.0
CG B:HIS204 3.0 45.2 1.0
CB B:CYS196 3.1 31.7 1.0
CB B:CYS200 3.4 36.8 1.0
CB B:HIS204 3.4 42.6 1.0
C B:GLU198 3.5 39.2 1.0
CA B:HIS204 3.6 44.1 1.0
N B:CYS200 3.6 45.8 1.0
O B:HIS204 3.8 40.3 1.0
O B:CYS196 3.8 48.4 1.0
N B:GLU198 4.0 31.4 1.0
C B:HIS204 4.1 42.1 1.0
C B:CYS196 4.1 45.2 1.0
NE2 B:HIS204 4.1 41.8 1.0
C B:ILE199 4.1 45.8 1.0
CA B:CYS200 4.2 43.1 1.0
CD2 B:HIS204 4.2 42.4 1.0
N B:ILE199 4.2 40.6 1.0
CA B:ILE199 4.2 43.8 1.0
CA B:CYS196 4.3 38.2 1.0
ND1 B:HIS161 4.3 25.7 1.0
CA B:GLU198 4.4 33.5 1.0
SD B:MET207 4.4 44.8 1.0
N B:SER197 4.8 44.0 1.0
CG B:MET207 4.8 37.7 1.0
N B:HIS204 4.9 43.0 1.0
O B:ILE199 4.9 42.1 1.0
CA B:HIS161 5.0 27.0 1.0

Copper binding site 4 out of 6 in 2ein

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Copper binding site 4 out of 6 in the Zinc 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 Zinc 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:48.3
occ:1.00
 NE2 N:HIS291 1.9 44.0 1.0
ND1 N:HIS240 2.0 48.4 1.0
NE2 N:HIS290 2.0 39.5 1.0
CE1 N:HIS291 2.4 46.4 1.0
CE1 N:HIS240 2.8 46.6 1.0
CE1 N:HIS290 3.0 48.4 1.0
CG N:HIS240 3.1 41.3 1.0
CD2 N:HIS290 3.2 43.4 1.0
CD2 N:HIS291 3.3 52.2 1.0
CB N:HIS240 3.6 37.8 1.0
ND1 N:HIS291 3.7 36.0 1.0
NE2 N:HIS240 4.0 42.2 1.0
CA N:HIS240 4.0 37.3 1.0
CG N:HIS291 4.1 47.1 1.0
CD2 N:HIS240 4.1 42.3 1.0
ND1 N:HIS290 4.2 39.7 1.0
NA N:HEA516 4.2 49.4 1.0
CG N:HIS290 4.3 42.4 1.0
C1A N:HEA516 4.3 49.3 1.0
FE N:HEA516 4.3 43.6 1.0
CG2 N:VAL243 4.6 49.0 1.0
C2A N:HEA516 4.6 50.3 1.0
C4A N:HEA516 4.7 50.1 1.0
ND N:HEA516 4.7 43.7 1.0
CG1 N:VAL243 4.7 56.0 1.0
CHA N:HEA516 4.7 42.3 1.0
C3A N:HEA516 4.8 49.8 1.0
NB N:HEA516 4.9 44.1 1.0
N N:HIS240 4.9 33.6 1.0
C4D N:HEA516 4.9 42.7 1.0
O N:HIS240 5.0 46.4 1.0

Copper binding site 5 out of 6 in 2ein

Go back to Copper Binding Sites List in 2ein
Copper binding site 5 out of 6 in the Zinc 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 Zinc 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:52.2
occ:1.00
 CU1 O:CUA228 0.0 52.2 1.0
ND1 O:HIS161 2.0 40.4 1.0
SG O:CYS196 2.2 43.4 1.0
CU2 O:CUA228 2.3 55.7 1.0
SG O:CYS200 2.3 43.2 1.0
SD O:MET207 2.9 63.6 1.0
CE1 O:HIS161 3.0 38.8 1.0
CG O:HIS161 3.1 43.8 1.0
CB O:CYS196 3.1 46.5 1.0
CE O:MET207 3.1 48.6 1.0
CB O:CYS200 3.4 53.0 1.0
CB O:HIS161 3.5 45.6 1.0
CG O:MET207 3.8 57.5 1.0
O O:GLU198 3.8 54.7 1.0
CA O:HIS161 4.0 44.7 1.0
ND1 O:HIS204 4.1 51.9 1.0
NE2 O:HIS161 4.2 42.9 1.0
CD2 O:HIS161 4.2 37.2 1.0
CA O:CYS196 4.5 50.3 1.0
CA O:CYS200 4.7 55.8 1.0
O O:LEU160 4.7 50.5 1.0
N O:SER162 4.8 49.2 1.0
N O:CYS200 4.9 57.1 1.0
CA O:HIS204 4.9 56.6 1.0
CZ2 O:TRP106 4.9 77.4 1.0
C O:CYS196 4.9 53.0 1.0
O O:HIS204 4.9 56.5 1.0
C O:HIS161 5.0 47.9 1.0
CE1 O:HIS204 5.0 55.7 1.0

Copper binding site 6 out of 6 in 2ein

Go back to Copper Binding Sites List in 2ein
Copper binding site 6 out of 6 in the Zinc 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 Zinc 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:55.7
occ:1.00
 CU2 O:CUA228 0.0 55.7 1.0
ND1 O:HIS204 2.0 51.9 1.0
CU1 O:CUA228 2.3 52.2 1.0
SG O:CYS200 2.3 43.2 1.0
SG O:CYS196 2.3 43.4 1.0
O O:GLU198 2.4 54.7 1.0
CG O:HIS204 2.9 54.3 1.0
CE1 O:HIS204 3.0 55.7 1.0
CB O:CYS200 3.2 53.0 1.0
CB O:HIS204 3.3 55.0 1.0
N O:CYS200 3.4 57.1 1.0
CB O:CYS196 3.5 46.5 1.0
C O:GLU198 3.5 46.8 1.0
CA O:HIS204 3.5 56.6 1.0
CA O:CYS200 3.9 55.8 1.0
ND1 O:HIS161 3.9 40.4 1.0
O O:HIS204 3.9 56.5 1.0
C O:ILE199 4.0 55.8 1.0
CD2 O:HIS204 4.0 51.5 1.0
NE2 O:HIS204 4.1 56.2 1.0
O O:CYS196 4.1 53.0 1.0
C O:HIS204 4.2 57.8 1.0
CA O:ILE199 4.2 54.4 1.0
N O:ILE199 4.3 48.0 1.0
N O:GLU198 4.3 47.1 1.0
SD O:MET207 4.4 63.6 1.0
C O:CYS196 4.4 53.0 1.0
CA O:GLU198 4.5 44.9 1.0
CE1 O:HIS161 4.6 38.8 1.0
CA O:CYS196 4.6 50.3 1.0
N O:HIS204 4.8 58.5 1.0
O O:ILE199 4.8 53.4 1.0
C O:CYS200 4.8 55.7 1.0
CG O:MET207 4.8 57.5 1.0
CG O:HIS161 4.9 43.8 1.0
CA O:HIS161 4.9 44.7 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 23:27:04 2024

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