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

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

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

Protein crystallography data

The structure of Zinc Ion Binding Structure of Bovine Heart Cytochrome C Oxidase in the Fully Reduced State, PDB code: 2eim 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 / 2.60
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 183.909, 206.721, 178.337, 90.00, 90.00, 90.00
R / Rfree (%) 20.4 / 25.6

Other elements in 2eim:

The structure of Zinc 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) 6 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 Reduced State (pdb code 2eim). 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 Reduced State, PDB code: 2eim:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6;

Copper binding site 1 out of 6 in 2eim

Go back to Copper Binding Sites List in 2eim
Copper binding site 1 out of 6 in the Zinc 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 Zinc 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:30.4
occ:1.00
NE2 A:HIS291 2.0 31.4 1.0
NE2 A:HIS290 2.0 34.6 1.0
ND1 A:HIS240 2.0 42.6 1.0
CE1 A:HIS290 2.9 36.0 1.0
CE1 A:HIS291 3.0 28.2 1.0
CE1 A:HIS240 3.0 35.9 1.0
CD2 A:HIS291 3.0 26.7 1.0
CD2 A:HIS290 3.1 32.4 1.0
CG A:HIS240 3.1 34.1 1.0
CB A:HIS240 3.5 31.4 1.0
CA A:HIS240 4.0 25.3 1.0
ND1 A:HIS290 4.1 32.8 1.0
ND1 A:HIS291 4.1 22.2 1.0
NE2 A:HIS240 4.1 43.5 1.0
CG A:HIS291 4.2 27.7 1.0
CG A:HIS290 4.2 34.5 1.0
CD2 A:HIS240 4.2 37.1 1.0
NA A:HEA516 4.5 47.5 1.0
C1A A:HEA516 4.6 39.9 1.0
CG2 A:VAL243 4.7 16.9 1.0
C4A A:HEA516 4.7 47.8 1.0
C2A A:HEA516 4.8 41.9 1.0
C3A A:HEA516 4.8 43.0 1.0
N A:HIS240 4.8 19.1 1.0
CHA A:HEA516 4.9 43.7 1.0

Copper binding site 2 out of 6 in 2eim

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

b:27.5
occ:1.00
CU1 B:CUA228 0.0 27.5 1.0
ND1 B:HIS161 2.0 23.9 1.0
SG B:CYS196 2.3 26.1 1.0
SG B:CYS200 2.3 24.7 1.0
CU2 B:CUA228 2.7 31.3 1.0
SD B:MET207 2.7 36.6 1.0
CG B:HIS161 3.0 17.2 1.0
CE B:MET207 3.0 21.9 1.0
CE1 B:HIS161 3.1 22.9 1.0
CB B:CYS200 3.2 34.4 1.0
CB B:HIS161 3.2 14.1 1.0
CB B:CYS196 3.4 22.0 1.0
CA B:HIS161 3.8 19.5 1.0
CG B:MET207 3.8 22.1 1.0
O B:GLU198 4.0 41.1 1.0
CD2 B:HIS161 4.2 20.0 1.0
NE2 B:HIS161 4.2 11.6 1.0
O B:LEU160 4.3 25.7 1.0
ND1 B:HIS204 4.6 31.9 1.0
CA B:CYS200 4.6 36.3 1.0
CD1 B:TRP104 4.8 37.5 1.0
CA B:CYS196 4.8 29.8 1.0
O B:HIS102 4.8 21.1 1.0
CA B:HIS204 4.8 29.2 1.0
N B:HIS161 4.8 23.7 1.0
N B:CYS200 4.9 38.0 1.0
CZ2 B:TRP106 4.9 24.0 1.0
C B:HIS161 4.9 20.8 1.0
N B:SER162 5.0 20.8 1.0
C B:LEU160 5.0 31.5 1.0

Copper binding site 3 out of 6 in 2eim

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

b:31.3
occ:1.00
CU2 B:CUA228 0.0 31.3 1.0
ND1 B:HIS204 2.0 31.9 1.0
SG B:CYS200 2.2 24.7 1.0
SG B:CYS196 2.3 26.1 1.0
O B:GLU198 2.4 41.1 1.0
CU1 B:CUA228 2.7 27.5 1.0
CG B:HIS204 2.9 28.4 1.0
CE1 B:HIS204 3.0 23.3 1.0
CB B:CYS196 3.1 22.0 1.0
CB B:HIS204 3.2 29.2 1.0
CA B:HIS204 3.3 29.2 1.0
CB B:CYS200 3.4 34.4 1.0
C B:GLU198 3.5 34.3 1.0
O B:HIS204 3.5 19.8 1.0
N B:CYS200 3.6 38.0 1.0
C B:HIS204 3.8 23.4 1.0
CD2 B:HIS204 4.1 24.8 1.0
NE2 B:HIS204 4.1 28.5 1.0
O B:CYS196 4.1 27.0 1.0
CA B:CYS200 4.1 36.3 1.0
C B:ILE199 4.2 35.3 1.0
CA B:ILE199 4.2 29.4 1.0
N B:GLU198 4.2 36.0 1.0
N B:ILE199 4.2 28.4 1.0
C B:CYS196 4.2 34.1 1.0
CA B:CYS196 4.3 29.8 1.0
SD B:MET207 4.4 36.6 1.0
ND1 B:HIS161 4.4 23.9 1.0
CA B:GLU198 4.5 31.2 1.0
N B:HIS204 4.6 37.0 1.0
CG B:MET207 4.6 22.1 1.0
CA B:HIS161 4.8 19.5 1.0
N B:SER197 4.8 35.2 1.0
O B:LEU160 5.0 25.7 1.0

Copper binding site 4 out of 6 in 2eim

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

b:36.1
occ:1.00
NE2 N:HIS291 1.9 37.3 1.0
ND1 N:HIS240 2.0 41.1 1.0
NE2 N:HIS290 2.0 29.8 1.0
CE1 N:HIS240 2.8 42.0 1.0
CE1 N:HIS290 2.9 34.5 1.0
CE1 N:HIS291 2.9 33.1 1.0
CD2 N:HIS291 3.0 35.5 1.0
CG N:HIS240 3.1 37.8 1.0
CD2 N:HIS290 3.1 30.5 1.0
CB N:HIS240 3.6 36.9 1.0
CA N:HIS240 4.0 35.5 1.0
NE2 N:HIS240 4.0 44.7 1.0
ND1 N:HIS291 4.1 33.3 1.0
ND1 N:HIS290 4.1 35.8 1.0
CG N:HIS291 4.1 36.0 1.0
CD2 N:HIS240 4.2 39.2 1.0
CG N:HIS290 4.2 36.1 1.0
NA N:HEA516 4.5 46.0 1.0
C1A N:HEA516 4.6 46.6 1.0
C4A N:HEA516 4.7 46.6 1.0
CG2 N:VAL243 4.7 32.4 1.0
C2A N:HEA516 4.8 46.5 1.0
C3A N:HEA516 4.8 48.4 1.0
N N:HIS240 4.8 36.9 1.0
CHA N:HEA516 4.9 46.8 1.0
FE N:HEA516 5.0 36.8 1.0

Copper binding site 5 out of 6 in 2eim

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Copper binding site 5 out of 6 in the Zinc 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 Zinc 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:50.8
occ:1.00
CU1 O:CUA228 0.0 50.8 1.0
ND1 O:HIS161 2.0 38.4 1.0
CU2 O:CUA228 2.3 51.0 1.0
SG O:CYS196 2.3 32.8 1.0
SG O:CYS200 2.3 44.5 1.0
SD O:MET207 2.7 46.0 1.0
CE1 O:HIS161 2.9 41.0 1.0
CG O:HIS161 3.1 32.2 1.0
CB O:CYS200 3.2 43.6 1.0
CE O:MET207 3.2 32.3 1.0
CB O:CYS196 3.3 41.9 1.0
CB O:HIS161 3.5 36.2 1.0
CG O:MET207 3.6 40.5 1.0
O O:GLU198 3.9 48.2 1.0
CA O:HIS161 4.0 34.7 1.0
NE2 O:HIS161 4.1 39.0 1.0
CD2 O:HIS161 4.2 30.7 1.0
ND1 O:HIS204 4.3 48.0 1.0
CA O:HIS204 4.4 42.3 1.0
O O:LEU160 4.5 38.6 1.0
CA O:CYS200 4.5 47.1 1.0
CA O:CYS196 4.7 37.5 1.0
N O:CYS200 4.7 49.0 1.0
CD1 O:TRP104 4.7 45.6 1.0
O O:HIS204 4.7 35.9 1.0
CB O:HIS204 4.9 43.4 1.0

Copper binding site 6 out of 6 in 2eim

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Copper binding site 6 out of 6 in the Zinc 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 Zinc 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:51.0
occ:1.00
CU2 O:CUA228 0.0 51.0 1.0
ND1 O:HIS204 2.1 48.0 1.0
CU1 O:CUA228 2.3 50.8 1.0
SG O:CYS200 2.3 44.5 1.0
SG O:CYS196 2.3 32.8 1.0
O O:GLU198 2.4 48.2 1.0
CG O:HIS204 3.0 42.3 1.0
CE1 O:HIS204 3.1 39.1 1.0
CB O:CYS196 3.2 41.9 1.0
CB O:HIS204 3.2 43.4 1.0
CA O:HIS204 3.3 42.3 1.0
CB O:CYS200 3.3 43.6 1.0
N O:CYS200 3.5 49.0 1.0
C O:GLU198 3.5 43.3 1.0
O O:HIS204 3.7 35.9 1.0
C O:HIS204 3.9 36.9 1.0
ND1 O:HIS161 4.0 38.4 1.0
CA O:CYS200 4.1 47.1 1.0
CD2 O:HIS204 4.2 31.4 1.0
C O:ILE199 4.2 46.0 1.0
CA O:ILE199 4.2 41.4 1.0
O O:CYS196 4.2 36.1 1.0
NE2 O:HIS204 4.2 33.7 1.0
N O:ILE199 4.3 41.6 1.0
N O:GLU198 4.3 45.5 1.0
C O:CYS196 4.3 37.7 1.0
CA O:CYS196 4.4 37.5 1.0
SD O:MET207 4.5 46.0 1.0
CA O:GLU198 4.6 45.3 1.0
N O:HIS204 4.6 48.6 1.0
CG O:MET207 4.7 40.5 1.0
CA O:HIS161 4.8 34.7 1.0
CE1 O:HIS161 4.8 41.0 1.0
CG O:HIS161 4.9 32.2 1.0
CB O:HIS161 4.9 36.2 1.0
O O:LEU160 4.9 38.6 1.0
N O:SER197 4.9 41.0 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: Wed Oct 28 14:19:26 2020
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