Atomistry » Copper » PDB 1mg2-1oe1 » 1occ
Atomistry »
  Copper »
    PDB 1mg2-1oe1 »
      1occ »

Copper in PDB 1occ: Structure of Bovine Heart Cytochrome C Oxidase at the Fully Oxidized State

Enzymatic activity of Structure of Bovine Heart Cytochrome C Oxidase at the Fully Oxidized State

All present enzymatic activity of Structure of Bovine Heart Cytochrome C Oxidase at the Fully Oxidized State:
1.9.3.1;

Protein crystallography data

The structure of Structure of Bovine Heart Cytochrome C Oxidase at the Fully Oxidized State, PDB code: 1occ was solved by T.Tsukihara, H.Aoyama, E.Yamashita, T.Tomizaki, H.Yamaguchi, K.Shinzawa-Itoh, R.Nakashima, R.Yaono, S.Yoshikawa, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 10.00 / 2.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 189.100, 210.500, 178.600, 90.00, 90.00, 90.00
R / Rfree (%) 20.1 / 25.2

Other elements in 1occ:

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

Magnesium (Mg) 2 atoms
Iron (Fe) 4 atoms
Zinc (Zn) 2 atoms

Copper Binding Sites:

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

Copper binding site 1 out of 6 in 1occ

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

b:15.3
occ:1.00
 ND1 A:HIS240 1.9 26.2 1.0
NE2 A:HIS291 2.2 7.0 1.0
NE2 A:HIS290 2.2 7.0 1.0
CE1 A:HIS240 2.6 27.2 1.0
CD2 A:HIS291 3.0 18.9 1.0
CG A:HIS240 3.1 18.8 1.0
CE1 A:HIS290 3.1 7.0 1.0
CE1 A:HIS291 3.2 23.1 1.0
CD2 A:HIS290 3.2 17.6 1.0
CB A:HIS240 3.6 11.4 1.0
NE2 A:HIS240 3.9 7.0 1.0
CD2 A:HIS240 4.1 15.7 1.0
CG A:HIS291 4.2 20.1 1.0
CA A:HIS240 4.2 13.6 1.0
ND1 A:HIS291 4.2 23.8 1.0
ND1 A:HIS290 4.2 7.9 1.0
CG A:HIS290 4.3 14.5 1.0
NA A:HEA516 4.4 14.8 1.0
C1A A:HEA516 4.5 7.0 1.0
C4A A:HEA516 4.7 14.3 1.0
FE A:HEA516 4.7 8.0 1.0
C2A A:HEA516 4.9 7.0 1.0
C3A A:HEA516 4.9 7.0 1.0
CHA A:HEA516 4.9 8.6 1.0

Copper binding site 2 out of 6 in 1occ

Go back to Copper Binding Sites List in 1occ
Copper binding site 2 out of 6 in the Structure of Bovine Heart Cytochrome C Oxidase at 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 Structure of Bovine Heart Cytochrome C Oxidase at the Fully Oxidized State within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu228

b:25.9
occ:1.00
 ND1 B:HIS161 1.9 7.0 1.0
SG B:CYS196 2.3 10.8 1.0
SG B:CYS200 2.3 10.4 1.0
CU B:CU229 2.4 13.4 1.0
SD B:MET207 2.5 14.2 1.0
CE1 B:HIS161 2.6 7.0 1.0
CG B:HIS161 3.1 7.0 1.0
CE B:MET207 3.2 10.6 1.0
CB B:CYS200 3.3 11.0 1.0
CB B:CYS196 3.5 17.1 1.0
CB B:HIS161 3.7 7.0 1.0
CG B:MET207 3.7 10.4 1.0
O B:GLU198 3.8 20.2 1.0
NE2 B:HIS161 3.9 7.0 1.0
CD2 B:HIS161 4.1 7.0 1.0
CA B:HIS161 4.1 7.0 1.0
ND1 B:HIS204 4.2 16.2 1.0
O B:LEU160 4.6 7.0 1.0
CA B:CYS200 4.7 10.1 1.0
O B:HIS204 4.8 17.7 1.0
CA B:CYS196 4.8 8.4 1.0
N B:CYS200 4.9 16.8 1.0
CA B:HIS204 5.0 9.2 1.0
CD1 B:TRP104 5.0 16.1 1.0

Copper binding site 3 out of 6 in 1occ

Go back to Copper Binding Sites List in 1occ
Copper binding site 3 out of 6 in the Structure of Bovine Heart Cytochrome C Oxidase at 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 Structure of Bovine Heart Cytochrome C Oxidase at the Fully Oxidized State within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu229

b:13.4
occ:1.00
 ND1 B:HIS204 1.9 16.2 1.0
O B:GLU198 2.2 20.2 1.0
SG B:CYS200 2.2 10.4 1.0
SG B:CYS196 2.3 10.8 1.0
CU B:CU228 2.4 25.9 1.0
CE1 B:HIS204 2.8 19.0 1.0
CG B:HIS204 3.0 9.0 1.0
CB B:CYS200 3.3 11.0 1.0
C B:GLU198 3.4 11.5 1.0
CB B:CYS196 3.4 17.1 1.0
CB B:HIS204 3.5 12.8 1.0
N B:CYS200 3.6 16.8 1.0
CA B:HIS204 3.6 9.2 1.0
O B:HIS204 3.6 17.7 1.0
NE2 B:HIS204 3.9 10.2 1.0
C B:HIS204 4.0 10.3 1.0
ND1 B:HIS161 4.1 7.0 1.0
CD2 B:HIS204 4.1 11.1 1.0
CA B:CYS200 4.1 10.1 1.0
SD B:MET207 4.1 14.2 1.0
C B:ILE199 4.1 12.8 1.0
CA B:ILE199 4.3 11.1 1.0
N B:ILE199 4.3 13.2 1.0
N B:GLU198 4.3 16.7 1.0
CA B:GLU198 4.4 8.4 1.0
O B:CYS196 4.5 15.9 1.0
CG B:MET207 4.5 10.4 1.0
C B:CYS196 4.6 14.1 1.0
CE1 B:HIS161 4.7 7.0 1.0
CA B:CYS196 4.7 8.4 1.0
N B:HIS204 4.9 15.7 1.0
C B:CYS200 4.9 7.5 1.0
O B:ILE199 4.9 8.4 1.0

Copper binding site 4 out of 6 in 1occ

Go back to Copper Binding Sites List in 1occ
Copper binding site 4 out of 6 in the Structure of Bovine Heart Cytochrome C Oxidase at 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 Structure of Bovine Heart Cytochrome C Oxidase at the Fully Oxidized State within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Cu517

b:15.3
occ:1.00
 ND1 N:HIS240 1.9 26.2 1.0
NE2 N:HIS291 2.2 7.0 1.0
NE2 N:HIS290 2.2 7.0 1.0
CE1 N:HIS240 2.6 27.2 1.0
CD2 N:HIS291 3.0 18.9 1.0
CG N:HIS240 3.1 18.8 1.0
CE1 N:HIS290 3.1 7.0 1.0
CE1 N:HIS291 3.2 23.1 1.0
CD2 N:HIS290 3.2 17.6 1.0
CB N:HIS240 3.6 11.4 1.0
NE2 N:HIS240 3.9 7.0 1.0
CD2 N:HIS240 4.1 15.7 1.0
CG N:HIS291 4.2 20.1 1.0
CA N:HIS240 4.2 13.6 1.0
ND1 N:HIS291 4.2 23.8 1.0
ND1 N:HIS290 4.2 7.9 1.0
CG N:HIS290 4.3 14.5 1.0
NA N:HEA516 4.4 14.8 1.0
C1A N:HEA516 4.5 7.0 1.0
C4A N:HEA516 4.7 14.3 1.0
FE N:HEA516 4.7 8.0 1.0
C2A N:HEA516 4.9 7.0 1.0
C3A N:HEA516 4.9 7.0 1.0
CHA N:HEA516 4.9 8.6 1.0

Copper binding site 5 out of 6 in 1occ

Go back to Copper Binding Sites List in 1occ
Copper binding site 5 out of 6 in the Structure of Bovine Heart Cytochrome C Oxidase at 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 Structure of Bovine Heart Cytochrome C Oxidase at the Fully Oxidized State within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Cu228

b:25.9
occ:1.00
 ND1 O:HIS161 1.9 7.0 1.0
SG O:CYS196 2.3 10.8 1.0
SG O:CYS200 2.3 10.4 1.0
CU O:CU229 2.4 13.4 1.0
SD O:MET207 2.5 14.2 1.0
CE1 O:HIS161 2.6 7.0 1.0
CG O:HIS161 3.1 7.0 1.0
CE O:MET207 3.2 10.6 1.0
CB O:CYS200 3.3 11.0 1.0
CB O:CYS196 3.5 17.1 1.0
CB O:HIS161 3.7 7.0 1.0
CG O:MET207 3.7 10.4 1.0
O O:GLU198 3.8 20.2 1.0
NE2 O:HIS161 3.9 7.0 1.0
CD2 O:HIS161 4.1 7.0 1.0
CA O:HIS161 4.1 7.0 1.0
ND1 O:HIS204 4.2 16.2 1.0
O O:LEU160 4.6 7.0 1.0
CA O:CYS200 4.7 10.1 1.0
O O:HIS204 4.8 17.7 1.0
CA O:CYS196 4.8 8.4 1.0
N O:CYS200 4.9 16.8 1.0
CA O:HIS204 5.0 9.2 1.0
CD1 O:TRP104 5.0 16.1 1.0

Copper binding site 6 out of 6 in 1occ

Go back to Copper Binding Sites List in 1occ
Copper binding site 6 out of 6 in the Structure of Bovine Heart Cytochrome C Oxidase at 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 Structure of Bovine Heart Cytochrome C Oxidase at the Fully Oxidized State within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Cu229

b:13.4
occ:1.00
 ND1 O:HIS204 1.9 16.2 1.0
O O:GLU198 2.2 20.2 1.0
SG O:CYS200 2.2 10.4 1.0
SG O:CYS196 2.3 10.8 1.0
CU O:CU228 2.4 25.9 1.0
CE1 O:HIS204 2.8 19.0 1.0
CG O:HIS204 3.0 9.0 1.0
CB O:CYS200 3.3 11.0 1.0
C O:GLU198 3.4 11.5 1.0
CB O:CYS196 3.4 17.1 1.0
CB O:HIS204 3.5 12.8 1.0
N O:CYS200 3.6 16.8 1.0
CA O:HIS204 3.6 9.2 1.0
O O:HIS204 3.6 17.7 1.0
NE2 O:HIS204 3.9 10.2 1.0
C O:HIS204 4.0 10.3 1.0
ND1 O:HIS161 4.1 7.0 1.0
CD2 O:HIS204 4.1 11.1 1.0
CA O:CYS200 4.1 10.1 1.0
SD O:MET207 4.1 14.2 1.0
C O:ILE199 4.1 12.8 1.0
CA O:ILE199 4.3 11.1 1.0
N O:ILE199 4.3 13.2 1.0
N O:GLU198 4.3 16.7 1.0
CA O:GLU198 4.4 8.4 1.0
O O:CYS196 4.5 15.9 1.0
CG O:MET207 4.5 10.4 1.0
C O:CYS196 4.6 14.1 1.0
CE1 O:HIS161 4.7 7.0 1.0
CA O:CYS196 4.7 8.4 1.0
N O:HIS204 4.9 15.7 1.0
C O:CYS200 4.9 7.5 1.0
O O:ILE199 4.9 8.4 1.0

Reference:

T.Tsukihara, H.Aoyama, E.Yamashita, T.Tomizaki, H.Yamaguchi, K.Shinzawa-Itoh, R.Nakashima, R.Yaono, S.Yoshikawa. The Whole Structure of the 13-Subunit Oxidized Cytochrome C Oxidase at 2.8 A. Science V. 272 1136 1996.
ISSN: ISSN 0036-8075
PubMed: 8638158
Page generated: Tue Jul 30 22:30:25 2024

Last articles

Zn in 9MJ5
Zn in 9HNW
Zn in 9G0L
Zn in 9FNE
Zn in 9DZN
Zn in 9E0I
Zn in 9D32
Zn in 9DAK
Zn in 8ZXC
Zn in 8ZUF
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy