Atomistry » Copper » PDB 2idq-2pp7 » 2occ
Atomistry »
  Copper »
    PDB 2idq-2pp7 »
      2occ »

Copper in PDB 2occ: Bovine Heart Cytochrome C Oxidase at the Fully Oxidized State

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

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

Protein crystallography data

The structure of Bovine Heart Cytochrome C Oxidase at the Fully Oxidized State, PDB code: 2occ was solved by T.Tsukihara, M.Yao, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 15.00 / 2.30
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 (%) 20.9 / 24.4

Other elements in 2occ:

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

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

Copper Binding Sites:

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

Copper binding site 1 out of 6 in 2occ

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

b:16.3
occ:1.00
 NE2 A:HIS290 1.9 12.6 1.0
NE2 A:HIS291 1.9 29.2 1.0
O2 A:PER520 2.1 15.3 1.0
ND1 A:HIS240 2.2 25.9 1.0
CE1 A:HIS291 2.8 25.4 1.0
O1 A:PER520 2.8 10.3 1.0
CE1 A:HIS290 2.9 22.4 1.0
CD2 A:HIS290 3.0 21.2 1.0
CD2 A:HIS291 3.1 26.0 1.0
CG A:HIS240 3.1 18.4 1.0
CE1 A:HIS240 3.2 22.7 1.0
CB A:HIS240 3.4 17.1 1.0
CA A:HIS240 3.9 17.0 1.0
ND1 A:HIS291 4.0 25.0 1.0
ND1 A:HIS290 4.1 17.1 1.0
CG A:HIS290 4.1 23.1 1.0
CG A:HIS291 4.1 27.2 1.0
CD2 A:HIS240 4.3 24.0 1.0
NE2 A:HIS240 4.3 28.7 1.0
NA A:HEA516 4.6 24.2 1.0
C1A A:HEA516 4.6 13.3 1.0
C4A A:HEA516 4.7 17.9 1.0
N A:HIS240 4.8 12.3 1.0
C2A A:HEA516 4.8 21.2 1.0
CG2 A:VAL243 4.8 15.2 1.0
C3A A:HEA516 4.8 17.3 1.0
FE A:HEA516 4.9 20.1 1.0

Copper binding site 2 out of 6 in 2occ

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

b:22.0
occ:1.00
 ND1 B:HIS161 1.9 10.9 1.0
SG B:CYS196 2.2 17.2 1.0
SG B:CYS200 2.3 15.5 1.0
CU B:CU229 2.4 24.3 1.0
CE1 B:HIS161 2.5 7.0 1.0
SD B:MET207 2.7 22.4 1.0
CE B:MET207 2.9 21.4 1.0
CG B:HIS161 3.2 7.0 1.0
CB B:CYS200 3.3 19.8 1.0
CB B:CYS196 3.4 26.2 1.0
CG B:MET207 3.7 25.8 1.0
NE2 B:HIS161 3.8 7.2 1.0
CB B:HIS161 3.9 17.1 1.0
O B:GLU198 4.0 32.3 1.0
CD2 B:HIS161 4.1 8.0 1.0
CA B:HIS161 4.2 14.6 1.0
ND1 B:HIS204 4.3 28.3 1.0
O B:LEU160 4.6 21.0 1.0
CA B:CYS196 4.7 23.2 1.0
CA B:CYS200 4.7 20.4 1.0
CA B:HIS204 4.9 21.4 1.0
O B:HIS102 4.9 13.5 1.0
O B:HIS204 4.9 20.1 1.0
N B:CYS200 5.0 20.8 1.0
CD1 B:TRP104 5.0 25.0 1.0

Copper binding site 3 out of 6 in 2occ

Go back to Copper Binding Sites List in 2occ
Copper binding site 3 out of 6 in the 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 Bovine Heart Cytochrome C Oxidase at the Fully Oxidized State within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu229

b:24.3
occ:1.00
 ND1 B:HIS204 1.9 28.3 1.0
SG B:CYS200 2.2 15.5 1.0
SG B:CYS196 2.3 17.2 1.0
O B:GLU198 2.4 32.3 1.0
CU B:CU228 2.4 22.0 1.0
CE1 B:HIS204 2.7 24.6 1.0
CG B:HIS204 3.1 19.1 1.0
CB B:CYS196 3.1 26.2 1.0
CB B:CYS200 3.5 19.8 1.0
C B:GLU198 3.6 22.7 1.0
CB B:HIS204 3.6 22.5 1.0
CA B:HIS204 3.7 21.4 1.0
O B:HIS204 3.7 20.1 1.0
N B:CYS200 3.7 20.8 1.0
NE2 B:HIS204 4.0 21.0 1.0
ND1 B:HIS161 4.1 10.9 1.0
C B:HIS204 4.1 19.6 1.0
CD2 B:HIS204 4.1 20.5 1.0
C B:ILE199 4.1 20.4 1.0
CA B:CYS200 4.2 20.4 1.0
CA B:ILE199 4.2 21.5 1.0
O B:CYS196 4.2 21.5 1.0
N B:GLU198 4.3 18.5 1.0
N B:ILE199 4.3 23.8 1.0
C B:CYS196 4.3 25.0 1.0
CA B:CYS196 4.3 23.2 1.0
SD B:MET207 4.4 22.4 1.0
CA B:GLU198 4.6 18.4 1.0
CE1 B:HIS161 4.6 7.0 1.0
CG B:MET207 4.7 25.8 1.0
N B:HIS204 4.9 27.4 1.0
N B:SER197 4.9 24.8 1.0
O B:ILE199 5.0 22.2 1.0
CE B:MET207 5.0 21.4 1.0

Copper binding site 4 out of 6 in 2occ

Go back to Copper Binding Sites List in 2occ
Copper binding site 4 out of 6 in the 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 Bovine Heart Cytochrome C Oxidase at the Fully Oxidized State within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Cu517

b:29.1
occ:1.00
 NE2 N:HIS290 2.0 18.9 1.0
NE2 N:HIS291 2.0 36.0 1.0
O2 N:PER520 2.0 21.1 1.0
ND1 N:HIS240 2.2 33.4 1.0
O1 N:PER520 2.7 22.6 1.0
CE1 N:HIS291 2.8 30.9 1.0
CE1 N:HIS290 2.9 27.4 1.0
CD2 N:HIS290 3.0 23.1 1.0
CG N:HIS240 3.1 29.1 1.0
CD2 N:HIS291 3.1 28.4 1.0
CE1 N:HIS240 3.2 30.2 1.0
CB N:HIS240 3.4 27.6 1.0
CA N:HIS240 3.9 28.6 1.0
ND1 N:HIS291 4.0 28.2 1.0
ND1 N:HIS290 4.1 22.6 1.0
CG N:HIS290 4.2 23.2 1.0
CG N:HIS291 4.2 26.9 1.0
CD2 N:HIS240 4.3 32.0 1.0
NE2 N:HIS240 4.3 31.3 1.0
NA N:HEA516 4.6 23.9 1.0
C1A N:HEA516 4.6 22.5 1.0
C4A N:HEA516 4.7 25.2 1.0
N N:HIS240 4.7 27.0 1.0
CG2 N:VAL243 4.7 21.4 1.0
C2A N:HEA516 4.8 25.6 1.0
C3A N:HEA516 4.8 21.6 1.0
FE N:HEA516 4.9 26.8 1.0

Copper binding site 5 out of 6 in 2occ

Go back to Copper Binding Sites List in 2occ
Copper binding site 5 out of 6 in the 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 Bovine Heart Cytochrome C Oxidase at the Fully Oxidized State within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Cu228

b:36.3
occ:1.00
 ND1 O:HIS161 2.0 26.7 1.0
SG O:CYS196 2.2 30.6 1.0
CU O:CU229 2.2 35.5 1.0
SG O:CYS200 2.2 26.3 1.0
CE1 O:HIS161 2.6 22.1 1.0
SD O:MET207 2.7 41.2 1.0
CE O:MET207 3.1 31.5 1.0
CG O:HIS161 3.3 24.6 1.0
CB O:CYS200 3.3 31.4 1.0
CB O:CYS196 3.4 35.0 1.0
O O:GLU198 3.8 39.9 1.0
CG O:MET207 3.8 37.1 1.0
NE2 O:HIS161 3.9 22.7 1.0
CB O:HIS161 3.9 26.4 1.0
ND1 O:HIS204 4.2 34.7 1.0
CD2 O:HIS161 4.2 24.9 1.0
CA O:HIS161 4.2 25.4 1.0
O O:LEU160 4.5 28.2 1.0
CA O:CYS200 4.6 33.1 1.0
CA O:CYS196 4.7 36.4 1.0
N O:CYS200 4.8 38.0 1.0
O O:HIS204 4.8 34.1 1.0
CA O:HIS204 4.8 36.5 1.0
CE1 O:HIS204 5.0 32.5 1.0

Copper binding site 6 out of 6 in 2occ

Go back to Copper Binding Sites List in 2occ
Copper binding site 6 out of 6 in the 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 Bovine Heart Cytochrome C Oxidase at the Fully Oxidized State within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Cu229

b:35.5
occ:1.00
 ND1 O:HIS204 2.0 34.7 1.0
SG O:CYS200 2.2 26.3 1.0
CU O:CU228 2.2 36.3 1.0
SG O:CYS196 2.2 30.6 1.0
O O:GLU198 2.4 39.9 1.0
CE1 O:HIS204 2.8 32.5 1.0
CG O:HIS204 3.2 34.5 1.0
CB O:CYS196 3.2 35.0 1.0
CB O:CYS200 3.4 31.4 1.0
C O:GLU198 3.6 31.8 1.0
N O:CYS200 3.6 38.0 1.0
CB O:HIS204 3.7 36.6 1.0
CA O:HIS204 3.7 36.5 1.0
O O:HIS204 3.7 34.1 1.0
ND1 O:HIS161 3.9 26.7 1.0
NE2 O:HIS204 4.1 33.1 1.0
C O:HIS204 4.1 34.7 1.0
CA O:CYS200 4.2 33.1 1.0
C O:ILE199 4.2 34.9 1.0
CD2 O:HIS204 4.2 30.8 1.0
CA O:ILE199 4.3 30.7 1.0
O O:CYS196 4.3 39.4 1.0
SD O:MET207 4.3 41.2 1.0
N O:GLU198 4.3 33.7 1.0
N O:ILE199 4.3 30.4 1.0
C O:CYS196 4.4 39.1 1.0
CA O:CYS196 4.4 36.4 1.0
CE1 O:HIS161 4.5 22.1 1.0
CA O:GLU198 4.6 30.5 1.0
CG O:MET207 4.7 37.1 1.0
CE O:MET207 4.9 31.5 1.0
N O:HIS204 4.9 41.2 1.0

Reference:

S.Yoshikawa, K.Shinzawa-Itoh, R.Nakashima, R.Yaono, E.Yamashita, N.Inoue, M.Yao, M.J.Fei, C.P.Libeu, T.Mizushima, H.Yamaguchi, T.Tomizaki, T.Tsukihara. Redox-Coupled Crystal Structural Changes in Bovine Heart Cytochrome C Oxidase. Science V. 280 1723 1998.
ISSN: ISSN 0036-8075
PubMed: 9624044
DOI: 10.1126/SCIENCE.280.5370.1723
Page generated: Tue Jul 30 23:50:41 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy