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

Copper in PDB 1oco: Bovine Heart Cytochrome C Oxidase in Carbon Monoxide-Bound State

Enzymatic activity of Bovine Heart Cytochrome C Oxidase in Carbon Monoxide-Bound State

All present enzymatic activity of Bovine Heart Cytochrome C Oxidase in Carbon Monoxide-Bound State:
1.9.3.1;

Protein crystallography data

The structure of Bovine Heart Cytochrome C Oxidase in Carbon Monoxide-Bound State, PDB code: 1oco 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) 7.00 / 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 (%) 21.3 / 25.6

Other elements in 1oco:

The structure of Bovine Heart Cytochrome C Oxidase in Carbon Monoxide-Bound 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 in Carbon Monoxide-Bound State (pdb code 1oco). 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 in Carbon Monoxide-Bound State, PDB code: 1oco:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6;

Copper binding site 1 out of 6 in 1oco

Go back to Copper Binding Sites List in 1oco
Copper binding site 1 out of 6 in the Bovine Heart Cytochrome C Oxidase in Carbon Monoxide-Bound 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 in Carbon Monoxide-Bound State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu517

b:10.1
occ:1.00
 NE2 A:HIS291 2.0 12.7 1.0
NE2 A:HIS290 2.0 7.0 1.0
ND1 A:HIS240 2.2 13.3 1.0
O A:CMO520 2.4 19.1 1.0
CD2 A:HIS291 2.7 20.9 1.0
CE1 A:HIS290 3.0 10.7 1.0
CD2 A:HIS290 3.1 14.5 1.0
CG A:HIS240 3.1 7.5 1.0
CE1 A:HIS291 3.1 17.9 1.0
CE1 A:HIS240 3.2 10.4 1.0
CB A:HIS240 3.4 7.0 1.0
C A:CMO520 3.7 12.2 1.0
CG A:HIS291 3.9 21.0 1.0
CA A:HIS240 4.0 7.0 1.0
ND1 A:HIS291 4.1 21.4 1.0
ND1 A:HIS290 4.2 7.0 1.0
CG A:HIS290 4.2 12.9 1.0
CD2 A:HIS240 4.3 14.2 1.0
NE2 A:HIS240 4.3 20.3 1.0
CG2 A:VAL243 4.8 7.0 1.0
N A:HIS240 4.8 7.0 1.0
O A:TRP288 4.9 18.9 1.0
CA A:TRP288 5.0 7.0 1.0

Copper binding site 2 out of 6 in 1oco

Go back to Copper Binding Sites List in 1oco
Copper binding site 2 out of 6 in the Bovine Heart Cytochrome C Oxidase in Carbon Monoxide-Bound 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 in Carbon Monoxide-Bound State within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu228

b:15.2
occ:1.00
 ND1 B:HIS161 1.9 10.8 1.0
SG B:CYS196 2.3 18.5 1.0
SG B:CYS200 2.4 20.9 1.0
CU B:CU229 2.4 19.9 1.0
SD B:MET207 2.7 22.5 1.0
CE1 B:HIS161 2.7 7.0 1.0
CE B:MET207 3.0 10.7 1.0
CG B:HIS161 3.1 7.0 1.0
CB B:CYS200 3.4 17.0 1.0
CB B:CYS196 3.5 18.6 1.0
CB B:HIS161 3.6 7.3 1.0
CG B:MET207 3.8 12.8 1.0
NE2 B:HIS161 3.9 7.0 1.0
O B:GLU198 4.1 26.8 1.0
CA B:HIS161 4.1 9.8 1.0
CD2 B:HIS161 4.1 7.0 1.0
ND1 B:HIS204 4.4 23.3 1.0
O B:LEU160 4.6 17.3 1.0
CD1 B:TRP104 4.7 17.9 1.0
CA B:HIS204 4.8 15.5 1.0
CA B:CYS200 4.8 9.9 1.0
CA B:CYS196 4.9 10.7 1.0
O B:HIS102 4.9 7.0 1.0
O B:HIS204 5.0 19.2 1.0

Copper binding site 3 out of 6 in 1oco

Go back to Copper Binding Sites List in 1oco
Copper binding site 3 out of 6 in the Bovine Heart Cytochrome C Oxidase in Carbon Monoxide-Bound 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 in Carbon Monoxide-Bound State within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu229

b:19.9
occ:1.00
 ND1 B:HIS204 2.1 23.3 1.0
SG B:CYS200 2.2 20.9 1.0
SG B:CYS196 2.2 18.5 1.0
O B:GLU198 2.4 26.8 1.0
CU B:CU228 2.4 15.2 1.0
CE1 B:HIS204 3.0 18.2 1.0
CG B:HIS204 3.0 14.9 1.0
CB B:CYS200 3.3 17.0 1.0
CA B:HIS204 3.3 15.5 1.0
CB B:HIS204 3.4 13.2 1.0
CB B:CYS196 3.5 18.6 1.0
N B:CYS200 3.6 11.3 1.0
C B:GLU198 3.6 14.4 1.0
O B:HIS204 3.7 19.2 1.0
C B:HIS204 4.0 18.2 1.0
CA B:CYS200 4.1 9.9 1.0
NE2 B:HIS204 4.1 13.9 1.0
ND1 B:HIS161 4.1 10.8 1.0
CD2 B:HIS204 4.1 10.4 1.0
C B:ILE199 4.1 13.3 1.0
CA B:ILE199 4.2 11.3 1.0
N B:ILE199 4.3 14.6 1.0
SD B:MET207 4.4 22.5 1.0
N B:GLU198 4.4 12.7 1.0
O B:CYS196 4.5 21.6 1.0
C B:CYS196 4.6 16.0 1.0
N B:HIS204 4.6 18.4 1.0
CA B:GLU198 4.6 8.4 1.0
CA B:CYS196 4.7 10.7 1.0
CG B:MET207 4.7 12.8 1.0
CE1 B:HIS161 4.7 7.0 1.0
O B:ILE199 4.9 10.7 1.0
C B:CYS200 4.9 14.9 1.0

Copper binding site 4 out of 6 in 1oco

Go back to Copper Binding Sites List in 1oco
Copper binding site 4 out of 6 in the Bovine Heart Cytochrome C Oxidase in Carbon Monoxide-Bound 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 in Carbon Monoxide-Bound State within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Cu517

b:21.6
occ:1.00
 NE2 N:HIS291 2.0 26.4 1.0
NE2 N:HIS290 2.1 9.5 1.0
ND1 N:HIS240 2.1 18.9 1.0
O N:CMO520 2.6 22.4 1.0
CD2 N:HIS291 2.8 26.9 1.0
CE1 N:HIS290 3.0 11.4 1.0
CE1 N:HIS240 3.1 8.8 1.0
CE1 N:HIS291 3.1 26.9 1.0
CD2 N:HIS290 3.2 13.6 1.0
CG N:HIS240 3.2 16.1 1.0
C N:CMO520 3.4 11.7 1.0
CB N:HIS240 3.5 16.3 1.0
CA N:HIS240 4.0 16.8 1.0
CG N:HIS291 4.0 23.4 1.0
ND1 N:HIS291 4.2 24.9 1.0
ND1 N:HIS290 4.2 11.4 1.0
NE2 N:HIS240 4.2 17.7 1.0
CG N:HIS290 4.3 13.2 1.0
CD2 N:HIS240 4.3 21.2 1.0
CG2 N:VAL243 4.7 24.2 1.0
N N:HIS240 4.8 9.7 1.0
NA N:HEA516 4.9 12.5 1.0

Copper binding site 5 out of 6 in 1oco

Go back to Copper Binding Sites List in 1oco
Copper binding site 5 out of 6 in the Bovine Heart Cytochrome C Oxidase in Carbon Monoxide-Bound 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 in Carbon Monoxide-Bound State within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Cu228

b:31.1
occ:1.00
 ND1 O:HIS161 2.0 16.9 1.0
SG O:CYS196 2.2 17.3 1.0
CU O:CU229 2.3 26.9 1.0
SG O:CYS200 2.4 19.4 1.0
SD O:MET207 2.7 32.6 1.0
CE1 O:HIS161 2.8 22.7 1.0
CE O:MET207 3.0 17.2 1.0
CG O:HIS161 3.2 19.3 1.0
CB O:CYS196 3.4 29.4 1.0
CB O:CYS200 3.5 24.4 1.0
CB O:HIS161 3.7 26.8 1.0
CG O:MET207 3.8 22.9 1.0
O O:GLU198 3.9 29.4 1.0
NE2 O:HIS161 4.1 21.2 1.0
CA O:HIS161 4.1 27.6 1.0
ND1 O:HIS204 4.2 29.8 1.0
CD2 O:HIS161 4.3 17.2 1.0
O O:LEU160 4.6 32.2 1.0
CA O:CYS196 4.7 26.6 1.0
CA O:HIS204 4.7 27.8 1.0
CA O:CYS200 4.8 27.5 1.0
O O:HIS204 4.8 29.2 1.0
CD1 O:TRP104 4.8 25.7 1.0
N O:CYS200 5.0 27.3 1.0

Copper binding site 6 out of 6 in 1oco

Go back to Copper Binding Sites List in 1oco
Copper binding site 6 out of 6 in the Bovine Heart Cytochrome C Oxidase in Carbon Monoxide-Bound 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 in Carbon Monoxide-Bound State within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Cu229

b:26.9
occ:1.00
 ND1 O:HIS204 2.0 29.8 1.0
SG O:CYS200 2.1 19.4 1.0
CU O:CU228 2.3 31.1 1.0
SG O:CYS196 2.4 17.3 1.0
O O:GLU198 2.4 29.4 1.0
CG O:HIS204 2.9 23.5 1.0
CE1 O:HIS204 3.1 26.9 1.0
CB O:CYS200 3.2 24.4 1.0
CB O:HIS204 3.3 24.9 1.0
CA O:HIS204 3.3 27.8 1.0
N O:CYS200 3.4 27.3 1.0
C O:GLU198 3.6 21.9 1.0
CB O:CYS196 3.6 29.4 1.0
O O:HIS204 3.7 29.2 1.0
CA O:CYS200 3.9 27.5 1.0
C O:HIS204 4.0 25.4 1.0
C O:ILE199 4.0 24.3 1.0
CD2 O:HIS204 4.1 17.1 1.0
ND1 O:HIS161 4.1 16.9 1.0
NE2 O:HIS204 4.1 25.3 1.0
CA O:ILE199 4.2 18.1 1.0
N O:ILE199 4.3 21.8 1.0
SD O:MET207 4.4 32.6 1.0
N O:HIS204 4.5 33.8 1.0
N O:GLU198 4.5 23.2 1.0
O O:CYS196 4.6 29.4 1.0
CE1 O:HIS161 4.7 22.7 1.0
CA O:GLU198 4.7 18.2 1.0
C O:CYS196 4.8 29.1 1.0
CG O:MET207 4.8 22.9 1.0
C O:CYS200 4.8 30.3 1.0
O O:ILE199 4.8 26.7 1.0
CA O:CYS196 4.8 26.6 1.0
O O:LEU160 5.0 32.2 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 22:30:24 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy