Atomistry » Copper » PDB 2cj3-2foy » 2dys
Atomistry »
  Copper »
    PDB 2cj3-2foy »
      2dys »

Copper in PDB 2dys: Bovine Heart Cytochrome C Oxidase Modified By Dccd

Enzymatic activity of Bovine Heart Cytochrome C Oxidase Modified By Dccd

All present enzymatic activity of Bovine Heart Cytochrome C Oxidase Modified By Dccd:
1.9.3.1;

Protein crystallography data

The structure of Bovine Heart Cytochrome C Oxidase Modified By Dccd, PDB code: 2dys was solved by K.Shinzawa-Itoh, H.Aoyama, K.Muramoto, T.Kurauchi, T.Mizushima, E.Yamashita, 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 / 2.20
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 184.130, 207.232, 178.242, 90.00, 90.00, 90.00
R / Rfree (%) 19.7 / 24.2

Other elements in 2dys:

The structure of Bovine Heart Cytochrome C Oxidase Modified By Dccd 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 Modified By Dccd (pdb code 2dys). 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 Modified By Dccd, PDB code: 2dys:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6;

Copper binding site 1 out of 6 in 2dys

Go back to Copper Binding Sites List in 2dys
Copper binding site 1 out of 6 in the Bovine Heart Cytochrome C Oxidase Modified By Dccd


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 Modified By Dccd within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu601

b:23.4
occ:1.00
NE2 A:HIS291 1.9 26.6 1.0
ND1 A:HIS240 2.0 36.1 1.0
NE2 A:HIS290 2.0 20.2 1.0
CE1 A:HIS240 2.9 31.7 1.0
CE1 A:HIS291 2.9 26.0 1.0
CE1 A:HIS290 2.9 23.1 1.0
CD2 A:HIS291 3.0 21.5 1.0
CG A:HIS240 3.1 25.7 1.0
CD2 A:HIS290 3.1 11.5 1.0
CB A:HIS240 3.5 21.7 1.0
CA A:HIS240 3.9 17.1 1.0
ND1 A:HIS291 4.1 23.2 1.0
NE2 A:HIS240 4.1 29.1 1.0
CG A:HIS291 4.1 27.8 1.0
ND1 A:HIS290 4.1 16.0 1.0
CD2 A:HIS240 4.2 27.6 1.0
CG A:HIS290 4.2 23.6 1.0
NA A:HEA605 4.4 27.3 1.0
C1A A:HEA605 4.5 18.4 1.0
CG2 A:VAL243 4.5 14.8 1.0
FE A:HEA605 4.6 23.2 1.0
C4A A:HEA605 4.7 27.4 1.0
N A:HIS240 4.8 16.4 1.0
C2A A:HEA605 4.8 26.1 1.0
C3A A:HEA605 4.9 26.0 1.0
CHA A:HEA605 4.9 21.6 1.0
ND A:HEA605 4.9 29.5 1.0
C A:HIS240 5.0 19.2 1.0

Copper binding site 2 out of 6 in 2dys

Go back to Copper Binding Sites List in 2dys
Copper binding site 2 out of 6 in the Bovine Heart Cytochrome C Oxidase Modified By Dccd


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 Modified By Dccd within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu301

b:24.7
occ:1.00
CU1 B:CUA301 0.0 24.7 1.0
ND1 B:HIS161 2.0 18.6 1.0
SG B:CYS196 2.2 21.3 1.0
SG B:CYS200 2.3 22.1 1.0
CU2 B:CUA301 2.6 27.0 1.0
SD B:MET207 2.7 26.3 1.0
CE1 B:HIS161 2.9 12.4 1.0
CE B:MET207 3.1 19.7 1.0
CG B:HIS161 3.2 12.3 1.0
CB B:CYS196 3.3 19.7 1.0
CB B:CYS200 3.3 24.0 1.0
CG B:MET207 3.7 25.6 1.0
CB B:HIS161 3.7 18.0 1.0
O B:GLU198 4.0 32.3 1.0
NE2 B:HIS161 4.1 9.5 1.0
CA B:HIS161 4.2 18.0 1.0
CD2 B:HIS161 4.3 13.6 1.0
ND1 B:HIS204 4.5 26.9 1.0
O B:LEU160 4.6 20.5 1.0
CA B:HIS204 4.7 24.6 1.0
CD1 B:TRP104 4.7 26.6 1.0
CA B:CYS196 4.7 24.0 1.0
O B:HIS102 4.7 18.5 1.0
CA B:CYS200 4.7 22.6 1.0
O B:HIS204 4.9 26.4 1.0
N B:CYS200 5.0 20.7 1.0
CZ2 B:TRP106 5.0 24.2 1.0

Copper binding site 3 out of 6 in 2dys

Go back to Copper Binding Sites List in 2dys
Copper binding site 3 out of 6 in the Bovine Heart Cytochrome C Oxidase Modified By Dccd


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 Modified By Dccd within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu301

b:27.0
occ:1.00
CU2 B:CUA301 0.0 27.0 1.0
ND1 B:HIS204 1.9 26.9 1.0
SG B:CYS200 2.2 22.1 1.0
SG B:CYS196 2.3 21.3 1.0
O B:GLU198 2.4 32.3 1.0
CU1 B:CUA301 2.6 24.7 1.0
CE1 B:HIS204 2.9 23.2 1.0
CG B:HIS204 3.0 20.5 1.0
CB B:CYS196 3.3 19.7 1.0
CB B:HIS204 3.3 21.8 1.0
CA B:HIS204 3.4 24.6 1.0
CB B:CYS200 3.5 24.0 1.0
C B:GLU198 3.5 26.4 1.0
O B:HIS204 3.6 26.4 1.0
N B:CYS200 3.6 20.7 1.0
C B:HIS204 3.9 22.2 1.0
NE2 B:HIS204 4.1 25.7 1.0
CD2 B:HIS204 4.1 22.3 1.0
O B:CYS196 4.1 20.9 1.0
C B:ILE199 4.1 24.7 1.0
N B:GLU198 4.1 23.2 1.0
CA B:ILE199 4.2 21.1 1.0
CA B:CYS200 4.2 22.6 1.0
N B:ILE199 4.2 24.3 1.0
C B:CYS196 4.2 24.2 1.0
ND1 B:HIS161 4.3 18.6 1.0
CA B:CYS196 4.4 24.0 1.0
CA B:GLU198 4.5 23.5 1.0
SD B:MET207 4.6 26.3 1.0
N B:HIS204 4.7 29.6 1.0
CG B:MET207 4.8 25.6 1.0
N B:SER197 4.8 21.6 1.0
O B:ILE199 5.0 22.9 1.0

Copper binding site 4 out of 6 in 2dys

Go back to Copper Binding Sites List in 2dys
Copper binding site 4 out of 6 in the Bovine Heart Cytochrome C Oxidase Modified By Dccd


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 Modified By Dccd within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Cu601

b:28.9
occ:1.00
NE2 N:HIS291 2.0 34.7 1.0
NE2 N:HIS290 2.0 18.9 1.0
ND1 N:HIS240 2.0 30.4 1.0
CE1 N:HIS290 2.9 26.4 1.0
CE1 N:HIS240 2.9 26.9 1.0
CE1 N:HIS291 2.9 34.1 1.0
CD2 N:HIS291 3.0 33.1 1.0
CG N:HIS240 3.1 33.8 1.0
CD2 N:HIS290 3.2 26.5 1.0
CB N:HIS240 3.5 30.5 1.0
CA N:HIS240 3.9 26.7 1.0
ND1 N:HIS291 4.1 31.6 1.0
NE2 N:HIS240 4.1 32.6 1.0
ND1 N:HIS290 4.1 23.5 1.0
CG N:HIS291 4.2 30.0 1.0
CD2 N:HIS240 4.2 29.2 1.0
CG N:HIS290 4.3 25.1 1.0
NA N:HEA605 4.4 30.9 1.0
CG2 N:VAL243 4.5 22.5 1.0
C1A N:HEA605 4.5 29.3 1.0
FE N:HEA605 4.6 27.0 1.0
C4A N:HEA605 4.6 28.0 1.0
N N:HIS240 4.8 25.3 1.0
C2A N:HEA605 4.8 28.1 1.0
ND N:HEA605 4.8 27.5 1.0
CHA N:HEA605 4.9 28.6 1.0
C3A N:HEA605 4.9 25.4 1.0
C4D N:HEA605 5.0 26.6 1.0
C N:HIS240 5.0 27.2 1.0

Copper binding site 5 out of 6 in 2dys

Go back to Copper Binding Sites List in 2dys
Copper binding site 5 out of 6 in the Bovine Heart Cytochrome C Oxidase Modified By Dccd


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 Modified By Dccd within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Cu301

b:36.8
occ:1.00
CU1 O:CUA301 0.0 36.8 1.0
ND1 O:HIS161 2.0 30.7 1.0
SG O:CYS196 2.3 26.5 1.0
SG O:CYS200 2.3 29.8 1.0
CU2 O:CUA301 2.3 36.2 1.0
CE1 O:HIS161 2.7 28.1 1.0
SD O:MET207 2.8 38.7 1.0
CE O:MET207 3.0 19.2 1.0
CG O:HIS161 3.2 24.0 1.0
CB O:CYS196 3.2 29.0 1.0
CB O:CYS200 3.3 40.0 1.0
CB O:HIS161 3.8 27.2 1.0
CG O:MET207 3.8 33.3 1.0
O O:GLU198 3.9 35.3 1.0
NE2 O:HIS161 4.0 16.9 1.0
CA O:HIS161 4.2 30.3 1.0
CD2 O:HIS161 4.2 21.9 1.0
ND1 O:HIS204 4.3 38.0 1.0
CA O:HIS204 4.6 34.7 1.0
CA O:CYS196 4.6 32.1 1.0
O O:LEU160 4.6 28.9 1.0
CD1 O:TRP104 4.7 33.5 1.0
CA O:CYS200 4.7 38.2 1.0
O O:HIS204 4.8 31.2 1.0
N O:CYS200 4.8 38.3 1.0
CZ2 O:TRP106 5.0 46.1 1.0
O O:HIS102 5.0 25.9 1.0

Copper binding site 6 out of 6 in 2dys

Go back to Copper Binding Sites List in 2dys
Copper binding site 6 out of 6 in the Bovine Heart Cytochrome C Oxidase Modified By Dccd


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 Modified By Dccd within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Cu301

b:36.2
occ:1.00
CU2 O:CUA301 0.0 36.2 1.0
ND1 O:HIS204 2.0 38.0 1.0
SG O:CYS196 2.3 26.5 1.0
SG O:CYS200 2.3 29.8 1.0
CU1 O:CUA301 2.3 36.8 1.0
O O:GLU198 2.4 35.3 1.0
CE1 O:HIS204 3.0 39.4 1.0
CG O:HIS204 3.0 36.5 1.0
CB O:CYS196 3.3 29.0 1.0
CB O:CYS200 3.4 40.0 1.0
CB O:HIS204 3.4 37.3 1.0
C O:GLU198 3.5 26.4 1.0
CA O:HIS204 3.5 34.7 1.0
N O:CYS200 3.6 38.3 1.0
O O:HIS204 3.8 31.2 1.0
ND1 O:HIS161 4.0 30.7 1.0
N O:GLU198 4.1 29.6 1.0
C O:ILE199 4.1 34.2 1.0
NE2 O:HIS204 4.1 36.7 1.0
C O:HIS204 4.1 30.9 1.0
CA O:CYS200 4.1 38.2 1.0
O O:CYS196 4.1 31.8 1.0
CD2 O:HIS204 4.2 30.8 1.0
CA O:ILE199 4.2 28.3 1.0
N O:ILE199 4.2 23.1 1.0
C O:CYS196 4.3 32.7 1.0
CA O:CYS196 4.4 32.1 1.0
CA O:GLU198 4.4 27.2 1.0
SD O:MET207 4.5 38.7 1.0
CE1 O:HIS161 4.7 28.1 1.0
CG O:MET207 4.8 33.3 1.0
N O:HIS204 4.8 36.1 1.0
N O:SER197 4.8 32.6 1.0
CA O:HIS161 4.9 30.3 1.0
O O:ILE199 5.0 31.2 1.0
CG O:HIS161 5.0 24.0 1.0
O O:LEU160 5.0 28.9 1.0

Reference:

K.Shinzawa-Itoh, H.Aoyama, K.Muramoto, H.Terada, T.Kurauchi, Y.Tadehara, A.Yamasaki, T.Sugimura, S.Kurono, K.Tsujimoto, T.Mizushima, E.Yamashita, T.Tsukihara, S.Yoshikawa. Structures and Physiological Roles of 13 Integral Lipids of Bovine Heart Cytochrome C Oxidase Embo J. V. 26 1713 2007.
ISSN: ISSN 0261-4189
PubMed: 17332748
DOI: 10.1038/SJ.EMBOJ.7601618
Page generated: Sun Dec 13 11:04:16 2020

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy