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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

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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

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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

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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

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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

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