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Copper in PDB 3ag4: Bovine Heart Cytochrome C Oxidase in the Cyanide Ion-Bound Fully Reduced State at 100 K

Enzymatic activity of Bovine Heart Cytochrome C Oxidase in the Cyanide Ion-Bound Fully Reduced State at 100 K

All present enzymatic activity of Bovine Heart Cytochrome C Oxidase in the Cyanide Ion-Bound Fully Reduced State at 100 K:
1.9.3.1;

Protein crystallography data

The structure of Bovine Heart Cytochrome C Oxidase in the Cyanide Ion-Bound Fully Reduced State at 100 K, PDB code: 3ag4 was solved by K.Muramoto, K.Ohta, K.Shinzawa-Itoh, K.Kanda, M.Taniguchi, H.Nabekura, 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 / 2.05
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 183.364, 206.648, 178.137, 90.00, 90.00, 90.00
R / Rfree (%) 18.6 / 21.9

Other elements in 3ag4:

The structure of Bovine Heart Cytochrome C Oxidase in the Cyanide Ion-Bound Fully Reduced State at 100 K 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 the Cyanide Ion-Bound Fully Reduced State at 100 K (pdb code 3ag4). 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 the Cyanide Ion-Bound Fully Reduced State at 100 K, PDB code: 3ag4:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6;

Copper binding site 1 out of 6 in 3ag4

Go back to Copper Binding Sites List in 3ag4
Copper binding site 1 out of 6 in the Bovine Heart Cytochrome C Oxidase in the Cyanide Ion-Bound Fully Reduced State at 100 K


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 the Cyanide Ion-Bound Fully Reduced State at 100 K within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu517

b:31.0
occ:1.00
 ND1 A:HIS240 2.0 33.7 1.0
NE2 A:HIS291 2.0 34.0 1.0
N A:CYN520 2.3 31.4 1.0
NE2 A:HIS290 2.8 36.2 1.0
C A:CYN520 2.9 31.3 1.0
CE1 A:HIS240 2.9 25.0 1.0
CE1 A:HIS291 3.0 27.5 1.0
CG A:HIS240 3.0 27.9 1.0
CD2 A:HIS291 3.0 28.4 1.0
CB A:HIS240 3.4 25.4 1.0
CE1 A:HIS290 3.7 31.7 1.0
CD2 A:HIS290 3.7 36.8 1.0
CA A:HIS240 3.8 23.6 1.0
NE2 A:HIS240 4.0 27.1 1.0
CD2 A:HIS240 4.1 27.3 1.0
ND1 A:HIS291 4.1 28.3 1.0
CG A:HIS291 4.2 30.4 1.0
CG2 A:VAL243 4.4 27.0 1.0
N A:HIS240 4.7 24.3 1.0
O A:HOH4310 4.7 38.4 1.0
ND1 A:HIS290 4.8 35.5 1.0
CG A:HIS290 4.9 32.7 1.0
C A:HIS240 4.9 25.6 1.0
ND A:HEA516 4.9 27.7 1.0
C1A A:HEA516 4.9 29.1 1.0
O A:HIS240 4.9 27.0 1.0
NA A:HEA516 4.9 30.2 1.0
FE A:HEA516 5.0 35.5 1.0
CZ3 A:TRP236 5.0 29.3 1.0

Copper binding site 2 out of 6 in 3ag4

Go back to Copper Binding Sites List in 3ag4
Copper binding site 2 out of 6 in the Bovine Heart Cytochrome C Oxidase in the Cyanide Ion-Bound Fully Reduced State at 100 K


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 the Cyanide Ion-Bound Fully Reduced State at 100 K within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu228

b:28.4
occ:1.00
 CU1 B:CUA228 0.0 28.4 1.0
ND1 B:HIS161 2.0 19.6 1.0
SD B:MET207 2.4 29.0 1.0
SG B:CYS200 2.4 29.1 1.0
SG B:CYS196 2.4 27.6 1.0
CU2 B:CUA228 2.5 28.8 1.0
CE1 B:HIS161 2.9 24.8 1.0
CE B:MET207 3.0 20.4 1.0
CG B:HIS161 3.1 24.5 1.0
CB B:CYS200 3.3 28.6 1.0
CB B:CYS196 3.5 24.7 1.0
CG B:MET207 3.5 26.4 1.0
CB B:HIS161 3.6 25.2 1.0
O B:GLU198 4.0 32.0 1.0
NE2 B:HIS161 4.0 23.2 1.0
CD2 B:HIS161 4.2 22.4 1.0
CA B:HIS161 4.2 25.5 1.0
ND1 B:HIS204 4.5 28.6 1.0
CD1 B:TRP104 4.5 25.6 1.0
O B:HIS102 4.6 26.8 1.0
CA B:HIS204 4.7 28.0 1.0
O B:LEU160 4.8 26.1 1.0
CA B:CYS200 4.8 27.9 1.0
CB B:MET207 4.8 27.5 1.0
CA B:CYS196 4.9 27.1 1.0
O B:HIS204 5.0 26.6 1.0
CZ2 B:TRP106 5.0 27.3 1.0

Copper binding site 3 out of 6 in 3ag4

Go back to Copper Binding Sites List in 3ag4
Copper binding site 3 out of 6 in the Bovine Heart Cytochrome C Oxidase in the Cyanide Ion-Bound Fully Reduced State at 100 K


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 the Cyanide Ion-Bound Fully Reduced State at 100 K within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu228

b:28.8
occ:1.00
 CU2 B:CUA228 0.0 28.8 1.0
ND1 B:HIS204 2.0 28.6 1.0
SG B:CYS196 2.3 27.6 1.0
SG B:CYS200 2.3 29.1 1.0
O B:GLU198 2.3 32.0 1.0
CU1 B:CUA228 2.5 28.4 1.0
CE1 B:HIS204 2.9 26.7 1.0
CG B:HIS204 3.2 28.1 1.0
CB B:CYS196 3.3 24.7 1.0
CA B:HIS204 3.5 28.0 1.0
CB B:CYS200 3.5 28.6 1.0
C B:GLU198 3.6 29.9 1.0
CB B:HIS204 3.6 26.3 1.0
N B:CYS200 3.7 26.9 1.0
O B:HIS204 3.8 26.6 1.0
NE2 B:HIS204 4.0 30.2 1.0
C B:HIS204 4.1 26.8 1.0
ND1 B:HIS161 4.1 19.6 1.0
C B:CYS196 4.2 27.0 1.0
CD2 B:HIS204 4.2 23.7 1.0
N B:GLU198 4.2 25.6 1.0
O B:CYS196 4.2 24.8 1.0
CA B:CYS200 4.3 27.9 1.0
CA B:ILE199 4.3 28.9 1.0
C B:ILE199 4.3 27.9 1.0
N B:ILE199 4.4 30.2 1.0
SD B:MET207 4.4 29.0 1.0
CA B:CYS196 4.4 27.1 1.0
N B:SER197 4.6 25.4 1.0
CA B:GLU198 4.6 26.9 1.0
CG B:MET207 4.7 26.4 1.0
N B:HIS204 4.7 30.4 1.0
CA B:HIS161 4.8 25.5 1.0
CG B:HIS161 5.0 24.5 1.0
CE1 B:HIS161 5.0 24.8 1.0
CB B:HIS161 5.0 25.2 1.0

Copper binding site 4 out of 6 in 3ag4

Go back to Copper Binding Sites List in 3ag4
Copper binding site 4 out of 6 in the Bovine Heart Cytochrome C Oxidase in the Cyanide Ion-Bound Fully Reduced State at 100 K


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 the Cyanide Ion-Bound Fully Reduced State at 100 K within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Cu517

b:37.5
occ:1.00
 ND1 N:HIS240 2.0 34.6 1.0
NE2 N:HIS291 2.0 40.0 1.0
N N:CYN520 2.4 42.3 1.0
NE2 N:HIS290 2.6 46.6 1.0
CE1 N:HIS291 2.9 28.6 1.0
CE1 N:HIS240 3.0 28.8 1.0
C N:CYN520 3.0 43.2 1.0
CG N:HIS240 3.0 37.2 1.0
CD2 N:HIS291 3.1 35.3 1.0
CB N:HIS240 3.3 34.7 1.0
CE1 N:HIS290 3.5 41.3 1.0
CD2 N:HIS290 3.7 41.0 1.0
CA N:HIS240 3.8 34.5 1.0
ND1 N:HIS291 4.0 35.1 1.0
NE2 N:HIS240 4.1 32.7 1.0
CD2 N:HIS240 4.1 32.4 1.0
CG N:HIS291 4.1 38.2 1.0
CG2 N:VAL243 4.4 32.4 1.0
N N:HIS240 4.6 30.7 1.0
ND1 N:HIS290 4.7 41.4 1.0
CG1 N:VAL243 4.8 37.1 1.0
CG N:HIS290 4.8 41.6 1.0
O N:HOH4406 4.8 40.0 1.0
C N:HIS240 4.9 34.3 1.0
CG2 N:VAL287 4.9 29.4 1.0
NA N:HEA516 4.9 40.0 1.0
O N:HIS240 4.9 33.8 1.0
C1A N:HEA516 5.0 34.0 1.0
ND N:HEA516 5.0 37.1 1.0

Copper binding site 5 out of 6 in 3ag4

Go back to Copper Binding Sites List in 3ag4
Copper binding site 5 out of 6 in the Bovine Heart Cytochrome C Oxidase in the Cyanide Ion-Bound Fully Reduced State at 100 K


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 the Cyanide Ion-Bound Fully Reduced State at 100 K within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Cu228

b:37.1
occ:1.00
 CU1 O:CUA228 0.0 37.1 1.0
ND1 O:HIS161 2.0 29.0 1.0
SG O:CYS196 2.3 35.6 1.0
SG O:CYS200 2.4 36.2 1.0
SD O:MET207 2.4 37.9 1.0
CU2 O:CUA228 2.6 36.7 1.0
CE1 O:HIS161 2.8 34.0 1.0
CE O:MET207 3.0 23.3 1.0
CG O:HIS161 3.1 31.9 1.0
CB O:CYS200 3.3 36.8 1.0
CB O:CYS196 3.4 37.1 1.0
CG O:MET207 3.5 35.0 1.0
CB O:HIS161 3.6 31.6 1.0
NE2 O:HIS161 4.0 33.2 1.0
O O:GLU198 4.0 35.8 1.0
CD2 O:HIS161 4.2 34.0 1.0
CA O:HIS161 4.3 34.5 1.0
CD1 O:TRP104 4.3 35.7 1.0
ND1 O:HIS204 4.6 37.3 1.0
O O:HIS102 4.7 31.6 1.0
CA O:CYS200 4.7 36.2 1.0
O O:LEU160 4.7 31.0 1.0
CA O:HIS204 4.8 37.5 1.0
CA O:CYS196 4.8 37.7 1.0
CB O:MET207 4.9 34.8 1.0

Copper binding site 6 out of 6 in 3ag4

Go back to Copper Binding Sites List in 3ag4
Copper binding site 6 out of 6 in the Bovine Heart Cytochrome C Oxidase in the Cyanide Ion-Bound Fully Reduced State at 100 K


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 the Cyanide Ion-Bound Fully Reduced State at 100 K within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Cu228

b:36.7
occ:1.00
 CU2 O:CUA228 0.0 36.7 1.0
ND1 O:HIS204 2.0 37.3 1.0
O O:GLU198 2.2 35.8 1.0
SG O:CYS196 2.3 35.6 1.0
SG O:CYS200 2.3 36.2 1.0
CU1 O:CUA228 2.6 37.1 1.0
CE1 O:HIS204 2.9 37.4 1.0
CG O:HIS204 3.1 36.0 1.0
CB O:CYS196 3.3 37.1 1.0
CB O:CYS200 3.4 36.8 1.0
C O:GLU198 3.4 35.9 1.0
CB O:HIS204 3.5 35.2 1.0
CA O:HIS204 3.5 37.5 1.0
N O:CYS200 3.7 37.6 1.0
O O:HIS204 3.9 38.5 1.0
NE2 O:HIS204 4.1 37.0 1.0
ND1 O:HIS161 4.1 29.0 1.0
CA O:CYS200 4.1 36.2 1.0
C O:HIS204 4.2 36.6 1.0
CD2 O:HIS204 4.2 32.1 1.0
O O:CYS196 4.2 34.1 1.0
N O:GLU198 4.2 36.2 1.0
C O:CYS196 4.2 37.9 1.0
N O:ILE199 4.3 34.9 1.0
CA O:ILE199 4.3 35.1 1.0
C O:ILE199 4.3 37.0 1.0
CA O:CYS196 4.4 37.7 1.0
CA O:GLU198 4.4 34.9 1.0
SD O:MET207 4.4 37.9 1.0
N O:HIS204 4.7 37.8 1.0
N O:SER197 4.7 38.8 1.0
CG O:MET207 4.8 35.0 1.0
CA O:HIS161 4.9 34.5 1.0
CE1 O:HIS161 4.9 34.0 1.0
CB O:HIS161 5.0 31.6 1.0

Reference:

K.Muramoto, K.Ohta, K.Shinzawa-Itoh, K.Kanda, M.Taniguchi, H.Nabekura, E.Yamashita, T.Tsukihara, S.Yoshikawa. Bovine Cytochrome C Oxidase Structures Enable O2 Reduction with Minimization of Reactive Oxygens and Provide A Proton-Pumping Gate Proc.Natl.Acad.Sci.Usa V. 107 7740 2010.
ISSN: ISSN 0027-8424
PubMed: 20385840
DOI: 10.1073/PNAS.0910410107
Page generated: Wed Jul 31 00:36:47 2024

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