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Copper in PDB 3ag1: Bovine Heart Cytochrome C Oxidase in the Carbon Monoxide-Bound Fully Reduced State at 280 K

Enzymatic activity of Bovine Heart Cytochrome C Oxidase in the Carbon Monoxide-Bound Fully Reduced State at 280 K

All present enzymatic activity of Bovine Heart Cytochrome C Oxidase in the Carbon Monoxide-Bound Fully Reduced State at 280 K:
1.9.3.1;

Protein crystallography data

The structure of Bovine Heart Cytochrome C Oxidase in the Carbon Monoxide-Bound Fully Reduced State at 280 K, PDB code: 3ag1 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 / 2.20
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 189.493, 210.887, 178.301, 90.00, 90.00, 90.00
R / Rfree (%) 16.2 / 19.2

Other elements in 3ag1:

The structure of Bovine Heart Cytochrome C Oxidase in the Carbon Monoxide-Bound Fully Reduced State at 280 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 Carbon Monoxide-Bound Fully Reduced State at 280 K (pdb code 3ag1). 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 Carbon Monoxide-Bound Fully Reduced State at 280 K, PDB code: 3ag1:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6;

Copper binding site 1 out of 6 in 3ag1

Go back to Copper Binding Sites List in 3ag1
Copper binding site 1 out of 6 in the Bovine Heart Cytochrome C Oxidase in the Carbon Monoxide-Bound Fully Reduced State at 280 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 Carbon Monoxide-Bound Fully Reduced State at 280 K within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu517

b:40.1
occ:1.00
 NE2 A:HIS291 2.0 38.8 1.0
ND1 A:HIS240 2.0 38.4 1.0
NE2 A:HIS290 2.1 39.6 1.0
O A:CMO520 2.7 41.8 1.0
CD2 A:HIS291 2.8 33.6 1.0
CG A:HIS240 3.0 35.9 1.0
CE1 A:HIS240 3.0 34.4 1.0
CE1 A:HIS291 3.1 44.4 1.0
CD2 A:HIS290 3.1 44.3 1.0
CE1 A:HIS290 3.1 43.1 1.0
CB A:HIS240 3.3 37.1 1.0
C A:CMO520 3.6 39.6 1.0
CA A:HIS240 3.9 35.8 1.0
CG A:HIS291 4.0 36.5 1.0
ND1 A:HIS291 4.1 42.2 1.0
CD2 A:HIS240 4.1 33.1 1.0
NE2 A:HIS240 4.1 42.9 1.0
ND1 A:HIS290 4.2 38.8 1.0
CG A:HIS290 4.2 41.9 1.0
N A:HIS240 4.7 36.5 1.0
CG2 A:VAL243 4.8 34.2 1.0
CG2 A:VAL287 4.9 35.8 1.0
CA A:TRP288 4.9 38.4 1.0
NA A:HEA516 5.0 40.6 1.0
O A:VAL287 5.0 40.2 1.0

Copper binding site 2 out of 6 in 3ag1

Go back to Copper Binding Sites List in 3ag1
Copper binding site 2 out of 6 in the Bovine Heart Cytochrome C Oxidase in the Carbon Monoxide-Bound Fully Reduced State at 280 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 Carbon Monoxide-Bound Fully Reduced State at 280 K within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu228

b:42.4
occ:1.00
 CU1 B:CUA228 0.0 42.4 1.0
ND1 B:HIS161 2.0 39.0 1.0
SG B:CYS196 2.3 40.1 1.0
SG B:CYS200 2.4 39.5 1.0
SD B:MET207 2.4 42.6 1.0
CU2 B:CUA228 2.6 41.4 1.0
CE1 B:HIS161 2.8 29.5 1.0
CE B:MET207 3.2 29.6 1.0
CG B:HIS161 3.2 32.9 1.0
CB B:CYS200 3.3 37.9 1.0
CB B:CYS196 3.4 38.6 1.0
CG B:MET207 3.5 39.4 1.0
CB B:HIS161 3.7 38.8 1.0
O B:GLU198 3.9 41.1 1.0
NE2 B:HIS161 4.0 37.8 1.0
CA B:HIS161 4.1 36.9 1.0
CD2 B:HIS161 4.2 32.7 1.0
CD1 B:TRP104 4.4 44.7 1.0
ND1 B:HIS204 4.5 40.2 1.0
O B:LEU160 4.7 38.2 1.0
CA B:CYS200 4.8 39.5 1.0
O B:HIS102 4.8 40.4 1.0
CA B:CYS196 4.8 38.3 1.0
CA B:HIS204 4.9 41.9 1.0
CB B:MET207 4.9 38.3 1.0

Copper binding site 3 out of 6 in 3ag1

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Copper binding site 3 out of 6 in the Bovine Heart Cytochrome C Oxidase in the Carbon Monoxide-Bound Fully Reduced State at 280 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 Carbon Monoxide-Bound Fully Reduced State at 280 K within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu228

b:41.4
occ:1.00
 CU2 B:CUA228 0.0 41.4 1.0
ND1 B:HIS204 2.0 40.2 1.0
SG B:CYS196 2.3 40.1 1.0
SG B:CYS200 2.3 39.5 1.0
O B:GLU198 2.3 41.1 1.0
CU1 B:CUA228 2.6 42.4 1.0
CE1 B:HIS204 2.8 43.3 1.0
CG B:HIS204 3.1 42.3 1.0
CB B:CYS196 3.2 38.6 1.0
C B:GLU198 3.5 39.5 1.0
CB B:CYS200 3.5 37.9 1.0
CB B:HIS204 3.6 42.4 1.0
CA B:HIS204 3.6 41.9 1.0
N B:CYS200 3.7 37.4 1.0
O B:HIS204 3.8 39.9 1.0
NE2 B:HIS204 4.0 44.8 1.0
N B:GLU198 4.1 40.1 1.0
CD2 B:HIS204 4.1 38.3 1.0
CA B:ILE199 4.2 40.3 1.0
C B:HIS204 4.2 41.8 1.0
C B:ILE199 4.2 40.2 1.0
N B:ILE199 4.2 40.2 1.0
ND1 B:HIS161 4.2 39.0 1.0
CA B:CYS200 4.2 39.5 1.0
C B:CYS196 4.3 38.5 1.0
O B:CYS196 4.3 38.0 1.0
CA B:CYS196 4.4 38.3 1.0
SD B:MET207 4.4 42.6 1.0
CA B:GLU198 4.5 38.9 1.0
CG B:MET207 4.6 39.4 1.0
N B:SER197 4.6 38.9 1.0
N B:HIS204 4.8 43.7 1.0
CA B:HIS161 4.9 36.9 1.0
CE1 B:HIS161 5.0 29.5 1.0

Copper binding site 4 out of 6 in 3ag1

Go back to Copper Binding Sites List in 3ag1
Copper binding site 4 out of 6 in the Bovine Heart Cytochrome C Oxidase in the Carbon Monoxide-Bound Fully Reduced State at 280 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 Carbon Monoxide-Bound Fully Reduced State at 280 K within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Cu517

b:49.0
occ:1.00
 NE2 N:HIS291 2.0 53.6 1.0
ND1 N:HIS240 2.0 47.4 1.0
NE2 N:HIS290 2.1 47.7 1.0
O N:CMO520 2.8 48.4 1.0
CE1 N:HIS291 2.9 48.5 1.0
CD2 N:HIS291 3.0 49.7 1.0
CG N:HIS240 3.0 46.4 1.0
CE1 N:HIS240 3.1 45.5 1.0
CE1 N:HIS290 3.1 46.3 1.0
CD2 N:HIS290 3.2 49.1 1.0
CB N:HIS240 3.2 44.8 1.0
C N:CMO520 3.7 47.9 1.0
CA N:HIS240 3.9 47.2 1.0
ND1 N:HIS291 4.0 44.4 1.0
CG N:HIS291 4.1 50.7 1.0
CD2 N:HIS240 4.1 44.7 1.0
NE2 N:HIS240 4.2 50.7 1.0
ND1 N:HIS290 4.2 46.1 1.0
CG N:HIS290 4.3 49.5 1.0
N N:HIS240 4.7 48.6 1.0
CG2 N:VAL243 4.8 46.1 1.0
NA N:HEA516 4.9 46.7 1.0
CG2 N:VAL287 4.9 44.9 1.0
C1A N:HEA516 5.0 50.5 1.0
O N:VAL287 5.0 49.9 1.0

Copper binding site 5 out of 6 in 3ag1

Go back to Copper Binding Sites List in 3ag1
Copper binding site 5 out of 6 in the Bovine Heart Cytochrome C Oxidase in the Carbon Monoxide-Bound Fully Reduced State at 280 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 Carbon Monoxide-Bound Fully Reduced State at 280 K within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Cu228

b:54.3
occ:1.00
 CU1 O:CUA228 0.0 54.3 1.0
ND1 O:HIS161 2.0 46.7 1.0
SG O:CYS196 2.3 50.7 1.0
SD O:MET207 2.3 57.3 1.0
SG O:CYS200 2.3 50.2 1.0
CU2 O:CUA228 2.6 52.2 1.0
CE1 O:HIS161 2.9 48.3 1.0
CG O:HIS161 3.1 49.5 1.0
CE O:MET207 3.2 47.9 1.0
CB O:CYS200 3.3 51.4 1.0
CB O:CYS196 3.4 51.9 1.0
CG O:MET207 3.5 52.9 1.0
CB O:HIS161 3.5 47.7 1.0
O O:GLU198 3.9 55.3 1.0
CA O:HIS161 4.0 50.6 1.0
NE2 O:HIS161 4.1 50.2 1.0
CD2 O:HIS161 4.2 47.9 1.0
ND1 O:HIS204 4.6 53.5 1.0
CD1 O:TRP104 4.6 55.0 1.0
CA O:CYS200 4.7 50.7 1.0
CB O:MET207 4.8 53.4 1.0
O O:HIS102 4.8 47.1 1.0
O O:LEU160 4.8 48.7 1.0
CA O:CYS196 4.8 52.3 1.0
CA O:HIS204 4.9 53.5 1.0
CZ2 O:TRP106 4.9 57.4 1.0
N O:CYS200 5.0 52.2 1.0

Copper binding site 6 out of 6 in 3ag1

Go back to Copper Binding Sites List in 3ag1
Copper binding site 6 out of 6 in the Bovine Heart Cytochrome C Oxidase in the Carbon Monoxide-Bound Fully Reduced State at 280 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 Carbon Monoxide-Bound Fully Reduced State at 280 K within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Cu228

b:52.2
occ:1.00
 CU2 O:CUA228 0.0 52.2 1.0
ND1 O:HIS204 2.0 53.5 1.0
O O:GLU198 2.2 55.3 1.0
SG O:CYS200 2.3 50.2 1.0
SG O:CYS196 2.3 50.7 1.0
CU1 O:CUA228 2.6 54.3 1.0
CE1 O:HIS204 2.8 49.5 1.0
CG O:HIS204 3.1 52.1 1.0
CB O:CYS196 3.2 51.9 1.0
CB O:CYS200 3.4 51.4 1.0
C O:GLU198 3.4 51.2 1.0
CA O:HIS204 3.5 53.5 1.0
CB O:HIS204 3.6 52.0 1.0
N O:CYS200 3.7 52.2 1.0
O O:HIS204 3.7 55.2 1.0
NE2 O:HIS204 4.0 52.8 1.0
C O:HIS204 4.1 53.7 1.0
CD2 O:HIS204 4.1 52.0 1.0
N O:GLU198 4.1 51.6 1.0
C O:CYS196 4.2 52.5 1.0
O O:CYS196 4.2 50.2 1.0
CA O:CYS200 4.2 50.7 1.0
SD O:MET207 4.2 57.3 1.0
CA O:ILE199 4.3 51.4 1.0
N O:ILE199 4.3 51.6 1.0
ND1 O:HIS161 4.3 46.7 1.0
CA O:CYS196 4.3 52.3 1.0
C O:ILE199 4.3 51.9 1.0
CA O:GLU198 4.5 51.0 1.0
CG O:MET207 4.5 52.9 1.0
N O:SER197 4.6 52.5 1.0
N O:HIS204 4.8 54.5 1.0
CA O:HIS161 4.9 50.6 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: Sun Dec 13 11:08:45 2020

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