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Copper in PDB 3aso: Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State Measured at 0.9 Angstrom Wavelength

Enzymatic activity of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State Measured at 0.9 Angstrom Wavelength

All present enzymatic activity of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State Measured at 0.9 Angstrom Wavelength:
1.9.3.1;

Protein crystallography data

The structure of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State Measured at 0.9 Angstrom Wavelength, PDB code: 3aso was solved by M.Suga, N.Yano, K.Muramoto, K.Shinzawa-Itoh, T.Maeda, 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) 15.00 / 2.30
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 181.874, 204.106, 177.874, 90.00, 90.00, 90.00
R / Rfree (%) 16.9 / 20.5

Other elements in 3aso:

The structure of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State Measured at 0.9 Angstrom Wavelength also contains other interesting chemical elements:

Zinc (Zn) 2 atoms
Magnesium (Mg) 2 atoms
Sodium (Na) 2 atoms
Iron (Fe) 4 atoms

Copper Binding Sites:

The binding sites of Copper atom in the Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State Measured at 0.9 Angstrom Wavelength (pdb code 3aso). 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 Fully Oxidized State Measured at 0.9 Angstrom Wavelength, PDB code: 3aso:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6;

Copper binding site 1 out of 6 in 3aso

Go back to Copper Binding Sites List in 3aso
Copper binding site 1 out of 6 in the Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State Measured at 0.9 Angstrom Wavelength


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 Fully Oxidized State Measured at 0.9 Angstrom Wavelength within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu517

b:20.8
occ:1.00
 NE2 A:HIS291 1.9 18.9 1.0
NE2 A:HIS290 2.0 22.4 1.0
ND1 A:HIS240 2.1 15.0 1.0
CD2 A:HIS291 2.9 16.9 1.0
CE1 A:HIS290 2.9 19.3 1.0
CE1 A:HIS291 3.0 18.5 1.0
CG A:HIS240 3.0 17.9 1.0
CE1 A:HIS240 3.1 14.7 1.0
CD2 A:HIS290 3.1 19.4 1.0
CB A:HIS240 3.3 16.7 1.0
CA A:HIS240 3.8 17.1 1.0
CG A:HIS291 4.0 18.4 1.0
ND1 A:HIS291 4.0 15.2 1.0
ND1 A:HIS290 4.1 19.1 1.0
CD2 A:HIS240 4.2 15.5 1.0
NE2 A:HIS240 4.2 20.5 1.0
CG A:HIS290 4.2 17.1 1.0
C1A A:HEA516 4.6 15.5 1.0
NA A:HEA516 4.7 18.1 1.0
N A:HIS240 4.7 16.9 1.0
CG2 A:VAL243 4.8 15.1 1.0
C4A A:HEA516 4.8 20.1 1.0
C2A A:HEA516 4.9 19.1 1.0
FE A:HEA516 4.9 19.8 1.0
CHA A:HEA516 5.0 11.6 1.0
C A:HIS240 5.0 18.0 1.0
C3A A:HEA516 5.0 18.7 1.0

Copper binding site 2 out of 6 in 3aso

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Copper binding site 2 out of 6 in the Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State Measured at 0.9 Angstrom Wavelength


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 Fully Oxidized State Measured at 0.9 Angstrom Wavelength within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu228

b:18.9
occ:1.00
 CU1 B:CUA228 0.0 18.9 1.0
ND1 B:HIS161 2.0 12.9 1.0
SG B:CYS196 2.3 18.7 1.0
SG B:CYS200 2.3 17.1 1.0
SD B:MET207 2.4 19.3 1.0
CU2 B:CUA228 2.6 18.2 1.0
CE1 B:HIS161 2.9 10.6 1.0
CG B:HIS161 3.1 14.9 1.0
CE B:MET207 3.2 9.1 1.0
CB B:CYS200 3.3 14.8 1.0
CB B:CYS196 3.4 17.8 1.0
CB B:HIS161 3.5 15.4 1.0
CG B:MET207 3.5 15.5 1.0
O B:GLU198 3.9 19.6 1.0
NE2 B:HIS161 4.1 9.7 1.0
CD2 B:HIS161 4.2 13.3 1.0
CA B:HIS161 4.2 16.6 1.0
ND1 B:HIS204 4.5 22.0 1.0
O B:HIS102 4.6 17.2 1.0
CD1 B:TRP104 4.7 13.1 1.0
O B:LEU160 4.7 15.4 1.0
CA B:CYS200 4.7 17.6 1.0
CA B:HIS204 4.8 18.5 1.0
CA B:CYS196 4.8 17.6 1.0
CB B:MET207 4.9 16.5 1.0
O B:HIS204 4.9 17.9 1.0

Copper binding site 3 out of 6 in 3aso

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Copper binding site 3 out of 6 in the Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State Measured at 0.9 Angstrom Wavelength


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 Fully Oxidized State Measured at 0.9 Angstrom Wavelength within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu228

b:18.2
occ:1.00
 CU2 B:CUA228 0.0 18.2 1.0
ND1 B:HIS204 2.0 22.0 1.0
O B:GLU198 2.2 19.6 1.0
SG B:CYS196 2.3 18.7 1.0
SG B:CYS200 2.3 17.1 1.0
CU1 B:CUA228 2.6 18.9 1.0
CE1 B:HIS204 2.9 20.8 1.0
CG B:HIS204 3.1 18.6 1.0
CB B:CYS196 3.3 17.8 1.0
C B:GLU198 3.4 17.8 1.0
CB B:CYS200 3.5 14.8 1.0
CB B:HIS204 3.6 17.4 1.0
CA B:HIS204 3.7 18.5 1.0
N B:CYS200 3.7 16.5 1.0
O B:HIS204 3.8 17.9 1.0
NE2 B:HIS204 4.0 23.1 1.0
N B:GLU198 4.1 17.4 1.0
C B:ILE199 4.2 17.0 1.0
C B:HIS204 4.2 17.7 1.0
N B:ILE199 4.2 16.4 1.0
CD2 B:HIS204 4.2 17.3 1.0
CA B:ILE199 4.2 17.3 1.0
C B:CYS196 4.2 17.5 1.0
CA B:CYS200 4.2 17.6 1.0
O B:CYS196 4.2 16.7 1.0
ND1 B:HIS161 4.2 12.9 1.0
SD B:MET207 4.4 19.3 1.0
CA B:CYS196 4.4 17.6 1.0
CA B:GLU198 4.4 17.6 1.0
N B:SER197 4.6 16.8 1.0
CG B:MET207 4.6 15.5 1.0
CA B:HIS161 4.9 16.6 1.0
CB B:HIS161 4.9 15.4 1.0
N B:HIS204 4.9 18.6 1.0
CG B:HIS161 5.0 14.9 1.0

Copper binding site 4 out of 6 in 3aso

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Copper binding site 4 out of 6 in the Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State Measured at 0.9 Angstrom Wavelength


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 Fully Oxidized State Measured at 0.9 Angstrom Wavelength within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Cu517

b:23.1
occ:1.00
 NE2 N:HIS291 2.0 21.9 1.0
NE2 N:HIS290 2.0 24.4 1.0
ND1 N:HIS240 2.0 18.4 1.0
CD2 N:HIS291 2.9 22.9 1.0
CE1 N:HIS291 2.9 22.1 1.0
CE1 N:HIS290 3.0 24.3 1.0
CG N:HIS240 3.0 20.5 1.0
CD2 N:HIS290 3.0 19.3 1.0
CE1 N:HIS240 3.0 15.5 1.0
CB N:HIS240 3.3 19.1 1.0
CA N:HIS240 3.9 19.8 1.0
ND1 N:HIS291 4.0 23.3 1.0
CG N:HIS291 4.1 23.7 1.0
ND1 N:HIS290 4.1 20.8 1.0
CG N:HIS290 4.1 20.7 1.0
NE2 N:HIS240 4.1 24.0 1.0
CD2 N:HIS240 4.1 22.4 1.0
C1A N:HEA516 4.6 18.9 1.0
NA N:HEA516 4.6 19.0 1.0
N N:HIS240 4.7 19.4 1.0
C4A N:HEA516 4.7 20.0 1.0
CG2 N:VAL243 4.9 13.4 1.0
FE N:HEA516 4.9 21.2 1.0
C2A N:HEA516 4.9 21.1 1.0
C3A N:HEA516 5.0 18.6 1.0

Copper binding site 5 out of 6 in 3aso

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Copper binding site 5 out of 6 in the Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State Measured at 0.9 Angstrom Wavelength


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 Fully Oxidized State Measured at 0.9 Angstrom Wavelength within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Cu228

b:22.9
occ:1.00
 CU1 O:CUA228 0.0 22.9 1.0
ND1 O:HIS161 2.0 20.1 1.0
SG O:CYS196 2.3 22.8 1.0
SG O:CYS200 2.3 22.7 1.0
SD O:MET207 2.3 24.2 1.0
CU2 O:CUA228 2.6 22.6 1.0
CE1 O:HIS161 2.9 17.0 1.0
CG O:HIS161 3.1 19.1 1.0
CE O:MET207 3.1 15.2 1.0
CB O:CYS196 3.3 21.7 1.0
CB O:CYS200 3.4 21.5 1.0
CG O:MET207 3.5 21.4 1.0
CB O:HIS161 3.6 21.2 1.0
O O:GLU198 3.9 22.6 1.0
NE2 O:HIS161 4.0 21.0 1.0
CD2 O:HIS161 4.2 18.8 1.0
CA O:HIS161 4.3 21.0 1.0
ND1 O:HIS204 4.5 22.4 1.0
O O:HIS102 4.6 19.4 1.0
CA O:CYS196 4.7 21.7 1.0
CD1 O:TRP104 4.7 19.6 1.0
CA O:HIS204 4.7 22.1 1.0
O O:LEU160 4.7 21.1 1.0
CA O:CYS200 4.8 22.3 1.0
CB O:MET207 4.9 20.9 1.0
O O:HIS204 4.9 21.4 1.0

Copper binding site 6 out of 6 in 3aso

Go back to Copper Binding Sites List in 3aso
Copper binding site 6 out of 6 in the Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State Measured at 0.9 Angstrom Wavelength


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 Fully Oxidized State Measured at 0.9 Angstrom Wavelength within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Cu228

b:22.6
occ:1.00
 CU2 O:CUA228 0.0 22.6 1.0
ND1 O:HIS204 2.0 22.4 1.0
O O:GLU198 2.2 22.6 1.0
SG O:CYS200 2.3 22.7 1.0
SG O:CYS196 2.3 22.8 1.0
CU1 O:CUA228 2.6 22.9 1.0
CE1 O:HIS204 2.9 22.1 1.0
CG O:HIS204 3.1 22.2 1.0
CB O:CYS196 3.3 21.7 1.0
C O:GLU198 3.4 21.6 1.0
CB O:CYS200 3.5 21.5 1.0
CB O:HIS204 3.5 22.2 1.0
CA O:HIS204 3.6 22.1 1.0
O O:HIS204 3.7 21.4 1.0
N O:CYS200 3.7 22.0 1.0
NE2 O:HIS204 4.0 23.9 1.0
N O:GLU198 4.1 21.1 1.0
C O:HIS204 4.1 22.3 1.0
CD2 O:HIS204 4.1 22.0 1.0
N O:ILE199 4.2 22.0 1.0
ND1 O:HIS161 4.2 20.1 1.0
C O:CYS196 4.2 22.6 1.0
CA O:ILE199 4.2 21.9 1.0
C O:ILE199 4.2 22.6 1.0
CA O:CYS200 4.2 22.3 1.0
O O:CYS196 4.3 19.9 1.0
CA O:CYS196 4.4 21.7 1.0
SD O:MET207 4.4 24.2 1.0
CA O:GLU198 4.4 21.5 1.0
N O:SER197 4.6 21.7 1.0
CG O:MET207 4.7 21.4 1.0
N O:HIS204 4.8 22.4 1.0
CA O:HIS161 5.0 21.0 1.0
CE1 O:HIS161 5.0 17.0 1.0

Reference:

M.Suga, N.Yano, K.Muramoto, K.Shinzawa-Itoh, T.Maeda, E.Yamashita, T.Tsukihara, S.Yoshikawa. Distinguishing Between Cl- and O2(2-) As the Bridging Element Between FE3+ and CU2+ in Resting-Oxidized Cytochrome C Oxidase Acta Crystallogr.,Sect.D V. 67 742 2011.
ISSN: ISSN 0907-4449
PubMed: 21795816
DOI: 10.1107/S0907444911022803
Page generated: Wed Jul 31 00:39:49 2024

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