Atomistry » Copper » PDB 2z7y-3aws » 3asn
Atomistry »
  Copper »
    PDB 2z7y-3aws »
      3asn »

Copper in PDB 3asn: Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State Measured at 1.7470 Angstrom Wavelength

Enzymatic activity of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State Measured at 1.7470 Angstrom Wavelength

All present enzymatic activity of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State Measured at 1.7470 Angstrom Wavelength:
1.9.3.1;

Protein crystallography data

The structure of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State Measured at 1.7470 Angstrom Wavelength, PDB code: 3asn 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 / 3.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 181.826, 204.098, 177.829, 90.00, 90.00, 90.00
R / Rfree (%) 15 / 18.7

Other elements in 3asn:

The structure of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State Measured at 1.7470 Angstrom Wavelength also contains other interesting chemical elements:

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

Copper Binding Sites:

The binding sites of Copper atom in the Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State Measured at 1.7470 Angstrom Wavelength (pdb code 3asn). 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 1.7470 Angstrom Wavelength, PDB code: 3asn:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6;

Copper binding site 1 out of 6 in 3asn

Go back to Copper Binding Sites List in 3asn
Copper binding site 1 out of 6 in the Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State Measured at 1.7470 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 1.7470 Angstrom Wavelength within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu517

b:22.5
occ:1.00
 NE2 A:HIS291 1.9 14.8 1.0
ND1 A:HIS240 2.1 14.3 1.0
NE2 A:HIS290 2.2 14.2 1.0
CE1 A:HIS291 2.9 15.7 1.0
CD2 A:HIS291 2.9 13.7 1.0
CG A:HIS240 3.0 12.4 1.0
CE1 A:HIS240 3.1 14.9 1.0
CE1 A:HIS290 3.1 12.6 1.0
CD2 A:HIS290 3.2 14.8 1.0
CB A:HIS240 3.3 13.8 1.0
CA A:HIS240 3.8 14.1 1.0
ND1 A:HIS291 4.0 17.3 1.0
CG A:HIS291 4.1 16.6 1.0
NE2 A:HIS240 4.2 16.5 1.0
CD2 A:HIS240 4.2 16.3 1.0
ND1 A:HIS290 4.2 12.3 1.0
CG A:HIS290 4.3 13.2 1.0
NA A:HEA516 4.5 17.3 1.0
C1A A:HEA516 4.5 15.7 1.0
FE A:HEA516 4.7 26.8 1.0
N A:HIS240 4.7 15.2 1.0
C4A A:HEA516 4.7 15.8 1.0
CG2 A:VAL243 4.9 9.1 1.0
CHA A:HEA516 4.9 13.8 1.0
C2A A:HEA516 4.9 15.1 1.0
C A:HIS240 5.0 15.2 1.0

Copper binding site 2 out of 6 in 3asn

Go back to Copper Binding Sites List in 3asn
Copper binding site 2 out of 6 in the Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State Measured at 1.7470 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 1.7470 Angstrom Wavelength within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu228

b:17.6
occ:1.00
 CU1 B:CUA228 0.0 17.6 1.0
ND1 B:HIS161 2.0 14.3 1.0
SG B:CYS196 2.3 13.3 1.0
SG B:CYS200 2.3 13.8 1.0
SD B:MET207 2.3 13.2 1.0
CU2 B:CUA228 2.6 18.3 1.0
CE1 B:HIS161 2.9 12.9 1.0
CG B:HIS161 3.1 12.1 1.0
CE B:MET207 3.2 4.2 1.0
CB B:CYS200 3.3 14.5 1.0
CB B:CYS196 3.4 13.9 1.0
CG B:MET207 3.5 10.5 1.0
CB B:HIS161 3.5 11.8 1.0
O B:GLU198 3.9 18.2 1.0
NE2 B:HIS161 4.1 14.2 1.0
CD2 B:HIS161 4.2 12.6 1.0
CA B:HIS161 4.2 12.6 1.0
ND1 B:HIS204 4.5 18.7 1.0
O B:HIS102 4.7 14.3 1.0
CA B:CYS200 4.7 14.7 1.0
CD1 B:TRP104 4.7 15.6 1.0
O B:LEU160 4.7 13.7 1.0
CA B:HIS204 4.7 16.6 1.0
CA B:CYS196 4.8 14.4 1.0
CB B:MET207 4.9 12.9 1.0
O B:HIS204 4.9 15.8 1.0
N B:CYS200 4.9 14.6 1.0

Copper binding site 3 out of 6 in 3asn

Go back to Copper Binding Sites List in 3asn
Copper binding site 3 out of 6 in the Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State Measured at 1.7470 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 1.7470 Angstrom Wavelength within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu228

b:18.3
occ:1.00
 CU2 B:CUA228 0.0 18.3 1.0
ND1 B:HIS204 2.0 18.7 1.0
O B:GLU198 2.1 18.2 1.0
SG B:CYS196 2.3 13.3 1.0
SG B:CYS200 2.3 13.8 1.0
CU1 B:CUA228 2.6 17.6 1.0
CE1 B:HIS204 2.8 19.2 1.0
CG B:HIS204 3.1 16.9 1.0
C B:GLU198 3.3 15.4 1.0
CB B:CYS196 3.4 13.9 1.0
CB B:CYS200 3.4 14.5 1.0
CB B:HIS204 3.6 16.6 1.0
N B:CYS200 3.6 14.6 1.0
CA B:HIS204 3.7 16.6 1.0
O B:HIS204 3.8 15.8 1.0
NE2 B:HIS204 4.0 20.6 1.0
N B:GLU198 4.1 15.4 1.0
C B:ILE199 4.1 14.2 1.0
N B:ILE199 4.1 13.8 1.0
CA B:CYS200 4.1 14.7 1.0
CA B:ILE199 4.2 13.1 1.0
CD2 B:HIS204 4.2 17.6 1.0
C B:HIS204 4.2 16.1 1.0
C B:CYS196 4.2 15.5 1.0
O B:CYS196 4.2 15.4 1.0
ND1 B:HIS161 4.2 14.3 1.0
CA B:GLU198 4.3 15.4 1.0
SD B:MET207 4.4 13.2 1.0
CA B:CYS196 4.4 14.4 1.0
N B:SER197 4.7 15.7 1.0
CG B:MET207 4.7 10.5 1.0
CA B:HIS161 4.9 12.6 1.0
N B:HIS204 5.0 17.0 1.0
CB B:HIS161 5.0 11.8 1.0
O B:ILE199 5.0 13.9 1.0

Copper binding site 4 out of 6 in 3asn

Go back to Copper Binding Sites List in 3asn
Copper binding site 4 out of 6 in the Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State Measured at 1.7470 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 1.7470 Angstrom Wavelength within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Cu517

b:24.9
occ:1.00
 NE2 N:HIS291 2.0 15.7 1.0
ND1 N:HIS240 2.0 15.0 1.0
NE2 N:HIS290 2.1 16.3 1.0
CE1 N:HIS291 2.9 15.2 1.0
CE1 N:HIS240 3.0 15.4 1.0
CG N:HIS240 3.0 15.7 1.0
CD2 N:HIS291 3.0 16.8 1.0
CE1 N:HIS290 3.0 16.4 1.0
CD2 N:HIS290 3.1 17.3 1.0
CB N:HIS240 3.3 17.5 1.0
CA N:HIS240 3.9 17.4 1.0
ND1 N:HIS291 4.1 18.3 1.0
NE2 N:HIS240 4.1 17.6 1.0
CD2 N:HIS240 4.1 18.1 1.0
CG N:HIS291 4.1 17.8 1.0
ND1 N:HIS290 4.2 15.7 1.0
CG N:HIS290 4.2 18.9 1.0
NA N:HEA516 4.4 20.1 1.0
C1A N:HEA516 4.5 19.3 1.0
FE N:HEA516 4.7 21.9 1.0
C4A N:HEA516 4.7 17.5 1.0
N N:HIS240 4.8 17.5 1.0
CHA N:HEA516 4.9 15.7 1.0
CG2 N:VAL243 4.9 15.0 1.0
C2A N:HEA516 4.9 16.0 1.0
ND N:HEA516 5.0 21.5 1.0
C3A N:HEA516 5.0 17.7 1.0

Copper binding site 5 out of 6 in 3asn

Go back to Copper Binding Sites List in 3asn
Copper binding site 5 out of 6 in the Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State Measured at 1.7470 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 1.7470 Angstrom Wavelength within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Cu228

b:20.6
occ:1.00
 CU1 O:CUA228 0.0 20.6 1.0
ND1 O:HIS161 2.0 19.7 1.0
SD O:MET207 2.3 17.3 1.0
SG O:CYS200 2.3 18.8 1.0
SG O:CYS196 2.3 16.1 1.0
CU2 O:CUA228 2.6 22.2 1.0
CE1 O:HIS161 2.8 19.0 1.0
CG O:HIS161 3.1 17.2 1.0
CE O:MET207 3.1 12.1 1.0
CB O:CYS196 3.3 16.7 1.0
CB O:CYS200 3.4 18.1 1.0
CG O:MET207 3.5 16.1 1.0
CB O:HIS161 3.6 17.9 1.0
O O:GLU198 3.9 21.5 1.0
NE2 O:HIS161 4.0 17.6 1.0
CD2 O:HIS161 4.2 15.8 1.0
CA O:HIS161 4.3 17.5 1.0
ND1 O:HIS204 4.5 19.6 1.0
O O:HIS102 4.6 16.1 1.0
CD1 O:TRP104 4.7 20.6 1.0
CA O:CYS196 4.7 17.7 1.0
CA O:HIS204 4.7 19.6 1.0
CA O:CYS200 4.8 18.9 1.0
O O:LEU160 4.8 17.9 1.0
CB O:MET207 4.9 16.6 1.0
O O:HIS204 4.9 18.7 1.0

Copper binding site 6 out of 6 in 3asn

Go back to Copper Binding Sites List in 3asn
Copper binding site 6 out of 6 in the Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State Measured at 1.7470 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 1.7470 Angstrom Wavelength within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Cu228

b:22.2
occ:1.00
 CU2 O:CUA228 0.0 22.2 1.0
ND1 O:HIS204 2.0 19.6 1.0
O O:GLU198 2.1 21.5 1.0
SG O:CYS196 2.3 16.1 1.0
SG O:CYS200 2.3 18.8 1.0
CU1 O:CUA228 2.6 20.6 1.0
CE1 O:HIS204 2.9 15.4 1.0
CG O:HIS204 3.1 19.6 1.0
CB O:CYS196 3.3 16.7 1.0
C O:GLU198 3.3 19.0 1.0
CB O:CYS200 3.4 18.1 1.0
CB O:HIS204 3.5 19.6 1.0
CA O:HIS204 3.6 19.6 1.0
N O:CYS200 3.7 18.2 1.0
O O:HIS204 3.8 18.7 1.0
NE2 O:HIS204 4.0 18.9 1.0
N O:GLU198 4.1 18.8 1.0
CD2 O:HIS204 4.1 20.0 1.0
C O:HIS204 4.1 19.4 1.0
CA O:CYS200 4.1 18.9 1.0
N O:ILE199 4.1 17.8 1.0
C O:ILE199 4.2 18.5 1.0
O O:CYS196 4.2 17.4 1.0
ND1 O:HIS161 4.2 19.7 1.0
CA O:ILE199 4.2 18.1 1.0
C O:CYS196 4.2 17.8 1.0
CA O:CYS196 4.4 17.7 1.0
CA O:GLU198 4.4 18.7 1.0
SD O:MET207 4.4 17.3 1.0
N O:SER197 4.7 18.1 1.0
CG O:MET207 4.8 16.1 1.0
N O:HIS204 4.8 19.9 1.0
CA O:HIS161 5.0 17.5 1.0
CE1 O:HIS161 5.0 19.0 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 00:39:30 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy