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Copper in PDB 2y69: Bovine Heart Cytochrome C Oxidase Re-Refined with Molecular Oxygen

Enzymatic activity of Bovine Heart Cytochrome C Oxidase Re-Refined with Molecular Oxygen

All present enzymatic activity of Bovine Heart Cytochrome C Oxidase Re-Refined with Molecular Oxygen:
1.9.3.1;

Protein crystallography data

The structure of Bovine Heart Cytochrome C Oxidase Re-Refined with Molecular Oxygen, PDB code: 2y69 was solved by V.R.I.Kaila, E.Oksanen, A.Goldman, M.I.Verkhovsky, D.Sundholm, M.Wikstrom, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 64.15 / 1.95
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 183.697, 206.991, 178.251, 90.00, 90.00, 90.00
R / Rfree (%) 21.1 / 24.5

Other elements in 2y69:

The structure of Bovine Heart Cytochrome C Oxidase Re-Refined with Molecular Oxygen also contains other interesting chemical elements:

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

Copper Binding Sites:

The binding sites of Copper atom in the Bovine Heart Cytochrome C Oxidase Re-Refined with Molecular Oxygen (pdb code 2y69). 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 Re-Refined with Molecular Oxygen, PDB code: 2y69:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6;

Copper binding site 1 out of 6 in 2y69

Go back to Copper Binding Sites List in 2y69
Copper binding site 1 out of 6 in the Bovine Heart Cytochrome C Oxidase Re-Refined with Molecular Oxygen


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 Re-Refined with Molecular Oxygen within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu517

b:28.5
occ:1.00
 NE2 A:HIS291 2.1 28.9 1.0
ND1 A:HIS240 2.1 28.6 1.0
NE2 A:HIS290 2.1 26.5 1.0
O1 A:OXY1515 2.5 41.0 1.0
O2 A:OXY1515 2.8 32.3 1.0
CD2 A:HIS291 3.0 25.8 1.0
CG A:HIS240 3.0 27.5 1.0
CE1 A:HIS291 3.0 24.5 1.0
CE1 A:HIS290 3.1 24.6 1.0
CE1 A:HIS240 3.1 26.1 1.0
CD2 A:HIS290 3.1 24.6 1.0
CB A:HIS240 3.3 26.3 1.0
CA A:HIS240 3.9 25.6 1.0
ND1 A:HIS291 4.1 25.4 1.0
CG A:HIS291 4.1 26.9 1.0
CD2 A:HIS240 4.2 27.1 1.0
NE2 A:HIS240 4.2 28.0 1.0
ND1 A:HIS290 4.2 24.0 1.0
CG A:HIS290 4.2 26.7 1.0
NA A:HEA516 4.5 24.9 1.0
C1A A:HEA516 4.6 24.1 1.0
N A:HIS240 4.8 25.6 1.0
C4A A:HEA516 4.8 22.2 1.0
CG2 A:VAL243 4.9 24.2 1.0
FE A:HEA516 4.9 26.4 1.0
CHA A:HEA516 4.9 23.9 1.0

Copper binding site 2 out of 6 in 2y69

Go back to Copper Binding Sites List in 2y69
Copper binding site 2 out of 6 in the Bovine Heart Cytochrome C Oxidase Re-Refined with Molecular Oxygen


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 Re-Refined with Molecular Oxygen within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu228

b:28.3
occ:1.00
 CU1 B:CUA228 0.0 28.3 1.0
ND1 B:HIS204 2.1 28.4 1.0
SG B:CYS200 2.3 29.1 1.0
SG B:CYS196 2.3 28.6 1.0
CU2 B:CUA228 2.6 30.4 1.0
O B:GLU198 2.6 28.6 1.0
CE1 B:HIS204 2.9 27.8 1.0
CG B:HIS204 3.1 27.6 1.0
CB B:CYS196 3.3 25.7 1.0
CB B:CYS200 3.5 28.1 1.0
C B:GLU198 3.5 28.4 1.0
CB B:HIS204 3.6 25.4 1.0
CA B:HIS204 3.6 26.6 1.0
N B:CYS200 3.7 27.7 1.0
O B:HIS204 3.8 25.5 1.0
NE2 B:HIS204 4.1 29.3 1.0
N B:GLU198 4.1 26.4 1.0
C B:ILE199 4.1 28.0 1.0
CD2 B:HIS204 4.2 27.7 1.0
O B:CYS196 4.2 26.0 1.0
C B:HIS204 4.2 26.3 1.0
C B:CYS196 4.2 27.8 1.0
CA B:ILE199 4.2 27.6 1.0
CA B:CYS200 4.3 27.9 1.0
N B:ILE199 4.3 28.0 1.0
ND1 B:HIS161 4.3 25.7 1.0
CA B:CYS196 4.4 27.1 1.0
SD B:MET207 4.4 28.8 1.0
CA B:GLU198 4.5 27.8 1.0
N B:SER197 4.7 27.1 1.0
CG B:MET207 4.7 27.9 1.0
N B:HIS204 4.9 27.1 1.0
CA B:HIS161 4.9 24.6 1.0
O B:ILE199 5.0 28.5 1.0

Copper binding site 3 out of 6 in 2y69

Go back to Copper Binding Sites List in 2y69
Copper binding site 3 out of 6 in the Bovine Heart Cytochrome C Oxidase Re-Refined with Molecular Oxygen


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 Re-Refined with Molecular Oxygen within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu228

b:30.4
occ:1.00
 CU2 B:CUA228 0.0 30.4 1.0
ND1 B:HIS161 2.0 25.7 1.0
SG B:CYS196 2.3 28.6 1.0
SD B:MET207 2.4 28.8 1.0
SG B:CYS200 2.4 29.1 1.0
CU1 B:CUA228 2.6 28.3 1.0
CE1 B:HIS161 3.0 21.5 1.0
CE B:MET207 3.1 22.4 1.0
CG B:HIS161 3.1 23.9 1.0
CB B:CYS196 3.4 25.7 1.0
CB B:CYS200 3.4 28.1 1.0
CG B:MET207 3.5 27.9 1.0
CB B:HIS161 3.5 23.3 1.0
NE2 B:HIS161 4.1 23.4 1.0
CA B:HIS161 4.2 24.6 1.0
CD2 B:HIS161 4.2 22.0 1.0
O B:GLU198 4.3 28.6 1.0
ND1 B:HIS204 4.6 28.4 1.0
O B:LEU160 4.7 26.8 1.0
O B:HIS102 4.7 26.9 1.0
CD1 B:TRP104 4.7 24.0 1.0
CA B:CYS196 4.8 27.1 1.0
CA B:HIS204 4.8 26.6 1.0
CA B:CYS200 4.8 27.9 1.0
CB B:MET207 4.9 28.4 1.0
CZ2 B:TRP106 5.0 27.3 1.0

Copper binding site 4 out of 6 in 2y69

Go back to Copper Binding Sites List in 2y69
Copper binding site 4 out of 6 in the Bovine Heart Cytochrome C Oxidase Re-Refined with Molecular Oxygen


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 Re-Refined with Molecular Oxygen within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Cu517

b:32.4
occ:1.00
 NE2 N:HIS290 2.0 29.8 1.0
ND1 N:HIS240 2.0 25.9 1.0
NE2 N:HIS291 2.1 47.3 1.0
O2 N:OXY1515 2.5 33.9 1.0
O1 N:OXY1515 2.6 31.2 1.0
CE1 N:HIS290 2.9 27.2 1.0
CG N:HIS240 2.9 44.1 1.0
CE1 N:HIS291 3.0 30.9 1.0
CD2 N:HIS291 3.0 32.6 1.0
CE1 N:HIS240 3.1 27.4 1.0
CD2 N:HIS290 3.1 28.3 1.0
CB N:HIS240 3.2 28.7 1.0
CA N:HIS240 3.9 39.9 1.0
ND1 N:HIS290 4.1 24.4 1.0
ND1 N:HIS291 4.1 29.6 1.0
CD2 N:HIS240 4.1 28.3 1.0
CG N:HIS291 4.1 45.4 1.0
NE2 N:HIS240 4.1 30.2 1.0
CG N:HIS290 4.2 22.9 1.0
NA N:HEA516 4.5 39.4 1.0
C1A N:HEA516 4.6 29.0 1.0
N N:HIS240 4.7 27.9 1.0
C4A N:HEA516 4.8 26.3 1.0
CG2 N:VAL243 4.8 34.6 1.0
FE N:HEA516 4.9 34.7 1.0
CHA N:HEA516 4.9 26.9 1.0

Copper binding site 5 out of 6 in 2y69

Go back to Copper Binding Sites List in 2y69
Copper binding site 5 out of 6 in the Bovine Heart Cytochrome C Oxidase Re-Refined with Molecular Oxygen


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 Re-Refined with Molecular Oxygen within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Cu228

b:39.5
occ:1.00
 CU1 O:CUA228 0.0 39.5 1.0
ND1 O:HIS204 2.1 41.5 1.0
SG O:CYS196 2.3 40.6 1.0
SG O:CYS200 2.3 40.2 1.0
O O:GLU198 2.6 40.1 1.0
CU2 O:CUA228 2.7 40.9 1.0
CE1 O:HIS204 2.9 33.9 1.0
CG O:HIS204 3.2 45.4 1.0
CB O:CYS196 3.4 33.2 1.0
CB O:CYS200 3.5 35.1 1.0
C O:GLU198 3.5 32.2 1.0
CA O:HIS204 3.6 29.1 1.0
CB O:HIS204 3.7 29.4 1.0
O O:HIS204 3.7 32.5 1.0
N O:CYS200 3.8 41.2 1.0
NE2 O:HIS204 4.0 36.2 1.0
N O:GLU198 4.1 32.3 1.0
C O:HIS204 4.1 41.1 1.0
O O:CYS196 4.2 34.6 1.0
CD2 O:HIS204 4.2 43.8 1.0
C O:CYS196 4.2 49.3 1.0
C O:ILE199 4.2 64.5 1.0
CA O:ILE199 4.2 31.5 1.0
CA O:CYS200 4.3 26.9 1.0
ND1 O:HIS161 4.3 49.5 1.0
N O:ILE199 4.3 31.0 1.0
CA O:CYS196 4.5 45.4 1.0
SD O:MET207 4.5 39.8 1.0
CA O:GLU198 4.5 37.6 1.0
N O:SER197 4.7 32.6 1.0
CG O:MET207 4.7 41.5 1.0
N O:HIS204 4.9 45.4 1.0

Copper binding site 6 out of 6 in 2y69

Go back to Copper Binding Sites List in 2y69
Copper binding site 6 out of 6 in the Bovine Heart Cytochrome C Oxidase Re-Refined with Molecular Oxygen


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 Re-Refined with Molecular Oxygen within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Cu228

b:40.9
occ:1.00
 CU2 O:CUA228 0.0 40.9 1.0
ND1 O:HIS161 2.1 49.5 1.0
SG O:CYS200 2.3 40.2 1.0
SG O:CYS196 2.3 40.6 1.0
SD O:MET207 2.4 39.8 1.0
CU1 O:CUA228 2.7 39.5 1.0
CE1 O:HIS161 2.9 28.8 1.0
CG O:HIS161 3.2 29.3 1.0
CE O:MET207 3.2 33.6 1.0
CB O:CYS200 3.4 35.1 1.0
CB O:CYS196 3.5 33.2 1.0
CG O:MET207 3.5 41.5 1.0
CB O:HIS161 3.6 33.4 1.0
NE2 O:HIS161 4.1 43.1 1.0
CD2 O:HIS161 4.2 38.6 1.0
O O:GLU198 4.3 40.1 1.0
CA O:HIS161 4.3 51.8 1.0
CD1 O:TRP104 4.6 37.1 1.0
ND1 O:HIS204 4.6 41.5 1.0
O O:LEU160 4.7 37.4 1.0
O O:HIS102 4.7 38.7 1.0
CA O:CYS200 4.8 26.9 1.0
CA O:HIS204 4.8 29.1 1.0
CA O:CYS196 4.9 45.4 1.0
CB O:MET207 4.9 38.1 1.0
O O:HIS204 4.9 32.5 1.0

Reference:

V.R.I.Kaila, E.Oksanen, A.Goldman, D.A.Bloch, M.I.Verkhovsky, D.Sundholm, M.Wikstrom. A Combined Quantum Chemical and Crystallographic Study on the Oxidized Binuclear Center of Cytochrome C Oxidase. Biochim.Biophys.Acta V.1807 769 2011.
ISSN: ISSN 0006-3002
PubMed: 21211513
DOI: 10.1016/J.BBABIO.2010.12.016
Page generated: Wed Jul 31 00:18:28 2024

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