Atomistry » Copper » PDB 2xv2-2z7w » 2y69
Atomistry »
  Copper »
    PDB 2xv2-2z7w »
      2y69 »

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: Sun Dec 13 11:07:56 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy