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:
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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