Copper in PDB 1h1i: Crystal Structure of Quercetin 2,3-Dioxygenase Anaerobically Complexed with the Substrate Quercetn
Enzymatic activity of Crystal Structure of Quercetin 2,3-Dioxygenase Anaerobically Complexed with the Substrate Quercetn
All present enzymatic activity of Crystal Structure of Quercetin 2,3-Dioxygenase Anaerobically Complexed with the Substrate Quercetn:
1.13.11.24;
Protein crystallography data
The structure of Crystal Structure of Quercetin 2,3-Dioxygenase Anaerobically Complexed with the Substrate Quercetn, PDB code: 1h1i
was solved by
R.A.Steiner,
B.W.Dijkstra,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
49.39 /
1.75
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
109.298,
55.745,
124.163,
90.00,
98.39,
90.00
|
R / Rfree (%)
|
14.8 /
18.3
|
Copper Binding Sites:
The binding sites of Copper atom in the Crystal Structure of Quercetin 2,3-Dioxygenase Anaerobically Complexed with the Substrate Quercetn
(pdb code 1h1i). This binding sites where shown within
5.0 Angstroms radius around Copper atom.
In total 4 binding sites of Copper where determined in the
Crystal Structure of Quercetin 2,3-Dioxygenase Anaerobically Complexed with the Substrate Quercetn, PDB code: 1h1i:
Jump to Copper binding site number:
1;
2;
3;
4;
Copper binding site 1 out
of 4 in 1h1i
Go back to
Copper Binding Sites List in 1h1i
Copper binding site 1 out
of 4 in the Crystal Structure of Quercetin 2,3-Dioxygenase Anaerobically Complexed with the Substrate Quercetn
Mono view
Stereo pair view
|
A full contact list of Copper with other atoms in the Cu binding
site number 1 of Crystal Structure of Quercetin 2,3-Dioxygenase Anaerobically Complexed with the Substrate Quercetn within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cu1357
b:19.6
occ:0.70
|
NE2
|
A:HIS112
|
2.1
|
14.4
|
1.0
|
O27
|
A:QUE1358
|
2.1
|
24.6
|
1.0
|
NE2
|
A:HIS68
|
2.1
|
13.6
|
1.0
|
NE2
|
A:HIS66
|
2.1
|
12.2
|
1.0
|
OE1
|
A:GLU73
|
2.3
|
27.4
|
1.0
|
CE1
|
A:HIS112
|
2.8
|
13.1
|
1.0
|
CE1
|
A:HIS68
|
2.9
|
13.1
|
1.0
|
C10
|
A:QUE1358
|
3.0
|
24.8
|
1.0
|
CE1
|
A:HIS66
|
3.1
|
13.7
|
1.0
|
CD
|
A:GLU73
|
3.1
|
28.5
|
1.0
|
CD2
|
A:HIS66
|
3.1
|
11.3
|
1.0
|
CD2
|
A:HIS68
|
3.1
|
15.1
|
1.0
|
CD2
|
A:HIS112
|
3.2
|
11.7
|
1.0
|
O13
|
A:QUE1358
|
3.3
|
25.5
|
1.0
|
OE2
|
A:GLU73
|
3.4
|
32.2
|
1.0
|
C9
|
A:QUE1358
|
3.5
|
23.4
|
1.0
|
ND1
|
A:HIS112
|
4.0
|
10.2
|
1.0
|
ND1
|
A:HIS68
|
4.0
|
11.6
|
1.0
|
C11
|
A:QUE1358
|
4.0
|
21.5
|
1.0
|
CG
|
A:HIS68
|
4.1
|
10.9
|
1.0
|
ND1
|
A:HIS66
|
4.2
|
12.7
|
1.0
|
CG
|
A:HIS66
|
4.2
|
9.9
|
1.0
|
CG
|
A:HIS112
|
4.2
|
9.8
|
1.0
|
CG
|
A:GLU73
|
4.3
|
18.7
|
1.0
|
C19
|
A:QUE1358
|
4.4
|
23.2
|
1.0
|
C14
|
A:QUE1358
|
4.7
|
23.1
|
1.0
|
C3
|
A:QUE1358
|
4.9
|
20.5
|
1.0
|
CZ
|
A:PHE75
|
4.9
|
13.4
|
1.0
|
CB
|
A:GLU73
|
5.0
|
12.0
|
1.0
|
|
Copper binding site 2 out
of 4 in 1h1i
Go back to
Copper Binding Sites List in 1h1i
Copper binding site 2 out
of 4 in the Crystal Structure of Quercetin 2,3-Dioxygenase Anaerobically Complexed with the Substrate Quercetn
Mono view
Stereo pair view
|
A full contact list of Copper with other atoms in the Cu binding
site number 2 of Crystal Structure of Quercetin 2,3-Dioxygenase Anaerobically Complexed with the Substrate Quercetn within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Cu1355
b:17.6
occ:0.70
|
NE2
|
B:HIS112
|
2.0
|
11.5
|
1.0
|
NE2
|
B:HIS66
|
2.1
|
9.8
|
1.0
|
NE2
|
B:HIS68
|
2.1
|
13.1
|
1.0
|
OE1
|
B:GLU73
|
2.3
|
28.9
|
1.0
|
O27
|
B:QUE1356
|
2.3
|
25.6
|
1.0
|
CE1
|
B:HIS112
|
2.8
|
10.1
|
1.0
|
CE1
|
B:HIS68
|
2.9
|
12.3
|
1.0
|
CD2
|
B:HIS66
|
2.9
|
8.6
|
1.0
|
CE1
|
B:HIS66
|
3.1
|
10.4
|
1.0
|
CD2
|
B:HIS112
|
3.1
|
11.5
|
1.0
|
C10
|
B:QUE1356
|
3.2
|
23.1
|
1.0
|
CD2
|
B:HIS68
|
3.2
|
14.3
|
1.0
|
CD
|
B:GLU73
|
3.3
|
27.5
|
1.0
|
O13
|
B:QUE1356
|
3.5
|
20.9
|
1.0
|
OE2
|
B:GLU73
|
3.6
|
31.0
|
1.0
|
C9
|
B:QUE1356
|
3.7
|
21.3
|
1.0
|
ND1
|
B:HIS112
|
3.9
|
10.2
|
1.0
|
ND1
|
B:HIS68
|
4.0
|
11.5
|
1.0
|
CG
|
B:HIS66
|
4.1
|
9.8
|
1.0
|
ND1
|
B:HIS66
|
4.1
|
12.3
|
1.0
|
CG
|
B:HIS112
|
4.1
|
10.1
|
1.0
|
C11
|
B:QUE1356
|
4.1
|
21.6
|
1.0
|
CG
|
B:HIS68
|
4.2
|
11.4
|
1.0
|
C19
|
B:QUE1356
|
4.4
|
24.2
|
1.0
|
CG
|
B:GLU73
|
4.6
|
19.5
|
1.0
|
C14
|
B:QUE1356
|
4.7
|
23.9
|
1.0
|
CZ
|
B:PHE75
|
4.9
|
14.7
|
1.0
|
|
Copper binding site 3 out
of 4 in 1h1i
Go back to
Copper Binding Sites List in 1h1i
Copper binding site 3 out
of 4 in the Crystal Structure of Quercetin 2,3-Dioxygenase Anaerobically Complexed with the Substrate Quercetn
Mono view
Stereo pair view
|
A full contact list of Copper with other atoms in the Cu binding
site number 3 of Crystal Structure of Quercetin 2,3-Dioxygenase Anaerobically Complexed with the Substrate Quercetn within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Cu1357
b:17.0
occ:0.70
|
NE2
|
C:HIS112
|
2.0
|
9.1
|
1.0
|
NE2
|
C:HIS68
|
2.1
|
11.7
|
1.0
|
NE2
|
C:HIS66
|
2.1
|
12.1
|
1.0
|
O27
|
C:QUE1358
|
2.2
|
20.4
|
1.0
|
OE1
|
C:GLU73
|
2.3
|
28.7
|
1.0
|
CE1
|
C:HIS112
|
2.8
|
9.7
|
1.0
|
CD2
|
C:HIS68
|
3.0
|
10.8
|
1.0
|
CE1
|
C:HIS68
|
3.1
|
12.8
|
1.0
|
CD2
|
C:HIS66
|
3.1
|
10.4
|
1.0
|
CE1
|
C:HIS66
|
3.1
|
10.0
|
1.0
|
CD2
|
C:HIS112
|
3.1
|
11.2
|
1.0
|
CD
|
C:GLU73
|
3.1
|
26.6
|
1.0
|
C10
|
C:QUE1358
|
3.2
|
18.2
|
1.0
|
OE2
|
C:GLU73
|
3.3
|
29.3
|
1.0
|
O13
|
C:QUE1358
|
3.5
|
20.1
|
1.0
|
C9
|
C:QUE1358
|
3.7
|
19.7
|
1.0
|
ND1
|
C:HIS112
|
4.0
|
9.1
|
1.0
|
ND1
|
C:HIS68
|
4.1
|
12.5
|
1.0
|
CG
|
C:HIS68
|
4.1
|
9.3
|
1.0
|
CG
|
C:HIS112
|
4.1
|
7.1
|
1.0
|
ND1
|
C:HIS66
|
4.2
|
10.3
|
1.0
|
C11
|
C:QUE1358
|
4.2
|
17.2
|
1.0
|
CG
|
C:HIS66
|
4.2
|
7.1
|
1.0
|
C19
|
C:QUE1358
|
4.4
|
20.4
|
1.0
|
CG
|
C:GLU73
|
4.5
|
21.0
|
1.0
|
C14
|
C:QUE1358
|
4.7
|
18.4
|
1.0
|
CZ
|
C:PHE75
|
4.8
|
13.0
|
1.0
|
|
Copper binding site 4 out
of 4 in 1h1i
Go back to
Copper Binding Sites List in 1h1i
Copper binding site 4 out
of 4 in the Crystal Structure of Quercetin 2,3-Dioxygenase Anaerobically Complexed with the Substrate Quercetn
Mono view
Stereo pair view
|
A full contact list of Copper with other atoms in the Cu binding
site number 4 of Crystal Structure of Quercetin 2,3-Dioxygenase Anaerobically Complexed with the Substrate Quercetn within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Cu1356
b:18.6
occ:0.70
|
NE2
|
D:HIS112
|
2.0
|
12.3
|
1.0
|
NE2
|
D:HIS66
|
2.1
|
13.4
|
1.0
|
O27
|
D:QUE1357
|
2.2
|
23.6
|
1.0
|
NE2
|
D:HIS68
|
2.2
|
16.5
|
1.0
|
OE1
|
D:GLU73
|
2.5
|
25.7
|
1.0
|
CE1
|
D:HIS112
|
2.8
|
9.9
|
1.0
|
CE1
|
D:HIS66
|
3.0
|
15.0
|
1.0
|
CD2
|
D:HIS66
|
3.0
|
9.9
|
1.0
|
CE1
|
D:HIS68
|
3.1
|
15.8
|
1.0
|
C10
|
D:QUE1357
|
3.1
|
22.4
|
1.0
|
CD
|
D:GLU73
|
3.1
|
26.6
|
1.0
|
CD2
|
D:HIS68
|
3.1
|
16.0
|
1.0
|
CD2
|
D:HIS112
|
3.2
|
8.4
|
1.0
|
OE2
|
D:GLU73
|
3.4
|
31.0
|
1.0
|
O13
|
D:QUE1357
|
3.4
|
22.9
|
1.0
|
C9
|
D:QUE1357
|
3.6
|
22.6
|
1.0
|
ND1
|
D:HIS112
|
3.9
|
7.9
|
1.0
|
ND1
|
D:HIS66
|
4.1
|
13.2
|
1.0
|
ND1
|
D:HIS68
|
4.1
|
11.6
|
1.0
|
C11
|
D:QUE1357
|
4.1
|
20.1
|
1.0
|
CG
|
D:HIS66
|
4.1
|
12.4
|
1.0
|
CG
|
D:HIS112
|
4.2
|
7.9
|
1.0
|
CG
|
D:HIS68
|
4.2
|
12.6
|
1.0
|
CG
|
D:GLU73
|
4.3
|
18.6
|
1.0
|
C19
|
D:QUE1357
|
4.4
|
22.6
|
1.0
|
C14
|
D:QUE1357
|
4.7
|
22.1
|
1.0
|
C3
|
D:QUE1357
|
5.0
|
20.2
|
1.0
|
|
Reference:
R.A.Steiner,
K.H.Kalk,
B.W.Dijkstra.
Anaerobic Enzyme.Substrate Structures Provide Insight Into the Reaction Mechanism of the Copper- Dependent Quercetin 2,3-Dioxygenase. Proc.Natl.Acad.Sci.Usa V. 99 16625 2002.
ISSN: ISSN 0027-8424
PubMed: 12486225
DOI: 10.1073/PNAS.262506299
Page generated: Tue Jul 30 21:52:44 2024
|