Copper in PDB 1h1m: Crystal Structure of Quercetin 2,3-Dioxygenase Anaerobically Complexed with the Substrate Kaempferol
Enzymatic activity of Crystal Structure of Quercetin 2,3-Dioxygenase Anaerobically Complexed with the Substrate Kaempferol
All present enzymatic activity of Crystal Structure of Quercetin 2,3-Dioxygenase Anaerobically Complexed with the Substrate Kaempferol:
1.13.11.24;
Protein crystallography data
The structure of Crystal Structure of Quercetin 2,3-Dioxygenase Anaerobically Complexed with the Substrate Kaempferol, PDB code: 1h1m
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 /
1.90
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
109.272,
55.377,
123.929,
90.00,
98.33,
90.00
|
R / Rfree (%)
|
15.4 /
20.4
|
Copper Binding Sites:
The binding sites of Copper atom in the Crystal Structure of Quercetin 2,3-Dioxygenase Anaerobically Complexed with the Substrate Kaempferol
(pdb code 1h1m). 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 Kaempferol, PDB code: 1h1m:
Jump to Copper binding site number:
1;
2;
3;
4;
Copper binding site 1 out
of 4 in 1h1m
Go back to
Copper Binding Sites List in 1h1m
Copper binding site 1 out
of 4 in the Crystal Structure of Quercetin 2,3-Dioxygenase Anaerobically Complexed with the Substrate Kaempferol
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 Kaempferol within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cu1361
b:9.4
occ:1.00
|
O27
|
A:KMP1360
|
2.0
|
20.1
|
1.0
|
NE2
|
A:HIS112
|
2.1
|
10.2
|
1.0
|
OE1
|
A:GLU73
|
2.1
|
23.2
|
1.0
|
NE2
|
A:HIS66
|
2.1
|
7.2
|
1.0
|
NE2
|
A:HIS68
|
2.1
|
9.4
|
1.0
|
C10
|
A:KMP1360
|
2.9
|
19.4
|
1.0
|
CD
|
A:GLU73
|
2.9
|
22.4
|
1.0
|
CD2
|
A:HIS66
|
3.0
|
4.3
|
1.0
|
CE1
|
A:HIS112
|
3.0
|
8.2
|
1.0
|
CE1
|
A:HIS68
|
3.0
|
8.3
|
1.0
|
CD2
|
A:HIS112
|
3.0
|
9.3
|
1.0
|
CD2
|
A:HIS68
|
3.1
|
9.9
|
1.0
|
CE1
|
A:HIS66
|
3.1
|
8.8
|
1.0
|
OE2
|
A:GLU73
|
3.3
|
23.9
|
1.0
|
O13
|
A:KMP1360
|
3.4
|
20.0
|
1.0
|
C9
|
A:KMP1360
|
3.5
|
17.8
|
1.0
|
C11
|
A:KMP1360
|
3.9
|
16.3
|
1.0
|
ND1
|
A:HIS112
|
4.1
|
7.7
|
1.0
|
ND1
|
A:HIS68
|
4.1
|
10.8
|
1.0
|
CG
|
A:HIS66
|
4.1
|
6.1
|
1.0
|
CG
|
A:HIS112
|
4.1
|
7.4
|
1.0
|
ND1
|
A:HIS66
|
4.2
|
8.2
|
1.0
|
CG
|
A:HIS68
|
4.2
|
9.1
|
1.0
|
CG
|
A:GLU73
|
4.2
|
14.6
|
1.0
|
C19
|
A:KMP1360
|
4.3
|
15.4
|
1.0
|
C14
|
A:KMP1360
|
4.6
|
15.1
|
1.0
|
C3
|
A:KMP1360
|
4.9
|
16.0
|
1.0
|
CB
|
A:GLU73
|
4.9
|
7.8
|
1.0
|
CZ
|
A:PHE75
|
5.0
|
10.4
|
1.0
|
|
Copper binding site 2 out
of 4 in 1h1m
Go back to
Copper Binding Sites List in 1h1m
Copper binding site 2 out
of 4 in the Crystal Structure of Quercetin 2,3-Dioxygenase Anaerobically Complexed with the Substrate Kaempferol
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 Kaempferol within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Cu1359
b:10.4
occ:1.00
|
OE1
|
B:GLU73
|
1.9
|
29.0
|
1.0
|
NE2
|
B:HIS66
|
2.0
|
6.7
|
1.0
|
NE2
|
B:HIS112
|
2.1
|
7.3
|
1.0
|
NE2
|
B:HIS68
|
2.1
|
13.1
|
1.0
|
O27
|
B:KMP1358
|
2.2
|
21.4
|
1.0
|
CD2
|
B:HIS66
|
2.9
|
4.7
|
1.0
|
CE1
|
B:HIS68
|
2.9
|
10.8
|
1.0
|
CD
|
B:GLU73
|
2.9
|
29.5
|
1.0
|
CE1
|
B:HIS112
|
3.0
|
6.3
|
1.0
|
C10
|
B:KMP1358
|
3.0
|
19.9
|
1.0
|
CD2
|
B:HIS112
|
3.1
|
7.0
|
1.0
|
CE1
|
B:HIS66
|
3.1
|
7.9
|
1.0
|
CD2
|
B:HIS68
|
3.2
|
10.9
|
1.0
|
O13
|
B:KMP1358
|
3.3
|
21.7
|
1.0
|
OE2
|
B:GLU73
|
3.3
|
30.9
|
1.0
|
C9
|
B:KMP1358
|
3.5
|
18.9
|
1.0
|
C11
|
B:KMP1358
|
4.0
|
17.2
|
1.0
|
CG
|
B:HIS66
|
4.1
|
6.8
|
1.0
|
ND1
|
B:HIS68
|
4.1
|
8.8
|
1.0
|
ND1
|
B:HIS112
|
4.1
|
7.6
|
1.0
|
ND1
|
B:HIS66
|
4.1
|
7.2
|
1.0
|
CG
|
B:HIS112
|
4.2
|
8.0
|
1.0
|
CG
|
B:GLU73
|
4.3
|
19.8
|
1.0
|
CG
|
B:HIS68
|
4.3
|
7.8
|
1.0
|
C19
|
B:KMP1358
|
4.3
|
16.9
|
1.0
|
C14
|
B:KMP1358
|
4.6
|
20.1
|
1.0
|
CZ
|
B:PHE75
|
4.8
|
11.7
|
1.0
|
CB
|
B:GLU73
|
4.8
|
12.6
|
1.0
|
C3
|
B:KMP1358
|
4.9
|
19.1
|
1.0
|
|
Copper binding site 3 out
of 4 in 1h1m
Go back to
Copper Binding Sites List in 1h1m
Copper binding site 3 out
of 4 in the Crystal Structure of Quercetin 2,3-Dioxygenase Anaerobically Complexed with the Substrate Kaempferol
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 Kaempferol within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Cu1359
b:11.2
occ:1.00
|
NE2
|
C:HIS66
|
1.9
|
8.3
|
1.0
|
OE1
|
C:GLU73
|
2.0
|
31.9
|
1.0
|
NE2
|
C:HIS112
|
2.1
|
5.2
|
1.0
|
NE2
|
C:HIS68
|
2.1
|
9.5
|
1.0
|
O27
|
C:KMP1358
|
2.1
|
18.0
|
1.0
|
CE1
|
C:HIS66
|
2.9
|
6.1
|
1.0
|
CE1
|
C:HIS112
|
2.9
|
5.5
|
1.0
|
CD2
|
C:HIS66
|
2.9
|
5.4
|
1.0
|
C10
|
C:KMP1358
|
3.0
|
18.9
|
1.0
|
CE1
|
C:HIS68
|
3.0
|
12.0
|
1.0
|
CD
|
C:GLU73
|
3.0
|
28.7
|
1.0
|
CD2
|
C:HIS112
|
3.1
|
5.3
|
1.0
|
CD2
|
C:HIS68
|
3.2
|
8.4
|
1.0
|
O13
|
C:KMP1358
|
3.3
|
23.3
|
1.0
|
OE2
|
C:GLU73
|
3.4
|
33.7
|
1.0
|
C9
|
C:KMP1358
|
3.4
|
20.1
|
1.0
|
C11
|
C:KMP1358
|
3.9
|
18.2
|
1.0
|
ND1
|
C:HIS66
|
4.0
|
5.3
|
1.0
|
CG
|
C:HIS66
|
4.1
|
5.1
|
1.0
|
ND1
|
C:HIS112
|
4.1
|
5.8
|
1.0
|
ND1
|
C:HIS68
|
4.1
|
8.2
|
1.0
|
CG
|
C:HIS112
|
4.2
|
6.8
|
1.0
|
CG
|
C:HIS68
|
4.2
|
7.4
|
1.0
|
CG
|
C:GLU73
|
4.3
|
21.5
|
1.0
|
C19
|
C:KMP1358
|
4.4
|
19.6
|
1.0
|
C14
|
C:KMP1358
|
4.6
|
20.4
|
1.0
|
C3
|
C:KMP1358
|
4.8
|
17.7
|
1.0
|
CZ
|
C:PHE75
|
4.9
|
14.2
|
1.0
|
CB
|
C:GLU73
|
4.9
|
12.6
|
1.0
|
|
Copper binding site 4 out
of 4 in 1h1m
Go back to
Copper Binding Sites List in 1h1m
Copper binding site 4 out
of 4 in the Crystal Structure of Quercetin 2,3-Dioxygenase Anaerobically Complexed with the Substrate Kaempferol
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 Kaempferol within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Cu1357
b:11.1
occ:1.00
|
NE2
|
D:HIS66
|
2.0
|
10.0
|
1.0
|
O27
|
D:KMP1356
|
2.1
|
17.0
|
1.0
|
NE2
|
D:HIS112
|
2.1
|
10.3
|
1.0
|
OE1
|
D:GLU73
|
2.2
|
23.0
|
1.0
|
NE2
|
D:HIS68
|
2.2
|
14.2
|
1.0
|
CE1
|
D:HIS66
|
3.0
|
8.8
|
1.0
|
C10
|
D:KMP1356
|
3.0
|
16.0
|
1.0
|
CD2
|
D:HIS66
|
3.0
|
7.9
|
1.0
|
CE1
|
D:HIS112
|
3.0
|
7.3
|
1.0
|
CD
|
D:GLU73
|
3.1
|
21.6
|
1.0
|
CD2
|
D:HIS112
|
3.1
|
7.9
|
1.0
|
CE1
|
D:HIS68
|
3.2
|
10.4
|
1.0
|
CD2
|
D:HIS68
|
3.2
|
13.2
|
1.0
|
OE2
|
D:GLU73
|
3.4
|
22.9
|
1.0
|
O13
|
D:KMP1356
|
3.4
|
17.6
|
1.0
|
C9
|
D:KMP1356
|
3.5
|
18.7
|
1.0
|
C11
|
D:KMP1356
|
4.0
|
17.0
|
1.0
|
ND1
|
D:HIS66
|
4.1
|
10.1
|
1.0
|
CG
|
D:HIS66
|
4.1
|
6.6
|
1.0
|
ND1
|
D:HIS112
|
4.2
|
7.3
|
1.0
|
CG
|
D:HIS112
|
4.2
|
7.9
|
1.0
|
ND1
|
D:HIS68
|
4.3
|
9.2
|
1.0
|
CG
|
D:HIS68
|
4.3
|
10.7
|
1.0
|
C19
|
D:KMP1356
|
4.3
|
19.6
|
1.0
|
CG
|
D:GLU73
|
4.4
|
13.5
|
1.0
|
C14
|
D:KMP1356
|
4.6
|
18.5
|
1.0
|
C3
|
D:KMP1356
|
4.9
|
15.4
|
1.0
|
CB
|
D:GLU73
|
4.9
|
10.2
|
1.0
|
CZ
|
D:PHE75
|
4.9
|
9.3
|
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 21:52:48 2024
|