Iodine in PDB 1gte: Dihydropyrimidine Dehydrogenase (Dpd) From Pig, Binary Complex with 5- Iodouracil
Enzymatic activity of Dihydropyrimidine Dehydrogenase (Dpd) From Pig, Binary Complex with 5- Iodouracil
All present enzymatic activity of Dihydropyrimidine Dehydrogenase (Dpd) From Pig, Binary Complex with 5- Iodouracil:
1.3.1.2;
Protein crystallography data
The structure of Dihydropyrimidine Dehydrogenase (Dpd) From Pig, Binary Complex with 5- Iodouracil, PDB code: 1gte
was solved by
D.Dobritzsch,
S.Ricagno,
G.Schneider,
K.D.Schnackerz,
Y.Lindqvist,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
24.98 /
1.65
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
81.710,
158.370,
162.330,
90.00,
95.84,
90.00
|
R / Rfree (%)
|
18.1 /
19.7
|
Other elements in 1gte:
The structure of Dihydropyrimidine Dehydrogenase (Dpd) From Pig, Binary Complex with 5- Iodouracil also contains other interesting chemical elements:
Iodine Binding Sites:
The binding sites of Iodine atom in the Dihydropyrimidine Dehydrogenase (Dpd) From Pig, Binary Complex with 5- Iodouracil
(pdb code 1gte). This binding sites where shown within
5.0 Angstroms radius around Iodine atom.
In total 4 binding sites of Iodine where determined in the
Dihydropyrimidine Dehydrogenase (Dpd) From Pig, Binary Complex with 5- Iodouracil, PDB code: 1gte:
Jump to Iodine binding site number:
1;
2;
3;
4;
Iodine binding site 1 out
of 4 in 1gte
Go back to
Iodine Binding Sites List in 1gte
Iodine binding site 1 out
of 4 in the Dihydropyrimidine Dehydrogenase (Dpd) From Pig, Binary Complex with 5- Iodouracil
Mono view
Stereo pair view
|
A full contact list of Iodine with other atoms in the I binding
site number 1 of Dihydropyrimidine Dehydrogenase (Dpd) From Pig, Binary Complex with 5- Iodouracil within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:I1034
b:29.6
occ:1.00
|
I5
|
A:IUR1034
|
0.0
|
29.6
|
1.0
|
C5
|
A:IUR1034
|
2.1
|
21.2
|
1.0
|
O
|
A:HOH2798
|
2.9
|
56.2
|
1.0
|
C4
|
A:IUR1034
|
3.0
|
20.9
|
1.0
|
C6
|
A:IUR1034
|
3.1
|
22.1
|
1.0
|
O4
|
A:IUR1034
|
3.2
|
19.8
|
1.0
|
O
|
A:HOH2372
|
3.5
|
32.9
|
1.0
|
CG2
|
A:ILE613
|
3.7
|
21.3
|
1.0
|
O4
|
A:FMN1030
|
3.7
|
18.6
|
1.0
|
N
|
A:ILE613
|
3.8
|
18.9
|
1.0
|
ND2
|
A:ASN668
|
3.8
|
18.7
|
1.0
|
C
|
A:LEU612
|
3.8
|
18.1
|
1.0
|
C4
|
A:FMN1030
|
3.9
|
16.4
|
1.0
|
CA
|
A:ILE613
|
4.0
|
18.9
|
1.0
|
O
|
A:LEU612
|
4.0
|
18.5
|
1.0
|
N3
|
A:FMN1030
|
4.1
|
16.1
|
1.0
|
N3
|
A:IUR1034
|
4.3
|
18.4
|
1.0
|
N1
|
A:IUR1034
|
4.4
|
19.1
|
1.0
|
CA
|
A:LEU612
|
4.4
|
17.7
|
1.0
|
CB
|
A:ILE613
|
4.5
|
19.8
|
1.0
|
O
|
A:GLU611
|
4.5
|
18.1
|
1.0
|
C4A
|
A:FMN1030
|
4.6
|
15.2
|
1.0
|
CG
|
A:ASN668
|
4.7
|
19.5
|
1.0
|
OD1
|
A:ASN668
|
4.9
|
22.4
|
1.0
|
C2
|
A:IUR1034
|
4.9
|
19.8
|
1.0
|
CB
|
A:THR575
|
4.9
|
16.1
|
1.0
|
O
|
A:HOH2797
|
4.9
|
24.5
|
1.0
|
C2
|
A:FMN1030
|
5.0
|
16.3
|
1.0
|
N5
|
A:FMN1030
|
5.0
|
16.0
|
1.0
|
|
Iodine binding site 2 out
of 4 in 1gte
Go back to
Iodine Binding Sites List in 1gte
Iodine binding site 2 out
of 4 in the Dihydropyrimidine Dehydrogenase (Dpd) From Pig, Binary Complex with 5- Iodouracil
Mono view
Stereo pair view
|
A full contact list of Iodine with other atoms in the I binding
site number 2 of Dihydropyrimidine Dehydrogenase (Dpd) From Pig, Binary Complex with 5- Iodouracil within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:I1034
b:30.1
occ:1.00
|
I5
|
B:IUR1034
|
0.0
|
30.1
|
1.0
|
C5
|
B:IUR1034
|
2.1
|
20.3
|
1.0
|
O
|
B:HOH2825
|
3.0
|
50.2
|
1.0
|
C4
|
B:IUR1034
|
3.0
|
21.3
|
1.0
|
C6
|
B:IUR1034
|
3.1
|
21.6
|
1.0
|
O
|
B:HOH3212
|
3.1
|
60.9
|
1.0
|
O4
|
B:IUR1034
|
3.2
|
19.4
|
1.0
|
O
|
B:HOH2402
|
3.5
|
35.3
|
1.0
|
O4
|
B:FMN1030
|
3.7
|
18.5
|
1.0
|
CG2
|
B:ILE613
|
3.7
|
21.6
|
1.0
|
N
|
B:ILE613
|
3.8
|
18.3
|
1.0
|
C
|
B:LEU612
|
3.8
|
18.6
|
1.0
|
ND2
|
B:ASN668
|
3.8
|
20.1
|
1.0
|
C4
|
B:FMN1030
|
3.9
|
17.2
|
1.0
|
O
|
B:LEU612
|
4.0
|
19.5
|
1.0
|
CA
|
B:ILE613
|
4.0
|
19.3
|
1.0
|
O
|
B:HOH2401
|
4.0
|
45.6
|
1.0
|
N3
|
B:FMN1030
|
4.2
|
16.7
|
1.0
|
N3
|
B:IUR1034
|
4.3
|
18.4
|
1.0
|
CA
|
B:LEU612
|
4.4
|
17.9
|
1.0
|
N1
|
B:IUR1034
|
4.4
|
19.4
|
1.0
|
O
|
B:GLU611
|
4.5
|
18.2
|
1.0
|
CB
|
B:ILE613
|
4.5
|
20.4
|
1.0
|
C4A
|
B:FMN1030
|
4.6
|
16.0
|
1.0
|
O
|
B:HOH2829
|
4.6
|
26.8
|
1.0
|
CG
|
B:ASN668
|
4.7
|
20.8
|
1.0
|
NZ
|
B:LYS574
|
4.8
|
23.0
|
1.0
|
C2
|
B:IUR1034
|
4.9
|
19.3
|
1.0
|
OD1
|
B:ASN668
|
4.9
|
23.3
|
1.0
|
CB
|
B:THR575
|
4.9
|
15.8
|
1.0
|
N5
|
B:FMN1030
|
5.0
|
17.2
|
1.0
|
OG1
|
B:THR575
|
5.0
|
16.7
|
1.0
|
C2
|
B:FMN1030
|
5.0
|
17.3
|
1.0
|
|
Iodine binding site 3 out
of 4 in 1gte
Go back to
Iodine Binding Sites List in 1gte
Iodine binding site 3 out
of 4 in the Dihydropyrimidine Dehydrogenase (Dpd) From Pig, Binary Complex with 5- Iodouracil
Mono view
Stereo pair view
|
A full contact list of Iodine with other atoms in the I binding
site number 3 of Dihydropyrimidine Dehydrogenase (Dpd) From Pig, Binary Complex with 5- Iodouracil within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:I1034
b:25.4
occ:1.00
|
I5
|
C:IUR1034
|
0.0
|
25.4
|
1.0
|
C5
|
C:IUR1034
|
2.1
|
18.8
|
1.0
|
C4
|
C:IUR1034
|
3.0
|
19.9
|
1.0
|
C6
|
C:IUR1034
|
3.0
|
20.4
|
1.0
|
O4
|
C:IUR1034
|
3.2
|
18.5
|
1.0
|
O
|
C:HOH2367
|
3.5
|
31.5
|
1.0
|
O4
|
C:FMN1030
|
3.7
|
15.9
|
1.0
|
ND2
|
C:ASN668
|
3.8
|
16.6
|
1.0
|
CG2
|
C:ILE613
|
3.8
|
20.0
|
1.0
|
N
|
C:ILE613
|
3.8
|
17.4
|
1.0
|
C
|
C:LEU612
|
3.9
|
17.3
|
1.0
|
C4
|
C:FMN1030
|
3.9
|
14.7
|
1.0
|
O
|
C:LEU612
|
4.0
|
17.7
|
1.0
|
CA
|
C:ILE613
|
4.1
|
17.9
|
1.0
|
N3
|
C:FMN1030
|
4.1
|
15.3
|
1.0
|
O
|
C:HOH2365
|
4.3
|
42.5
|
1.0
|
N3
|
C:IUR1034
|
4.3
|
17.3
|
1.0
|
N1
|
C:IUR1034
|
4.4
|
18.2
|
1.0
|
CA
|
C:LEU612
|
4.4
|
16.5
|
1.0
|
C4A
|
C:FMN1030
|
4.5
|
14.4
|
1.0
|
O
|
C:GLU611
|
4.6
|
17.0
|
1.0
|
CB
|
C:ILE613
|
4.6
|
18.9
|
1.0
|
O
|
C:HOH2794
|
4.7
|
22.4
|
1.0
|
CG
|
C:ASN668
|
4.7
|
19.7
|
1.0
|
NZ
|
C:LYS574
|
4.8
|
23.0
|
1.0
|
C2
|
C:IUR1034
|
4.9
|
19.7
|
1.0
|
C2
|
C:FMN1030
|
4.9
|
16.0
|
1.0
|
N5
|
C:FMN1030
|
4.9
|
15.2
|
1.0
|
CB
|
C:THR575
|
4.9
|
14.6
|
1.0
|
CB
|
C:SER670
|
5.0
|
29.5
|
1.0
|
OD1
|
C:ASN668
|
5.0
|
22.4
|
1.0
|
OG1
|
C:THR575
|
5.0
|
13.8
|
1.0
|
OG
|
C:SER670
|
5.0
|
29.9
|
1.0
|
|
Iodine binding site 4 out
of 4 in 1gte
Go back to
Iodine Binding Sites List in 1gte
Iodine binding site 4 out
of 4 in the Dihydropyrimidine Dehydrogenase (Dpd) From Pig, Binary Complex with 5- Iodouracil
Mono view
Stereo pair view
|
A full contact list of Iodine with other atoms in the I binding
site number 4 of Dihydropyrimidine Dehydrogenase (Dpd) From Pig, Binary Complex with 5- Iodouracil within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:I1034
b:25.2
occ:1.00
|
I5
|
D:IUR1034
|
0.0
|
25.2
|
1.0
|
C5
|
D:IUR1034
|
2.1
|
17.9
|
1.0
|
C4
|
D:IUR1034
|
3.0
|
17.2
|
1.0
|
C6
|
D:IUR1034
|
3.1
|
19.7
|
1.0
|
O4
|
D:IUR1034
|
3.2
|
15.7
|
1.0
|
O
|
D:HOH2423
|
3.4
|
31.8
|
1.0
|
CG2
|
D:ILE613
|
3.7
|
19.2
|
1.0
|
O4
|
D:FMN1030
|
3.7
|
14.4
|
1.0
|
ND2
|
D:ASN668
|
3.8
|
17.2
|
1.0
|
N
|
D:ILE613
|
3.8
|
16.9
|
1.0
|
C
|
D:LEU612
|
3.8
|
17.0
|
1.0
|
C4
|
D:FMN1030
|
3.9
|
13.5
|
1.0
|
O
|
D:LEU612
|
4.0
|
17.1
|
1.0
|
CA
|
D:ILE613
|
4.0
|
17.1
|
1.0
|
N3
|
D:FMN1030
|
4.1
|
13.8
|
1.0
|
N3
|
D:IUR1034
|
4.3
|
15.4
|
1.0
|
N1
|
D:IUR1034
|
4.4
|
17.0
|
1.0
|
CA
|
D:LEU612
|
4.4
|
16.9
|
1.0
|
CB
|
D:ILE613
|
4.5
|
18.8
|
1.0
|
O
|
D:GLU611
|
4.5
|
15.1
|
1.0
|
C4A
|
D:FMN1030
|
4.6
|
13.3
|
1.0
|
CG
|
D:ASN668
|
4.7
|
19.7
|
1.0
|
O
|
D:HOH2868
|
4.7
|
21.7
|
1.0
|
O
|
D:HOH2939
|
4.8
|
36.2
|
1.0
|
OD1
|
D:ASN668
|
4.9
|
21.5
|
1.0
|
C2
|
D:IUR1034
|
4.9
|
16.4
|
1.0
|
CB
|
D:THR575
|
4.9
|
14.3
|
1.0
|
C2
|
D:FMN1030
|
4.9
|
13.6
|
1.0
|
N5
|
D:FMN1030
|
5.0
|
15.1
|
1.0
|
OG1
|
D:THR575
|
5.0
|
14.0
|
1.0
|
NZ
|
D:LYS574
|
5.0
|
19.6
|
1.0
|
CB
|
D:SER670
|
5.0
|
27.4
|
1.0
|
|
Reference:
D.Dobritzsch,
S.Ricagno,
G.Schneider,
K.D.Schnackerz,
Y.Lindqvist.
Crystal Structure of the Productive Ternary Complex of Dihydropyrimidine Dehydrogenase with Nadph and 5-Iodouracil. Implications For Mechanism of Inhibition and Electron Transfer. J. Biol. Chem. V. 277 13155 2002.
ISSN: ISSN 0021-9258
PubMed: 11796730
DOI: 10.1074/JBC.M111877200
Page generated: Sun Aug 11 09:58:37 2024
|