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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:

Iron (Fe) 64 atoms

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 Dec 13 19:19:41 2020

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