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Iodine in PDB 1gth: Dihydropyrimidine Dehydrogenase (Dpd) From Pig, Ternary Complex with Nadph and 5-Iodouracil

Enzymatic activity of Dihydropyrimidine Dehydrogenase (Dpd) From Pig, Ternary Complex with Nadph and 5-Iodouracil

All present enzymatic activity of Dihydropyrimidine Dehydrogenase (Dpd) From Pig, Ternary Complex with Nadph and 5-Iodouracil:
1.3.1.2;

Protein crystallography data

The structure of Dihydropyrimidine Dehydrogenase (Dpd) From Pig, Ternary Complex with Nadph and 5-Iodouracil, PDB code: 1gth 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) 25.00 / 2.25
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 82.210, 159.690, 167.590, 90.00, 97.11, 90.00
R / Rfree (%) 17.7 / 20.9

Other elements in 1gth:

The structure of Dihydropyrimidine Dehydrogenase (Dpd) From Pig, Ternary Complex with Nadph and 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, Ternary Complex with Nadph and 5-Iodouracil (pdb code 1gth). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 2 binding sites of Iodine where determined in the Dihydropyrimidine Dehydrogenase (Dpd) From Pig, Ternary Complex with Nadph and 5-Iodouracil, PDB code: 1gth:
Jump to Iodine binding site number: 1; 2;

Iodine binding site 1 out of 2 in 1gth

Go back to Iodine Binding Sites List in 1gth
Iodine binding site 1 out of 2 in the Dihydropyrimidine Dehydrogenase (Dpd) From Pig, Ternary Complex with Nadph and 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, Ternary Complex with Nadph and 5-Iodouracil within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I1034

b:52.3
occ:0.20
I5 B:IDH1034 0.0 52.3 0.2
C5 B:IDH1034 2.2 45.2 1.0
C6 B:IDH1034 3.0 46.0 1.0
C4 B:IDH1034 3.0 44.1 1.0
O4 B:IDH1034 3.1 39.5 1.0
SG B:CYS671 3.2 47.0 1.0
CG2 B:ILE613 3.3 26.3 1.0
C B:LEU612 3.5 24.9 1.0
N B:ILE613 3.6 25.4 1.0
CB B:CYS671 3.6 41.7 1.0
O B:LEU612 3.7 24.0 1.0
CA B:ILE613 3.8 25.1 1.0
O4 B:FMN1030 3.9 21.7 1.0
C4 B:FMN1030 4.0 20.1 1.0
ND2 B:ASN668 4.1 15.9 1.0
CA B:LEU612 4.1 24.7 1.0
CB B:ILE613 4.2 25.9 1.0
CG B:MET675 4.3 48.1 1.0
N3 B:IDH1034 4.3 42.6 1.0
N1 B:IDH1034 4.4 43.1 1.0
O B:GLU611 4.4 22.4 1.0
N3 B:FMN1030 4.4 17.9 1.0
C4A B:FMN1030 4.6 19.8 1.0
CA B:CYS671 4.6 40.1 1.0
C2 B:IDH1034 4.9 42.3 1.0
CE B:MET642 4.9 31.4 1.0
N5 B:FMN1030 4.9 20.5 1.0

Iodine binding site 2 out of 2 in 1gth

Go back to Iodine Binding Sites List in 1gth
Iodine binding site 2 out of 2 in the Dihydropyrimidine Dehydrogenase (Dpd) From Pig, Ternary Complex with Nadph and 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, Ternary Complex with Nadph and 5-Iodouracil within 5.0Å range:
probe atom residue distance (Å) B Occ
C:I1034

b:38.4
occ:0.20
I5 C:IUR1034 0.0 38.4 0.2
C5 C:IUR1034 2.1 32.1 1.0
C4 C:IUR1034 3.0 30.8 1.0
CG2 C:ILE613 3.1 26.3 1.0
C6 C:IUR1034 3.1 30.7 1.0
O4 C:IUR1034 3.2 28.9 1.0
SG C:CYS671 3.2 50.5 1.0
O4 C:FMN1030 3.6 22.8 1.0
ND2 C:ASN668 3.7 22.3 1.0
C4 C:FMN1030 3.7 22.0 1.0
CB C:CYS671 3.7 46.1 1.0
N C:ILE613 3.7 26.7 1.0
CA C:ILE613 3.8 26.5 1.0
C C:LEU612 3.8 26.6 1.0
N3 C:FMN1030 3.9 19.9 1.0
O C:LEU612 3.9 25.0 1.0
CB C:ILE613 4.0 28.5 1.0
N3 C:IUR1034 4.3 28.0 1.0
N1 C:IUR1034 4.4 29.3 1.0
CG C:MET675 4.4 60.8 1.0
C4A C:FMN1030 4.4 21.4 1.0
CG C:ASN668 4.6 21.9 1.0
CA C:LEU612 4.6 26.0 1.0
CA C:CYS671 4.7 44.6 1.0
OG1 C:THR575 4.7 19.1 1.0
CB C:THR575 4.7 20.6 1.0
C2 C:FMN1030 4.7 21.5 1.0
OD1 C:ASN668 4.8 23.4 1.0
N5 C:FMN1030 4.9 21.0 1.0
C2 C:IUR1034 4.9 28.1 1.0
O C:GLU611 5.0 26.7 1.0
NZ C:LYS574 5.0 31.1 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 19:19:40 2020

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