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Fluorine in PDB 1h7x: Dihydropyrimidine Dehydrogenase (Dpd) From Pig, Ternary Complex of A Mutant Enzyme (C671A), Nadph and 5-Fluorouracil

Enzymatic activity of Dihydropyrimidine Dehydrogenase (Dpd) From Pig, Ternary Complex of A Mutant Enzyme (C671A), Nadph and 5-Fluorouracil

All present enzymatic activity of Dihydropyrimidine Dehydrogenase (Dpd) From Pig, Ternary Complex of A Mutant Enzyme (C671A), Nadph and 5-Fluorouracil:
1.3.1.2;

Protein crystallography data

The structure of Dihydropyrimidine Dehydrogenase (Dpd) From Pig, Ternary Complex of A Mutant Enzyme (C671A), Nadph and 5-Fluorouracil, PDB code: 1h7x was solved by D.Dobritzsch, 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) 25.08 / 2.01
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 81.950, 159.290, 163.570, 90.00, 96.04, 90.00
R / Rfree (%) 17.1 / 19.2

Other elements in 1h7x:

The structure of Dihydropyrimidine Dehydrogenase (Dpd) From Pig, Ternary Complex of A Mutant Enzyme (C671A), Nadph and 5-Fluorouracil also contains other interesting chemical elements:

Iron (Fe) 64 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Dihydropyrimidine Dehydrogenase (Dpd) From Pig, Ternary Complex of A Mutant Enzyme (C671A), Nadph and 5-Fluorouracil (pdb code 1h7x). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Dihydropyrimidine Dehydrogenase (Dpd) From Pig, Ternary Complex of A Mutant Enzyme (C671A), Nadph and 5-Fluorouracil, PDB code: 1h7x:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 1h7x

Go back to Fluorine Binding Sites List in 1h7x
Fluorine binding site 1 out of 4 in the Dihydropyrimidine Dehydrogenase (Dpd) From Pig, Ternary Complex of A Mutant Enzyme (C671A), Nadph and 5-Fluorouracil


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Dihydropyrimidine Dehydrogenase (Dpd) From Pig, Ternary Complex of A Mutant Enzyme (C671A), Nadph and 5-Fluorouracil within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1033

b:26.6
occ:1.00
 F5 A:URF1033 0.0 26.6 1.0
C5 A:URF1033 1.3 24.4 1.0
C6 A:URF1033 2.3 23.2 1.0
C4 A:URF1033 2.4 23.2 1.0
O4 A:URF1033 2.8 23.5 1.0
N3 A:URF1033 3.6 22.7 1.0
N1 A:URF1033 3.6 23.2 1.0
O4 A:FMN1030 3.6 15.8 1.0
CG2 A:ILE613 3.6 18.6 1.0
C4 A:FMN1030 3.7 14.4 1.0
O A:HOH2339 3.7 38.0 1.0
C A:LEU612 3.8 17.6 1.0
O A:LEU612 3.9 18.0 1.0
N A:ILE613 3.9 17.7 1.0
N3 A:FMN1030 4.0 14.0 1.0
ND2 A:ASN668 4.0 18.8 1.0
CA A:ILE613 4.1 18.1 1.0
C4A A:FMN1030 4.1 13.9 1.0
C2 A:URF1033 4.2 24.1 1.0
O A:GLU611 4.3 16.9 1.0
CA A:LEU612 4.4 17.8 1.0
N5 A:FMN1030 4.5 14.0 1.0
CB A:ILE613 4.5 17.9 1.0
O A:HOH2696 4.6 25.7 1.0
C2 A:FMN1030 4.7 13.6 1.0
O A:HOH2752 4.7 37.4 1.0
C10 A:FMN1030 4.8 13.4 1.0
NZ A:LYS574 4.9 22.9 1.0
OG A:SER670 4.9 30.6 1.0
CG A:ASN668 5.0 18.3 1.0
N1 A:FMN1030 5.0 12.1 1.0

Fluorine binding site 2 out of 4 in 1h7x

Go back to Fluorine Binding Sites List in 1h7x
Fluorine binding site 2 out of 4 in the Dihydropyrimidine Dehydrogenase (Dpd) From Pig, Ternary Complex of A Mutant Enzyme (C671A), Nadph and 5-Fluorouracil


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Dihydropyrimidine Dehydrogenase (Dpd) From Pig, Ternary Complex of A Mutant Enzyme (C671A), Nadph and 5-Fluorouracil within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1033

b:23.6
occ:1.00
 F5 B:URF1033 0.0 23.6 1.0
C5 B:URF1033 1.3 21.4 1.0
C6 B:URF1033 2.3 20.4 1.0
C4 B:URF1033 2.4 20.9 1.0
O4 B:URF1033 2.9 19.3 1.0
O4 B:FMN1030 3.6 16.9 1.0
C4 B:FMN1030 3.6 15.5 1.0
N1 B:URF1033 3.6 20.5 1.0
N3 B:URF1033 3.6 19.2 1.0
CG2 B:ILE613 3.7 17.2 1.0
C B:LEU612 3.8 17.3 1.0
O B:LEU612 3.8 17.7 1.0
N B:ILE613 3.9 17.0 1.0
N3 B:FMN1030 3.9 14.3 1.0
ND2 B:ASN668 4.0 17.2 1.0
C4A B:FMN1030 4.0 14.6 1.0
CA B:ILE613 4.1 17.7 1.0
C2 B:URF1033 4.2 20.2 1.0
O B:GLU611 4.3 16.0 1.0
N5 B:FMN1030 4.4 14.8 1.0
CA B:LEU612 4.4 17.0 1.0
CB B:ILE613 4.5 17.7 1.0
C2 B:FMN1030 4.7 15.1 1.0
O B:HOH2696 4.7 27.9 1.0
C10 B:FMN1030 4.8 13.4 1.0
NZ B:LYS574 4.8 22.1 1.0
O B:HOH3048 4.8 47.1 1.0
N1 B:FMN1030 5.0 14.0 1.0
CG B:ASN668 5.0 19.0 1.0

Fluorine binding site 3 out of 4 in 1h7x

Go back to Fluorine Binding Sites List in 1h7x
Fluorine binding site 3 out of 4 in the Dihydropyrimidine Dehydrogenase (Dpd) From Pig, Ternary Complex of A Mutant Enzyme (C671A), Nadph and 5-Fluorouracil


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Dihydropyrimidine Dehydrogenase (Dpd) From Pig, Ternary Complex of A Mutant Enzyme (C671A), Nadph and 5-Fluorouracil within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F1033

b:23.8
occ:1.00
 F5 C:URF1033 0.0 23.8 1.0
C5 C:URF1033 1.3 21.3 1.0
C6 C:URF1033 2.3 22.1 1.0
C4 C:URF1033 2.4 21.4 1.0
O4 C:URF1033 2.9 20.2 1.0
O4 C:FMN1030 3.5 17.4 1.0
C4 C:FMN1030 3.6 14.2 1.0
CG2 C:ILE613 3.6 16.7 1.0
N3 C:URF1033 3.6 20.4 1.0
N1 C:URF1033 3.6 20.1 1.0
C C:LEU612 3.8 16.4 1.0
N C:ILE613 3.9 16.3 1.0
O C:LEU612 3.9 15.5 1.0
N3 C:FMN1030 3.9 12.7 1.0
ND2 C:ASN668 4.0 17.2 1.0
C4A C:FMN1030 4.0 14.4 1.0
CA C:ILE613 4.1 15.6 1.0
C2 C:URF1033 4.2 20.6 1.0
O C:GLU611 4.4 13.2 1.0
N5 C:FMN1030 4.4 14.9 1.0
CA C:LEU612 4.4 16.0 1.0
CB C:ILE613 4.5 17.0 1.0
C2 C:FMN1030 4.6 13.4 1.0
O C:HOH2714 4.7 25.1 1.0
C10 C:FMN1030 4.8 13.7 1.0
O C:HOH2772 4.9 44.5 1.0
NZ C:LYS574 4.9 23.7 1.0
N1 C:FMN1030 4.9 13.1 1.0
CG C:ASN668 5.0 18.2 1.0
OG C:SER670 5.0 29.8 1.0

Fluorine binding site 4 out of 4 in 1h7x

Go back to Fluorine Binding Sites List in 1h7x
Fluorine binding site 4 out of 4 in the Dihydropyrimidine Dehydrogenase (Dpd) From Pig, Ternary Complex of A Mutant Enzyme (C671A), Nadph and 5-Fluorouracil


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Dihydropyrimidine Dehydrogenase (Dpd) From Pig, Ternary Complex of A Mutant Enzyme (C671A), Nadph and 5-Fluorouracil within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F1033

b:25.1
occ:1.00
 F5 D:URF1033 0.0 25.1 1.0
C5 D:URF1033 1.3 20.7 1.0
C6 D:URF1033 2.3 19.6 1.0
C4 D:URF1033 2.4 19.6 1.0
O4 D:URF1033 2.8 17.1 1.0
O D:HOH2731 3.5 48.6 1.0
CG2 D:ILE613 3.5 17.4 1.0
O4 D:FMN1030 3.6 14.4 1.0
C4 D:FMN1030 3.6 13.3 1.0
N3 D:URF1033 3.6 18.8 1.0
N1 D:URF1033 3.6 19.8 1.0
C D:LEU612 3.8 16.4 1.0
O D:LEU612 3.8 15.8 1.0
N D:ILE613 3.9 16.1 1.0
ND2 D:ASN668 3.9 16.4 1.0
N3 D:FMN1030 3.9 12.4 1.0
CA D:ILE613 4.0 16.2 1.0
C4A D:FMN1030 4.1 13.2 1.0
C2 D:URF1033 4.2 19.9 1.0
O D:GLU611 4.4 14.3 1.0
CB D:ILE613 4.4 16.7 1.0
N5 D:FMN1030 4.5 12.0 1.0
CA D:LEU612 4.5 15.8 1.0
C2 D:FMN1030 4.6 13.1 1.0
O D:HOH2735 4.7 22.1 1.0
C10 D:FMN1030 4.8 12.9 1.0
NZ D:LYS574 4.8 21.4 1.0
CG D:ASN668 4.9 17.6 1.0
OG D:SER670 4.9 28.6 1.0
N1 D:FMN1030 5.0 12.1 1.0

Reference:

D.Dobritzsch, G.Schneider, K.D.Schnackerz, Y.Lindqvist. Crystal Structure of Dihydropyrimidine Dehydrogenase, A Major Determinant of the Pharmacokinetics of the Anti-Cancer Drug 5-Fluorouracil Embo J. V. 20 650 2001.
ISSN: ISSN 0261-4189
PubMed: 11179210
DOI: 10.1093/EMBOJ/20.4.650
Page generated: Sun Dec 13 11:30:05 2020

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