Atomistry » Fluorine » PDB 1h2j-1j97 » 1h7x
Atomistry »
  Fluorine »
    PDB 1h2j-1j97 »
      1h7x »

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: Wed Jul 31 11:30:38 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy