Iron in PDB 1h7x: 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;

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

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:

Fluorine

(F)

4 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 40; Page 5, Binding sites: 41 - 50; Page 6, Binding sites: 51 - 60; Page 7, Binding sites: 61 - 64;

Binding sites:

The binding sites of Iron 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 Iron atom.
In total 64 binding sites of Iron 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 Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 64 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 Iron with other atoms in the Fe 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:Fe1026 b:14.5 occ:1.00 FE1 A:SF41026 0.0 14.5 1.0 SG A:CYS91 2.4 12.4 1.0 S3 A:SF41026 2.4 15.4 1.0 S2 A:SF41026 2.5 14.7 1.0 S4 A:SF41026 2.6 15.6 1.0 FE4 A:SF41026 2.8 14.7 1.0 FE2 A:SF41026 2.9 14.9 1.0 FE3 A:SF41026 2.9 14.9 1.0 CB A:CYS91 3.1 11.6 1.0 CA A:CYS91 3.9 11.6 1.0 S1 A:SF41026 4.2 15.3 1.0 OG1 A:THR93 4.2 15.6 1.0 CG2 A:VAL490 4.4 8.2 1.0 CD2 A:LEU95 4.4 18.4 1.0 C A:CYS91 4.6 11.8 1.0 CB A:LEU95 4.6 15.6 1.0 CD A:PRO92 4.6 12.4 1.0 OE1 A:GLN156 4.7 13.4 1.0 CB A:CYS136 4.7 11.6 1.0 N A:PRO92 4.8 12.0 1.0 SG A:CYS136 4.8 11.4 1.0 CG A:LEU95 4.9 17.6 1.0 CD1 A:LEU95 5.0 19.0 1.0 SG A:CYS130 5.0 15.2 1.0

Iron binding site 2 out of 64 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 Iron with other atoms in the Fe 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 A:Fe1026 b:14.9 occ:1.00 FE2 A:SF41026 0.0 14.9 1.0 SG A:CYS136 2.2 11.4 1.0 S1 A:SF41026 2.6 15.3 1.0 S3 A:SF41026 2.6 15.4 1.0 S4 A:SF41026 2.7 15.6 1.0 FE4 A:SF41026 2.8 14.7 1.0 FE1 A:SF41026 2.9 14.5 1.0 FE3 A:SF41026 3.0 14.9 1.0 CB A:CYS136 3.0 11.6 1.0 CG2 A:THR132 4.2 12.0 1.0 S2 A:SF41026 4.3 14.7 1.0 CA A:CYS136 4.3 12.1 1.0 CG2 A:ILE152 4.3 9.4 1.0 N A:CYS136 4.3 11.2 1.0 CB A:CYS91 4.7 11.6 1.0 OE1 A:GLN156 4.7 13.4 1.0 CB A:CYS130 4.8 13.6 1.0 CB A:ILE152 4.9 9.8 1.0 SG A:CYS91 4.9 12.4 1.0 SG A:CYS130 4.9 15.2 1.0 CB A:THR132 5.0 11.7 1.0 CD1 A:ILE97 5.0 12.6 1.0

Iron binding site 3 out of 64 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 Iron with other atoms in the Fe 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 A:Fe1026 b:14.9 occ:1.00 FE3 A:SF41026 0.0 14.9 1.0 OE1 A:GLN156 2.0 13.4 1.0 S2 A:SF41026 2.4 14.7 1.0 S1 A:SF41026 2.4 15.3 1.0 S4 A:SF41026 2.6 15.6 1.0 FE4 A:SF41026 2.9 14.7 1.0 CD A:GLN156 2.9 12.4 1.0 FE1 A:SF41026 2.9 14.5 1.0 FE2 A:SF41026 3.0 14.9 1.0 NE2 A:GLN156 3.2 10.4 1.0 CD2 A:LEU95 3.6 18.4 1.0 CG A:GLN156 4.2 9.1 1.0 S3 A:SF41026 4.3 15.4 1.0 CB A:GLN156 4.5 9.7 1.0 CG2 A:ILE152 4.8 9.4 1.0 CG A:LEU95 4.9 17.6 1.0 SG A:CYS130 4.9 15.2 1.0 SG A:CYS91 5.0 12.4 1.0 SG A:CYS136 5.0 11.4 1.0

Iron binding site 4 out of 64 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 Iron with other atoms in the Fe 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 A:Fe1026 b:14.7 occ:1.00 FE4 A:SF41026 0.0 14.7 1.0 S3 A:SF41026 2.4 15.4 1.0 SG A:CYS130 2.4 15.2 1.0 S1 A:SF41026 2.4 15.3 1.0 S2 A:SF41026 2.6 14.7 1.0 FE1 A:SF41026 2.8 14.5 1.0 FE2 A:SF41026 2.8 14.9 1.0 FE3 A:SF41026 2.9 14.9 1.0 CB A:CYS130 3.1 13.6 1.0 S4 A:SF41026 4.3 15.6 1.0 CB A:CYS126 4.3 10.9 1.0 CG2 A:VAL490 4.3 8.2 1.0 O A:CYS126 4.4 12.7 1.0 CB A:VAL490 4.4 9.2 1.0 CA A:CYS130 4.6 12.7 1.0 OE1 A:GLN156 4.7 13.4 1.0 CG1 A:VAL490 4.7 8.6 1.0 C A:CYS126 4.8 11.9 1.0 NE2 A:GLN156 4.8 10.4 1.0 SG A:CYS136 4.9 11.4 1.0 CD1 A:LEU135 5.0 10.4 1.0 SG A:CYS91 5.0 12.4 1.0

Iron binding site 5 out of 64 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 Iron with other atoms in the Fe binding site number 5 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:Fe1027 b:14.1 occ:1.00 FE1 A:SF41027 0.0 14.1 1.0 SG A:CYS140 2.4 13.2 1.0 S3 A:SF41027 2.4 12.8 1.0 S2 A:SF41027 2.5 14.4 1.0 S4 A:SF41027 2.6 15.8 1.0 FE4 A:SF41027 2.8 14.5 1.0 FE2 A:SF41027 2.8 14.0 1.0 FE3 A:SF41027 2.9 12.9 1.0 CB A:CYS140 3.4 11.6 1.0 CA A:CYS140 3.7 13.7 1.0 N A:ASN141 3.8 12.5 1.0 CG1 A:ILE150 4.1 9.5 1.0 C A:CYS140 4.1 12.7 1.0 S1 A:SF41027 4.2 15.7 1.0 N A:LEU142 4.4 11.1 1.0 CB A:ILE150 4.5 11.4 1.0 SG A:CYS87 4.7 10.6 1.0 CB A:CYS87 4.8 11.2 1.0 CA A:ASN141 4.8 10.5 1.0 CB A:LEU142 4.8 11.6 1.0 SG A:CYS82 4.9 12.3 1.0 CG A:LEU142 5.0 12.7 1.0 N A:ILE150 5.0 12.2 1.0

Iron binding site 6 out of 64 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 Iron with other atoms in the Fe binding site number 6 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:Fe1027 b:14.0 occ:1.00 FE2 A:SF41027 0.0 14.0 1.0 SG A:CYS87 2.2 10.6 1.0 S1 A:SF41027 2.6 15.7 1.0 S3 A:SF41027 2.6 12.8 1.0 S4 A:SF41027 2.7 15.8 1.0 FE4 A:SF41027 2.8 14.5 1.0 FE1 A:SF41027 2.8 14.1 1.0 FE3 A:SF41027 3.0 12.9 1.0 CB A:CYS87 3.2 11.2 1.0 CB A:ALA85 4.2 11.2 1.0 S2 A:SF41027 4.2 14.4 1.0 CG2 A:ILE97 4.3 12.5 1.0 CA A:CYS87 4.4 11.5 1.0 N A:CYS87 4.4 11.3 1.0 CD1 A:ILE152 4.6 8.8 1.0 CB A:ILE97 4.8 11.6 1.0 SG A:CYS140 5.0 13.2 1.0 SG A:CYS79 5.0 12.5 1.0

Iron binding site 7 out of 64 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 Iron with other atoms in the Fe binding site number 7 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:Fe1027 b:12.9 occ:1.00 FE3 A:SF41027 0.0 12.9 1.0 SG A:CYS79 2.4 12.5 1.0 S2 A:SF41027 2.4 14.4 1.0 S1 A:SF41027 2.4 15.7 1.0 S4 A:SF41027 2.6 15.8 1.0 FE4 A:SF41027 2.8 14.5 1.0 FE1 A:SF41027 2.9 14.1 1.0 FE2 A:SF41027 3.0 14.0 1.0 CB A:CYS79 3.5 11.5 1.0 N A:LEU80 3.9 11.7 1.0 N A:LYS81 3.9 12.8 1.0 CA A:CYS79 4.0 11.1 1.0 CG1 A:ILE150 4.0 9.5 1.0 C A:CYS79 4.3 11.2 1.0 S3 A:SF41027 4.3 12.8 1.0 CA A:LYS81 4.6 13.2 1.0 CD1 A:ILE101 4.6 9.0 1.0 CB A:ILE150 4.7 11.4 1.0 CA A:LEU80 4.8 11.4 1.0 SG A:CYS82 4.8 12.3 1.0 C A:LEU80 4.8 12.9 1.0 N A:CYS82 4.9 12.0 1.0 SG A:CYS140 5.0 13.2 1.0

Iron binding site 8 out of 64 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 Iron with other atoms in the Fe binding site number 8 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:Fe1027 b:14.5 occ:1.00 FE4 A:SF41027 0.0 14.5 1.0 S3 A:SF41027 2.4 12.8 1.0 SG A:CYS82 2.4 12.3 1.0 S1 A:SF41027 2.4 15.7 1.0 S2 A:SF41027 2.6 14.4 1.0 FE1 A:SF41027 2.8 14.1 1.0 FE2 A:SF41027 2.8 14.0 1.0 FE3 A:SF41027 2.8 12.9 1.0 CB A:CYS82 3.3 10.0 1.0 N A:CYS82 3.8 12.0 1.0 CA A:CYS82 4.2 12.3 1.0 ND2 A:ASN141 4.2 8.6 1.0 S4 A:SF41027 4.3 15.8 1.0 N A:LYS81 4.3 12.8 1.0 CB A:LEU80 4.5 10.7 1.0 CB A:ASN141 4.7 9.6 1.0 N A:LEU80 4.7 11.7 1.0 N A:ASN141 4.7 12.5 1.0 SG A:CYS79 4.7 12.5 1.0 SG A:CYS87 4.8 10.6 1.0 C A:LYS81 4.8 12.8 1.0 C A:LEU80 4.9 12.9 1.0 CA A:LYS81 4.9 13.2 1.0 CG A:ASN141 4.9 9.4 1.0 CB A:ALA85 4.9 11.2 1.0 CA A:LEU80 4.9 11.4 1.0 SG A:CYS140 5.0 13.2 1.0

Iron binding site 9 out of 64 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 Iron with other atoms in the Fe binding site number 9 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:Fe1028 b:16.4 occ:1.00 FE1 A:SF41028 0.0 16.4 1.0 SG A:CYS996 2.4 14.9 1.0 S3 A:SF41028 2.4 15.2 1.0 S2 A:SF41028 2.5 16.4 1.0 S4 A:SF41028 2.6 17.7 1.0 FE4 A:SF41028 2.8 15.8 1.0 FE2 A:SF41028 2.9 16.7 1.0 FE3 A:SF41028 2.9 15.1 1.0 CB A:CYS996 3.4 13.3 1.0 CD A:PRO997 3.9 13.8 1.0 CA A:CYS996 4.0 12.6 1.0 S1 A:SF41028 4.2 16.0 1.0 SG A:CYS1001 4.3 17.8 1.0 CD1 A:ILE1002 4.4 13.7 1.0 N A:PRO997 4.5 12.4 1.0 CG1 A:ILE1002 4.6 13.6 1.0 C A:CYS996 4.6 12.5 1.0 CG A:PRO997 4.7 14.8 1.0 CB A:CYS1001 4.7 16.1 1.0 SG A:CYS956 4.8 13.3 1.0 SG A:CYS959 4.9 13.7 1.0 N A:ILE998 5.0 13.5 1.0

Iron binding site 10 out of 64 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 Iron with other atoms in the Fe binding site number 10 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:Fe1028 b:16.7 occ:1.00 FE2 A:SF41028 0.0 16.7 1.0 SG A:CYS959 2.3 13.7 1.0 S1 A:SF41028 2.6 16.0 1.0 S3 A:SF41028 2.6 15.2 1.0 S4 A:SF41028 2.8 17.7 1.0 FE4 A:SF41028 2.8 15.8 1.0 FE1 A:SF41028 2.9 16.4 1.0 FE3 A:SF41028 3.0 15.1 1.0 CB A:CYS959 3.2 11.2 1.0 N A:CYS959 3.7 10.4 1.0 CG A:PRO980 4.0 14.6 1.0 CA A:CYS959 4.1 10.4 1.0 S2 A:SF41028 4.3 16.4 1.0 N A:LYS958 4.5 10.8 1.0 CB A:PRO980 4.6 14.7 1.0 N A:GLY957 4.6 11.0 1.0 CD1 A:ILE1002 4.6 13.7 1.0 CA A:GLY957 4.8 10.9 1.0 C A:GLY957 4.8 10.6 1.0 SG A:CYS956 4.8 13.3 1.0 SG A:CYS953 4.9 13.7 1.0 C A:LYS958 4.9 10.0 1.0 CD1 A:ILE948 4.9 17.7 1.0 CD A:PRO980 4.9 14.1 1.0 N A:TYR960 5.0 10.4 1.0

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