Iron in PDB 1gth: 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;

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

The structure of Dihydropyrimidine Dehydrogenase (Dpd) From Pig, Ternary Complex with Nadph and 5-Iodouracil also contains other interesting chemical elements:

Iodine

(I)

2 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 with Nadph and 5-Iodouracil (pdb code 1gth). 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 with Nadph and 5-Iodouracil, PDB code: 1gth:
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 with Nadph and 5-Iodouracil


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 with Nadph and 5-Iodouracil within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1026 b:23.4 occ:1.00 FE1 A:SF41026 0.0 23.4 1.0 SG A:CYS91 2.3 18.7 1.0 S3 A:SF41026 2.4 21.8 1.0 S2 A:SF41026 2.5 23.4 1.0 S4 A:SF41026 2.6 23.4 1.0 FE4 A:SF41026 2.8 22.7 1.0 FE2 A:SF41026 2.8 24.0 1.0 FE3 A:SF41026 2.9 23.4 1.0 CB A:CYS91 3.2 18.7 1.0 CA A:CYS91 4.0 19.5 1.0 OG1 A:THR93 4.1 19.5 1.0 S1 A:SF41026 4.2 22.9 1.0 CD1 A:LEU95 4.2 25.8 1.0 CG A:LEU95 4.3 26.3 1.0 CG2 A:VAL490 4.4 19.0 1.0 CD A:PRO92 4.6 18.4 1.0 C A:CYS91 4.6 19.0 1.0 CB A:CYS136 4.7 19.4 1.0 CB A:LEU95 4.7 24.8 1.0 OE1 A:GLN156 4.8 22.5 1.0 N A:PRO92 4.8 19.0 1.0 SG A:CYS136 4.8 19.1 1.0 SG A:CYS130 5.0 20.2 1.0

Iron binding site 2 out of 64 in the Dihydropyrimidine Dehydrogenase (Dpd) From Pig, Ternary Complex with Nadph and 5-Iodouracil


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 with Nadph and 5-Iodouracil within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1026 b:24.0 occ:1.00 FE2 A:SF41026 0.0 24.0 1.0 SG A:CYS136 2.2 19.1 1.0 S1 A:SF41026 2.6 22.9 1.0 S3 A:SF41026 2.7 21.8 1.0 S4 A:SF41026 2.7 23.4 1.0 FE4 A:SF41026 2.8 22.7 1.0 FE1 A:SF41026 2.8 23.4 1.0 FE3 A:SF41026 3.0 23.4 1.0 CB A:CYS136 3.1 19.4 1.0 CG2 A:THR132 4.1 16.1 1.0 CG2 A:ILE152 4.2 16.5 1.0 S2 A:SF41026 4.3 23.4 1.0 CA A:CYS136 4.3 20.4 1.0 N A:CYS136 4.3 21.1 1.0 CB A:CYS91 4.7 18.7 1.0 CB A:CYS130 4.8 19.9 1.0 SG A:CYS91 4.8 18.7 1.0 SG A:CYS130 4.8 20.2 1.0 CB A:ILE152 4.9 17.1 1.0 OE1 A:GLN156 4.9 22.5 1.0 CB A:THR132 4.9 18.3 1.0

Iron binding site 3 out of 64 in the Dihydropyrimidine Dehydrogenase (Dpd) From Pig, Ternary Complex with Nadph and 5-Iodouracil


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 with Nadph and 5-Iodouracil within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1026 b:23.4 occ:1.00 FE3 A:SF41026 0.0 23.4 1.0 OE1 A:GLN156 2.1 22.5 1.0 S2 A:SF41026 2.4 23.4 1.0 S1 A:SF41026 2.4 22.9 1.0 S4 A:SF41026 2.6 23.4 1.0 FE4 A:SF41026 2.8 22.7 1.0 CD A:GLN156 2.9 19.3 1.0 FE1 A:SF41026 2.9 23.4 1.0 FE2 A:SF41026 3.0 24.0 1.0 NE2 A:GLN156 3.1 18.6 1.0 CD1 A:LEU95 3.6 25.8 1.0 CG A:GLN156 4.2 19.2 1.0 S3 A:SF41026 4.3 21.8 1.0 CB A:GLN156 4.5 17.8 1.0 CG A:LEU95 4.6 26.3 1.0 CG2 A:ILE152 4.6 16.5 1.0 SG A:CYS130 4.9 20.2 1.0 SG A:CYS91 4.9 18.7 1.0 SG A:CYS136 5.0 19.1 1.0

Iron binding site 4 out of 64 in the Dihydropyrimidine Dehydrogenase (Dpd) From Pig, Ternary Complex with Nadph and 5-Iodouracil


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 with Nadph and 5-Iodouracil within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1026 b:22.7 occ:1.00 FE4 A:SF41026 0.0 22.7 1.0 SG A:CYS130 2.3 20.2 1.0 S3 A:SF41026 2.4 21.8 1.0 S1 A:SF41026 2.4 22.9 1.0 S2 A:SF41026 2.6 23.4 1.0 FE1 A:SF41026 2.8 23.4 1.0 FE2 A:SF41026 2.8 24.0 1.0 FE3 A:SF41026 2.8 23.4 1.0 CB A:CYS130 3.2 19.9 1.0 CB A:CYS126 4.3 20.7 1.0 S4 A:SF41026 4.3 23.4 1.0 CG2 A:VAL490 4.3 19.0 1.0 O A:CYS126 4.3 22.7 1.0 CB A:VAL490 4.4 19.4 1.0 CG1 A:VAL490 4.6 20.0 1.0 CA A:CYS130 4.6 20.2 1.0 C A:CYS126 4.7 22.5 1.0 NE2 A:GLN156 4.7 18.6 1.0 OE1 A:GLN156 4.8 22.5 1.0 SG A:CYS136 4.9 19.1 1.0 SG A:CYS91 4.9 18.7 1.0 CG2 A:THR132 5.0 16.1 1.0

Iron binding site 5 out of 64 in the Dihydropyrimidine Dehydrogenase (Dpd) From Pig, Ternary Complex with Nadph and 5-Iodouracil


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 with Nadph and 5-Iodouracil within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1027 b:20.2 occ:1.00 FE1 A:SF41027 0.0 20.2 1.0 SG A:CYS140 2.3 17.6 1.0 S3 A:SF41027 2.4 17.0 1.0 S2 A:SF41027 2.5 20.5 1.0 S4 A:SF41027 2.6 20.2 1.0 FE4 A:SF41027 2.8 20.9 1.0 FE2 A:SF41027 2.8 21.2 1.0 FE3 A:SF41027 2.9 20.8 1.0 CB A:CYS140 3.3 16.4 1.0 CA A:CYS140 3.7 18.6 1.0 N A:ASN141 3.8 19.6 1.0 C A:CYS140 4.1 18.6 1.0 CG1 A:ILE150 4.1 17.9 1.0 S1 A:SF41027 4.2 19.7 1.0 N A:LEU142 4.4 19.1 1.0 CB A:ILE150 4.5 19.7 1.0 SG A:CYS87 4.7 13.4 1.0 CB A:CYS87 4.8 17.2 1.0 CB A:LEU142 4.8 17.7 1.0 CG A:LEU142 4.9 17.9 1.0 CA A:ASN141 4.9 20.2 1.0 SG A:CYS82 4.9 19.2 1.0 N A:CYS140 5.0 18.1 1.0

Iron binding site 6 out of 64 in the Dihydropyrimidine Dehydrogenase (Dpd) From Pig, Ternary Complex with Nadph and 5-Iodouracil


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 with Nadph and 5-Iodouracil within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1027 b:21.2 occ:1.00 FE2 A:SF41027 0.0 21.2 1.0 SG A:CYS87 2.2 13.4 1.0 S1 A:SF41027 2.6 19.7 1.0 S3 A:SF41027 2.6 17.0 1.0 S4 A:SF41027 2.7 20.2 1.0 FE4 A:SF41027 2.8 20.9 1.0 FE1 A:SF41027 2.8 20.2 1.0 FE3 A:SF41027 3.0 20.8 1.0 CB A:CYS87 3.1 17.2 1.0 CB A:ALA85 4.2 17.8 1.0 CG2 A:ILE97 4.2 17.1 1.0 S2 A:SF41027 4.2 20.5 1.0 CA A:CYS87 4.4 17.5 1.0 N A:CYS87 4.4 17.9 1.0 CD1 A:ILE152 4.7 13.9 1.0 CB A:ILE97 4.7 18.8 1.0 SG A:CYS140 4.9 17.6 1.0 SG A:CYS82 5.0 19.2 1.0 SG A:CYS79 5.0 18.1 1.0

Iron binding site 7 out of 64 in the Dihydropyrimidine Dehydrogenase (Dpd) From Pig, Ternary Complex with Nadph and 5-Iodouracil


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 with Nadph and 5-Iodouracil within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1027 b:20.8 occ:1.00 FE3 A:SF41027 0.0 20.8 1.0 SG A:CYS79 2.4 18.1 1.0 S2 A:SF41027 2.4 20.5 1.0 S1 A:SF41027 2.4 19.7 1.0 S4 A:SF41027 2.5 20.2 1.0 FE4 A:SF41027 2.8 20.9 1.0 FE1 A:SF41027 2.9 20.2 1.0 FE2 A:SF41027 3.0 21.2 1.0 CB A:CYS79 3.5 19.4 1.0 N A:LEU80 3.8 20.2 1.0 N A:LYS81 3.9 21.2 1.0 CA A:CYS79 3.9 20.2 1.0 CG1 A:ILE150 4.0 17.9 1.0 C A:CYS79 4.2 21.4 1.0 S3 A:SF41027 4.3 17.0 1.0 CD1 A:ILE101 4.5 17.5 1.0 CA A:LYS81 4.6 19.9 1.0 CB A:ILE150 4.7 19.7 1.0 SG A:CYS82 4.8 19.2 1.0 CA A:LEU80 4.8 20.4 1.0 C A:LEU80 4.8 20.3 1.0 SG A:CYS140 4.9 17.6 1.0 N A:CYS82 5.0 18.7 1.0

Iron binding site 8 out of 64 in the Dihydropyrimidine Dehydrogenase (Dpd) From Pig, Ternary Complex with Nadph and 5-Iodouracil


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 with Nadph and 5-Iodouracil within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1027 b:20.9 occ:1.00 FE4 A:SF41027 0.0 20.9 1.0 SG A:CYS82 2.4 19.2 1.0 S3 A:SF41027 2.4 17.0 1.0 S1 A:SF41027 2.4 19.7 1.0 S2 A:SF41027 2.6 20.5 1.0 FE1 A:SF41027 2.8 20.2 1.0 FE2 A:SF41027 2.8 21.2 1.0 FE3 A:SF41027 2.8 20.8 1.0 CB A:CYS82 3.3 18.4 1.0 N A:CYS82 3.8 18.7 1.0 ND2 A:ASN141 4.2 19.9 1.0 CA A:CYS82 4.2 19.2 1.0 S4 A:SF41027 4.3 20.2 1.0 N A:LYS81 4.3 21.2 1.0 CB A:LEU80 4.4 18.8 1.0 N A:LEU80 4.7 20.2 1.0 N A:ASN141 4.7 19.6 1.0 SG A:CYS87 4.7 13.4 1.0 CB A:ASN141 4.7 19.9 1.0 SG A:CYS79 4.8 18.1 1.0 CB A:ALA85 4.8 17.8 1.0 C A:LEU80 4.9 20.3 1.0 CG A:ASN141 4.9 21.2 1.0 CA A:LEU80 4.9 20.4 1.0 C A:LYS81 4.9 19.5 1.0 SG A:CYS140 4.9 17.6 1.0 CA A:LYS81 4.9 19.9 1.0

Iron binding site 9 out of 64 in the Dihydropyrimidine Dehydrogenase (Dpd) From Pig, Ternary Complex with Nadph and 5-Iodouracil


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 with Nadph and 5-Iodouracil within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1028 b:24.7 occ:1.00 FE1 A:SF41028 0.0 24.7 1.0 SG A:CYS996 2.4 21.5 1.0 S3 A:SF41028 2.4 21.2 1.0 S2 A:SF41028 2.5 24.3 1.0 S4 A:SF41028 2.6 24.1 1.0 FE4 A:SF41028 2.8 23.6 1.0 FE2 A:SF41028 2.9 24.7 1.0 FE3 A:SF41028 2.9 23.4 1.0 CB A:CYS996 3.4 21.8 1.0 CD A:PRO997 3.9 18.7 1.0 CA A:CYS996 4.0 20.9 1.0 CD1 A:ILE1002 4.2 19.2 1.0 S1 A:SF41028 4.2 22.9 1.0 SG A:CYS1001 4.2 23.3 1.0 CG1 A:ILE1002 4.5 21.4 1.0 N A:PRO997 4.6 20.9 1.0 CB A:CYS1001 4.6 21.1 1.0 CG A:PRO997 4.7 19.9 1.0 C A:CYS996 4.7 21.1 1.0 SG A:CYS956 4.8 18.5 1.0 SG A:CYS959 5.0 17.7 1.0

Iron binding site 10 out of 64 in the Dihydropyrimidine Dehydrogenase (Dpd) From Pig, Ternary Complex with Nadph and 5-Iodouracil


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 with Nadph and 5-Iodouracil within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1028 b:24.7 occ:1.00 FE2 A:SF41028 0.0 24.7 1.0 SG A:CYS959 2.3 17.7 1.0 S1 A:SF41028 2.6 22.9 1.0 S3 A:SF41028 2.6 21.2 1.0 S4 A:SF41028 2.7 24.1 1.0 FE4 A:SF41028 2.8 23.6 1.0 FE1 A:SF41028 2.9 24.7 1.0 FE3 A:SF41028 3.0 23.4 1.0 CB A:CYS959 3.2 15.2 1.0 N A:CYS959 3.7 15.6 1.0 CG A:PRO980 3.9 24.0 1.0 CA A:CYS959 4.1 17.6 1.0 S2 A:SF41028 4.2 24.3 1.0 CD1 A:ILE1002 4.5 19.2 1.0 N A:LYS958 4.5 16.4 1.0 CB A:PRO980 4.6 23.7 1.0 N A:GLY957 4.6 17.5 1.0 CD1 A:ILE948 4.7 23.1 1.0 CA A:GLY957 4.8 16.9 1.0 SG A:CYS956 4.8 18.5 1.0 SG A:CYS953 4.8 19.0 1.0 C A:GLY957 4.9 17.9 1.0 CD A:PRO980 4.9 23.8 1.0 C A:LYS958 4.9 18.4 1.0 N A:TYR960 4.9 16.6 1.0

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