Iron in PDB 7ljs: Porcine Dihydropyrimidine Dehydrogenase (Dpd) Complexed with 5- Ethynyluracil (5EU) - Open Form

All present enzymatic activity of Porcine Dihydropyrimidine Dehydrogenase (Dpd) Complexed with 5- Ethynyluracil (5EU) - Open Form:
1.3.1.2;

The structure of Porcine Dihydropyrimidine Dehydrogenase (Dpd) Complexed with 5- Ethynyluracil (5EU) - Open Form, PDB code: 7ljs was solved by A.Butrin, D.Forouzesh, B.Beaupre, Z.Wawrzak, D.Liu, G.Moran, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.62 / 2.00
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	82.031, 160.046, 164.074, 90, 95.95, 90
R / Rfree (%)	17.2 / 22.9

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 Porcine Dihydropyrimidine Dehydrogenase (Dpd) Complexed with 5- Ethynyluracil (5EU) - Open Form (pdb code 7ljs). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 64 binding sites of Iron where determined in the Porcine Dihydropyrimidine Dehydrogenase (Dpd) Complexed with 5- Ethynyluracil (5EU) - Open Form, PDB code: 7ljs:
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 Porcine Dihydropyrimidine Dehydrogenase (Dpd) Complexed with 5- Ethynyluracil (5EU) - Open Form


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Porcine Dihydropyrimidine Dehydrogenase (Dpd) Complexed with 5- Ethynyluracil (5EU) - Open Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1101 b:19.2 occ:1.00 FE1 A:SF41101 0.0 19.2 1.0 S2 A:SF41101 1.9 20.3 1.0 S3 A:SF41101 2.0 20.7 1.0 S4 A:SF41101 2.1 19.9 1.0 FE2 A:SF41101 2.4 19.9 1.0 FE4 A:SF41101 2.4 19.7 1.0 FE3 A:SF41101 2.4 19.2 1.0 SG A:CYS91 2.5 20.6 1.0 CB A:CYS91 3.4 20.5 1.0 S1 A:SF41101 3.4 20.3 1.0 CD2 A:LEU95 4.1 25.4 1.0 OE1 A:GLN156 4.2 32.2 1.0 CA A:CYS91 4.2 20.5 1.0 SG A:CYS136 4.3 22.0 1.0 CG2 A:VAL490 4.4 22.9 1.0 SG A:CYS130 4.5 24.3 1.0 OG1 A:THR93 4.5 22.3 1.0 CB A:CYS136 4.6 22.0 1.0 CD1 A:LEU95 4.7 25.5 1.0 CB A:LEU95 4.7 23.9 1.0 CG A:LEU95 4.7 25.0 1.0 CD A:PRO92 4.8 20.7 1.0 C A:CYS91 5.0 20.6 1.0

Iron binding site 2 out of 64 in the Porcine Dihydropyrimidine Dehydrogenase (Dpd) Complexed with 5- Ethynyluracil (5EU) - Open Form


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Porcine Dihydropyrimidine Dehydrogenase (Dpd) Complexed with 5- Ethynyluracil (5EU) - Open Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1101 b:19.9 occ:1.00 FE2 A:SF41101 0.0 19.9 1.0 S1 A:SF41101 1.9 20.3 1.0 S3 A:SF41101 2.1 20.7 1.0 S4 A:SF41101 2.2 19.9 1.0 FE3 A:SF41101 2.3 19.2 1.0 SG A:CYS136 2.3 22.0 1.0 FE4 A:SF41101 2.3 19.7 1.0 FE1 A:SF41101 2.4 19.2 1.0 S2 A:SF41101 3.4 20.3 1.0 CB A:CYS136 3.4 22.0 1.0 OE1 A:GLN156 4.1 32.2 1.0 SG A:CYS130 4.3 24.3 1.0 CG2 A:THR132 4.3 19.3 1.0 SG A:CYS91 4.5 20.6 1.0 N A:CYS136 4.7 21.9 1.0 CG2 A:ILE152 4.7 20.0 1.0 CA A:CYS136 4.7 21.9 1.0 CB A:CYS130 4.7 23.7 1.0 CB A:CYS91 4.7 20.5 1.0 CD1 A:ILE97 5.0 21.7 1.0

Iron binding site 3 out of 64 in the Porcine Dihydropyrimidine Dehydrogenase (Dpd) Complexed with 5- Ethynyluracil (5EU) - Open Form


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Porcine Dihydropyrimidine Dehydrogenase (Dpd) Complexed with 5- Ethynyluracil (5EU) - Open Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1101 b:19.2 occ:1.00 FE3 A:SF41101 0.0 19.2 1.0 OE1 A:GLN156 2.0 32.2 1.0 S2 A:SF41101 2.0 20.3 1.0 S4 A:SF41101 2.0 19.9 1.0 S1 A:SF41101 2.0 20.3 1.0 FE2 A:SF41101 2.3 19.9 1.0 FE4 A:SF41101 2.3 19.7 1.0 FE1 A:SF41101 2.4 19.2 1.0 CD A:GLN156 3.1 30.0 1.0 S3 A:SF41101 3.4 20.7 1.0 NE2 A:GLN156 3.6 29.5 1.0 CD2 A:LEU95 3.7 25.4 1.0 SG A:CYS136 4.3 22.0 1.0 SG A:CYS130 4.4 24.3 1.0 CG A:GLN156 4.4 28.0 1.0 SG A:CYS91 4.7 20.6 1.0 CB A:GLN156 4.7 26.1 1.0 CG A:LEU95 4.9 25.0 1.0 CG2 A:ILE152 4.9 20.0 1.0

Iron binding site 4 out of 64 in the Porcine Dihydropyrimidine Dehydrogenase (Dpd) Complexed with 5- Ethynyluracil (5EU) - Open Form


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Porcine Dihydropyrimidine Dehydrogenase (Dpd) Complexed with 5- Ethynyluracil (5EU) - Open Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1101 b:19.7 occ:1.00 FE4 A:SF41101 0.0 19.7 1.0 S3 A:SF41101 1.9 20.7 1.0 S2 A:SF41101 2.1 20.3 1.0 S1 A:SF41101 2.1 20.3 1.0 SG A:CYS130 2.3 24.3 1.0 FE2 A:SF41101 2.3 19.9 1.0 FE3 A:SF41101 2.3 19.2 1.0 FE1 A:SF41101 2.4 19.2 1.0 CB A:CYS130 3.4 23.7 1.0 S4 A:SF41101 3.5 19.9 1.0 OE1 A:GLN156 4.0 32.2 1.0 CG2 A:VAL490 4.4 22.9 1.0 SG A:CYS136 4.4 22.0 1.0 CB A:CYS126 4.4 24.2 1.0 CB A:VAL490 4.6 23.5 1.0 SG A:CYS91 4.7 20.6 1.0 O A:CYS126 4.7 23.6 1.0 CG1 A:VAL490 4.8 23.7 1.0 NE2 A:GLN156 4.8 29.5 1.0 CD A:GLN156 4.8 30.0 1.0 CA A:CYS130 4.9 23.0 1.0 C A:CYS126 5.0 23.6 1.0

Iron binding site 5 out of 64 in the Porcine Dihydropyrimidine Dehydrogenase (Dpd) Complexed with 5- Ethynyluracil (5EU) - Open Form


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Porcine Dihydropyrimidine Dehydrogenase (Dpd) Complexed with 5- Ethynyluracil (5EU) - Open Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1102 b:18.9 occ:1.00 FE1 A:SF41102 0.0 18.9 1.0 S2 A:SF41102 2.0 18.2 1.0 S4 A:SF41102 2.0 18.5 1.0 S3 A:SF41102 2.0 18.6 1.0 FE4 A:SF41102 2.3 18.6 1.0 SG A:CYS140 2.4 22.4 1.0 FE2 A:SF41102 2.4 18.4 1.0 FE3 A:SF41102 2.5 18.0 1.0 S1 A:SF41102 3.6 17.7 1.0 CB A:CYS140 3.6 22.2 1.0 N A:ASN141 4.0 22.0 1.0 CA A:CYS140 4.0 22.6 1.0 CG1 A:ILE150 4.1 19.6 1.0 C A:CYS140 4.4 22.8 1.0 SG A:CYS87 4.4 23.7 1.0 SG A:CYS82 4.4 21.2 1.0 N A:LEU142 4.5 22.2 1.0 CB A:ILE150 4.5 20.0 1.0 SG A:CYS79 4.8 19.6 1.0 CB A:CYS87 4.8 22.8 1.0 CA A:ASN141 4.9 22.0 1.0 CB A:LEU142 5.0 21.9 1.0 CG A:LEU142 5.0 21.6 1.0 CB A:ASN141 5.0 21.4 1.0

Iron binding site 6 out of 64 in the Porcine Dihydropyrimidine Dehydrogenase (Dpd) Complexed with 5- Ethynyluracil (5EU) - Open Form


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Porcine Dihydropyrimidine Dehydrogenase (Dpd) Complexed with 5- Ethynyluracil (5EU) - Open Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1102 b:18.4 occ:1.00 FE2 A:SF41102 0.0 18.4 1.0 S4 A:SF41102 2.1 18.5 1.0 S3 A:SF41102 2.1 18.6 1.0 S1 A:SF41102 2.1 17.7 1.0 FE4 A:SF41102 2.2 18.6 1.0 SG A:CYS87 2.3 23.7 1.0 FE1 A:SF41102 2.4 18.9 1.0 FE3 A:SF41102 2.4 18.0 1.0 S2 A:SF41102 3.4 18.2 1.0 CB A:CYS87 3.5 22.8 1.0 CB A:ALA85 4.3 21.9 1.0 SG A:CYS82 4.3 21.2 1.0 SG A:CYS79 4.5 19.6 1.0 N A:CYS87 4.5 22.4 1.0 CG2 A:ILE97 4.5 21.0 1.0 SG A:CYS140 4.6 22.4 1.0 CA A:CYS87 4.6 22.6 1.0 CD1 A:ILE152 4.8 18.9 1.0

Iron binding site 7 out of 64 in the Porcine Dihydropyrimidine Dehydrogenase (Dpd) Complexed with 5- Ethynyluracil (5EU) - Open Form


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Porcine Dihydropyrimidine Dehydrogenase (Dpd) Complexed with 5- Ethynyluracil (5EU) - Open Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1102 b:18.0 occ:1.00 FE3 A:SF41102 0.0 18.0 1.0 S4 A:SF41102 1.9 18.5 1.0 S2 A:SF41102 2.1 18.2 1.0 S1 A:SF41102 2.2 17.7 1.0 FE4 A:SF41102 2.3 18.6 1.0 SG A:CYS79 2.3 19.6 1.0 FE2 A:SF41102 2.4 18.4 1.0 FE1 A:SF41102 2.5 18.9 1.0 CB A:CYS79 3.6 19.0 1.0 S3 A:SF41102 3.6 18.6 1.0 CA A:CYS79 4.1 19.4 1.0 CG1 A:ILE150 4.1 19.6 1.0 N A:LYS81 4.1 19.8 1.0 N A:LEU80 4.1 19.2 1.0 SG A:CYS82 4.3 21.2 1.0 C A:CYS79 4.5 19.4 1.0 CD1 A:ILE101 4.5 17.5 1.0 SG A:CYS87 4.6 23.7 1.0 SG A:CYS140 4.6 22.4 1.0 CB A:ILE150 4.7 20.0 1.0 CA A:LYS81 4.8 20.1 1.0 N A:CYS82 4.9 21.4 1.0 CG2 A:ILE150 5.0 19.9 1.0

Iron binding site 8 out of 64 in the Porcine Dihydropyrimidine Dehydrogenase (Dpd) Complexed with 5- Ethynyluracil (5EU) - Open Form


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Porcine Dihydropyrimidine Dehydrogenase (Dpd) Complexed with 5- Ethynyluracil (5EU) - Open Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1102 b:18.6 occ:1.00 FE4 A:SF41102 0.0 18.6 1.0 S1 A:SF41102 2.0 17.7 1.0 S2 A:SF41102 2.1 18.2 1.0 S3 A:SF41102 2.1 18.6 1.0 FE2 A:SF41102 2.2 18.4 1.0 FE3 A:SF41102 2.3 18.0 1.0 FE1 A:SF41102 2.3 18.9 1.0 SG A:CYS82 2.4 21.2 1.0 S4 A:SF41102 3.2 18.5 1.0 CB A:CYS82 3.7 21.4 1.0 N A:CYS82 4.0 21.4 1.0 SG A:CYS79 4.2 19.6 1.0 SG A:CYS87 4.3 23.7 1.0 N A:LYS81 4.4 19.8 1.0 CA A:CYS82 4.5 21.9 1.0 SG A:CYS140 4.5 22.4 1.0 ND2 A:ASN141 4.6 20.4 1.0 N A:LEU80 4.7 19.2 1.0 N A:ASN141 4.8 22.0 1.0 CB A:ALA85 4.8 21.9 1.0 CB A:ASN141 4.8 21.4 1.0 CB A:LEU80 4.8 19.3 1.0 CA A:LYS81 5.0 20.1 1.0

Iron binding site 9 out of 64 in the Porcine Dihydropyrimidine Dehydrogenase (Dpd) Complexed with 5- Ethynyluracil (5EU) - Open Form


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Porcine Dihydropyrimidine Dehydrogenase (Dpd) Complexed with 5- Ethynyluracil (5EU) - Open Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1103 b:20.3 occ:1.00 FE1 A:SF41103 0.0 20.3 1.0 S3 A:SF41103 2.0 20.4 1.0 S4 A:SF41103 2.0 20.8 1.0 S2 A:SF41103 2.1 21.2 1.0 FE4 A:SF41103 2.3 20.5 1.0 FE3 A:SF41103 2.4 19.5 1.0 SG A:CYS996 2.5 25.8 1.0 FE2 A:SF41103 2.5 19.8 1.0 S1 A:SF41103 3.6 20.8 1.0 CB A:CYS996 3.7 25.3 1.0 CD A:PRO997 4.1 23.5 1.0 CA A:CYS996 4.2 24.6 1.0 SG A:CYS956 4.2 22.2 1.0 SG A:CYS1001 4.3 26.2 1.0 CG1 A:ILE1002 4.6 26.7 1.0 CD1 A:ILE1002 4.7 26.4 1.0 SG A:CYS959 4.7 24.1 1.0 SG A:CYS953 4.7 22.7 1.0 N A:PRO997 4.8 23.6 1.0 C A:CYS996 4.9 24.2 1.0 CG A:PRO997 4.9 23.4 1.0 CB A:CYS1001 4.9 26.0 1.0

Iron binding site 10 out of 64 in the Porcine Dihydropyrimidine Dehydrogenase (Dpd) Complexed with 5- Ethynyluracil (5EU) - Open Form


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Porcine Dihydropyrimidine Dehydrogenase (Dpd) Complexed with 5- Ethynyluracil (5EU) - Open Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1103 b:19.8 occ:1.00 FE2 A:SF41103 0.0 19.8 1.0 S4 A:SF41103 2.0 20.8 1.0 S3 A:SF41103 2.0 20.4 1.0 S1 A:SF41103 2.1 20.8 1.0 FE4 A:SF41103 2.3 20.5 1.0 SG A:CYS959 2.4 24.1 1.0 FE3 A:SF41103 2.4 19.5 1.0 FE1 A:SF41103 2.5 20.3 1.0 CB A:CYS959 3.5 23.6 1.0 S2 A:SF41103 3.5 21.2 1.0 N A:CYS959 3.9 22.2 1.0 CG A:PRO980 4.0 24.6 1.0 SG A:CYS956 4.2 22.2 1.0 CA A:CYS959 4.3 22.8 1.0 SG A:CYS953 4.5 22.7 1.0 N A:GLY957 4.6 22.2 1.0 N A:LYS958 4.6 21.6 1.0 CB A:PRO980 4.7 24.7 1.0 SG A:CYS996 4.7 25.8 1.0 CD1 A:ILE1002 4.8 26.4 1.0 CA A:GLY957 4.8 22.1 1.0 CD A:PRO980 4.9 24.9 1.0 C A:GLY957 4.9 21.6 1.0

D.C.Forouzesh, B.A.Beaupre, A.Butrin, Z.Wawrzak, D.Liu, G.R.Moran. The Interaction of Porcine Dihydropyrimidine Dehydrogenase with the Chemotherapy Sensitizer: 5-Ethynyluracil. Biochemistry 2021.
ISSN: ISSN 0006-2960
PubMed: 33755421
DOI: 10.1021/ACS.BIOCHEM.1C00096