Iron in PDB 8f5w: Dihydropyrimidine Dehydrogenase (Dpd) C671S Mutant Soaked with Dihydrothymine and Nadph Quasi-Anaerobically

All present enzymatic activity of Dihydropyrimidine Dehydrogenase (Dpd) C671S Mutant Soaked with Dihydrothymine and Nadph Quasi-Anaerobically:
1.3.1.2;

The structure of Dihydropyrimidine Dehydrogenase (Dpd) C671S Mutant Soaked with Dihydrothymine and Nadph Quasi-Anaerobically, PDB code: 8f5w was solved by N.Kaley, M.Smith, D.Forouzesh, D.Liu, G.Moran, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.23 / 1.97
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	81.735, 158.003, 162.404, 90, 96.06, 90
R / Rfree (%)	17.9 / 21.7

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) C671S Mutant Soaked with Dihydrothymine and Nadph Quasi-Anaerobically (pdb code 8f5w). 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) C671S Mutant Soaked with Dihydrothymine and Nadph Quasi-Anaerobically, PDB code: 8f5w:
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) C671S Mutant Soaked with Dihydrothymine and Nadph Quasi-Anaerobically


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) C671S Mutant Soaked with Dihydrothymine and Nadph Quasi-Anaerobically within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1101 b:23.4 occ:1.00 FE1 A:SF41101 0.0 23.4 1.0 S3 A:SF41101 2.3 20.4 1.0 S4 A:SF41101 2.3 21.3 1.0 S2 A:SF41101 2.3 21.7 1.0 SG A:CYS996 2.3 19.3 1.0 FE4 A:SF41101 2.7 22.0 1.0 FE3 A:SF41101 2.7 22.8 1.0 FE2 A:SF41101 2.8 22.3 1.0 CB A:CYS996 3.3 17.1 1.0 CD A:PRO997 3.9 22.2 1.0 S1 A:SF41101 3.9 21.7 1.0 CA A:CYS996 4.0 20.4 1.0 CD1 A:ILE1002 4.2 20.7 1.0 SG A:CYS1001 4.2 23.6 1.0 CG1 A:ILE1002 4.3 17.5 1.0 N A:PRO997 4.5 20.3 1.0 C A:CYS996 4.6 21.8 1.0 CB A:CYS1001 4.7 23.9 1.0 SG A:CYS956 4.7 19.8 1.0 SG A:CYS959 4.8 22.3 1.0 CG A:PRO997 4.9 24.5 1.0 SG A:CYS953 5.0 24.1 1.0

Iron binding site 2 out of 64 in the Dihydropyrimidine Dehydrogenase (Dpd) C671S Mutant Soaked with Dihydrothymine and Nadph Quasi-Anaerobically


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) C671S Mutant Soaked with Dihydrothymine and Nadph Quasi-Anaerobically within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1101 b:22.3 occ:1.00 FE2 A:SF41101 0.0 22.3 1.0 SG A:CYS956 2.3 19.8 1.0 S3 A:SF41101 2.3 20.4 1.0 S4 A:SF41101 2.3 21.3 1.0 S1 A:SF41101 2.3 21.7 1.0 FE4 A:SF41101 2.7 22.0 1.0 FE3 A:SF41101 2.7 22.8 1.0 FE1 A:SF41101 2.8 23.4 1.0 N A:CYS956 3.5 21.0 1.0 CB A:CYS956 3.6 19.3 1.0 N A:GLY957 3.7 17.1 1.0 S2 A:SF41101 3.9 21.7 1.0 CA A:CYS956 3.9 19.8 1.0 CD A:PRO997 4.0 22.2 1.0 N A:LYS958 4.1 18.9 1.0 C A:CYS956 4.2 21.7 1.0 N A:ASN955 4.3 19.7 1.0 CG A:PRO997 4.5 24.5 1.0 C A:ASN955 4.6 22.6 1.0 SG A:CYS953 4.6 24.1 1.0 CA A:GLY957 4.7 18.1 1.0 SG A:CYS996 4.7 19.3 1.0 SG A:CYS959 4.8 22.3 1.0 CB A:LYS958 4.8 20.5 1.0 CA A:ASN955 4.9 21.0 1.0 C A:GLY957 4.9 22.1 1.0 N A:CYS959 4.9 17.2 1.0 CG1 A:ILE954 4.9 23.3 1.0 N A:ILE954 4.9 19.9 1.0 C A:ILE954 4.9 19.6 1.0

Iron binding site 3 out of 64 in the Dihydropyrimidine Dehydrogenase (Dpd) C671S Mutant Soaked with Dihydrothymine and Nadph Quasi-Anaerobically


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) C671S Mutant Soaked with Dihydrothymine and Nadph Quasi-Anaerobically within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1101 b:22.8 occ:1.00 FE3 A:SF41101 0.0 22.8 1.0 S2 A:SF41101 2.3 21.7 1.0 S4 A:SF41101 2.3 21.3 1.0 SG A:CYS953 2.3 24.1 1.0 S1 A:SF41101 2.3 21.7 1.0 FE4 A:SF41101 2.7 22.0 1.0 FE2 A:SF41101 2.7 22.3 1.0 FE1 A:SF41101 2.7 23.4 1.0 CB A:CYS953 3.2 24.4 1.0 CA A:CYS953 3.6 22.8 1.0 N A:ILE954 3.9 19.9 1.0 S3 A:SF41101 3.9 20.4 1.0 N A:ASN955 3.9 19.7 1.0 CG A:PRO980 4.1 23.3 1.0 C A:CYS953 4.2 22.5 1.0 SG A:CYS1001 4.4 23.6 1.0 CD A:PRO980 4.4 23.3 1.0 CA A:ASN955 4.6 21.0 1.0 N A:CYS956 4.7 21.0 1.0 C A:ILE954 4.8 19.6 1.0 SG A:CYS959 4.8 22.3 1.0 SG A:CYS996 4.9 19.3 1.0 CA A:ILE954 4.9 22.4 1.0 N A:CYS953 4.9 21.7 1.0 SG A:CYS956 4.9 19.8 1.0 CG2 A:ILE948 5.0 24.5 1.0

Iron binding site 4 out of 64 in the Dihydropyrimidine Dehydrogenase (Dpd) C671S Mutant Soaked with Dihydrothymine and Nadph Quasi-Anaerobically


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) C671S Mutant Soaked with Dihydrothymine and Nadph Quasi-Anaerobically within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1101 b:22.0 occ:1.00 FE4 A:SF41101 0.0 22.0 1.0 S2 A:SF41101 2.2 21.7 1.0 S3 A:SF41101 2.3 20.4 1.0 S1 A:SF41101 2.3 21.7 1.0 SG A:CYS959 2.3 22.3 1.0 FE3 A:SF41101 2.7 22.8 1.0 FE2 A:SF41101 2.7 22.3 1.0 FE1 A:SF41101 2.7 23.4 1.0 CB A:CYS959 3.3 18.2 1.0 S4 A:SF41101 3.9 21.3 1.0 N A:CYS959 3.9 17.2 1.0 CG A:PRO980 3.9 23.3 1.0 CA A:CYS959 4.2 20.4 1.0 CD1 A:ILE1002 4.4 20.7 1.0 N A:LYS958 4.5 18.9 1.0 N A:GLY957 4.6 17.1 1.0 CB A:PRO980 4.6 21.0 1.0 SG A:CYS953 4.6 24.1 1.0 SG A:CYS956 4.6 19.8 1.0 CD1 A:ILE948 4.7 21.0 1.0 CA A:GLY957 4.8 18.1 1.0 SG A:CYS996 4.9 19.3 1.0 CD A:PRO980 4.9 23.3 1.0 C A:GLY957 4.9 22.1 1.0

Iron binding site 5 out of 64 in the Dihydropyrimidine Dehydrogenase (Dpd) C671S Mutant Soaked with Dihydrothymine and Nadph Quasi-Anaerobically


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) C671S Mutant Soaked with Dihydrothymine and Nadph Quasi-Anaerobically within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1102 b:22.5 occ:1.00 FE1 A:SF41102 0.0 22.5 1.0 S4 A:SF41102 2.2 22.7 1.0 SG A:CYS992 2.3 26.7 1.0 S3 A:SF41102 2.3 20.4 1.0 S2 A:SF41102 2.3 20.3 1.0 FE4 A:SF41102 2.7 21.9 1.0 FE3 A:SF41102 2.7 23.9 1.0 FE2 A:SF41102 2.7 23.6 1.0 CB A:CYS992 3.2 20.7 1.0 N A:CYS992 3.8 22.3 1.0 S1 A:SF41102 3.9 23.8 1.0 CB A:ALA946 4.0 20.8 1.0 CA A:CYS992 4.1 22.4 1.0 CD1 A:ILE971 4.5 20.9 1.0 SG A:CYS986 4.5 20.5 1.0 SG A:CYS989 4.6 23.8 1.0 SG A:CYS963 4.7 23.0 1.0 N A:LEU991 4.8 23.3 1.0 N A:THR990 4.8 22.8 1.0 CB A:CYS963 5.0 20.4 1.0

Iron binding site 6 out of 64 in the Dihydropyrimidine Dehydrogenase (Dpd) C671S Mutant Soaked with Dihydrothymine and Nadph Quasi-Anaerobically


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) C671S Mutant Soaked with Dihydrothymine and Nadph Quasi-Anaerobically within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1102 b:23.6 occ:1.00 FE2 A:SF41102 0.0 23.6 1.0 S3 A:SF41102 2.3 20.4 1.0 SG A:CYS989 2.3 23.8 1.0 S4 A:SF41102 2.3 22.7 1.0 S1 A:SF41102 2.3 23.8 1.0 FE3 A:SF41102 2.7 23.9 1.0 FE1 A:SF41102 2.7 22.5 1.0 FE4 A:SF41102 2.8 21.9 1.0 CB A:CYS989 3.5 25.3 1.0 N A:CYS989 3.5 23.2 1.0 N A:THR990 3.7 22.8 1.0 CA A:CYS989 3.9 25.2 1.0 S2 A:SF41102 3.9 20.3 1.0 C A:CYS989 4.2 23.7 1.0 N A:LEU991 4.3 23.3 1.0 C A:GLY988 4.4 24.0 1.0 N A:GLY988 4.5 22.9 1.0 SG A:CYS963 4.7 23.0 1.0 SG A:CYS986 4.7 20.5 1.0 OG1 A:THR987 4.7 24.6 1.0 CA A:THR990 4.7 22.9 1.0 CA A:GLY988 4.8 24.0 1.0 CD1 A:TYR968 4.8 26.2 1.0 SG A:CYS992 4.8 26.7 1.0 N A:CYS992 4.9 22.3 1.0 C A:THR990 4.9 23.1 1.0 CB A:LEU991 5.0 19.4 1.0

Iron binding site 7 out of 64 in the Dihydropyrimidine Dehydrogenase (Dpd) C671S Mutant Soaked with Dihydrothymine and Nadph Quasi-Anaerobically


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) C671S Mutant Soaked with Dihydrothymine and Nadph Quasi-Anaerobically within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1102 b:23.9 occ:1.00 FE3 A:SF41102 0.0 23.9 1.0 S2 A:SF41102 2.2 20.3 1.0 SG A:CYS963 2.3 23.0 1.0 S4 A:SF41102 2.3 22.7 1.0 S1 A:SF41102 2.3 23.8 1.0 FE4 A:SF41102 2.7 21.9 1.0 FE2 A:SF41102 2.7 23.6 1.0 FE1 A:SF41102 2.7 22.5 1.0 CB A:CYS963 3.3 20.4 1.0 S3 A:SF41102 3.8 20.4 1.0 CB A:ALA970 4.1 22.7 1.0 CA A:CYS963 4.1 22.6 1.0 CD1 A:ILE971 4.6 20.9 1.0 SG A:CYS989 4.6 23.8 1.0 N A:TYR968 4.6 20.8 1.0 CG1 A:ILE971 4.7 19.6 1.0 SG A:CYS986 4.8 20.5 1.0 SG A:CYS992 4.8 26.7 1.0 N A:ALA970 4.9 22.8 1.0 CB A:TYR968 5.0 22.8 1.0

Iron binding site 8 out of 64 in the Dihydropyrimidine Dehydrogenase (Dpd) C671S Mutant Soaked with Dihydrothymine and Nadph Quasi-Anaerobically


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) C671S Mutant Soaked with Dihydrothymine and Nadph Quasi-Anaerobically within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1102 b:21.9 occ:1.00 FE4 A:SF41102 0.0 21.9 1.0 SG A:CYS986 2.2 20.5 1.0 S2 A:SF41102 2.3 20.3 1.0 S3 A:SF41102 2.3 20.4 1.0 S1 A:SF41102 2.3 23.8 1.0 FE3 A:SF41102 2.7 23.9 1.0 FE1 A:SF41102 2.7 22.5 1.0 FE2 A:SF41102 2.8 23.6 1.0 CB A:CYS986 3.2 20.1 1.0 CA A:CYS986 3.6 19.6 1.0 N A:GLY988 3.8 22.9 1.0 N A:THR987 3.8 22.7 1.0 S4 A:SF41102 3.9 22.7 1.0 C A:CYS986 4.2 22.3 1.0 CA A:GLY988 4.4 24.0 1.0 CB A:ALA946 4.5 20.8 1.0 CG1 A:VAL982 4.6 19.6 1.0 N A:CYS989 4.6 23.2 1.0 CB A:ALA970 4.7 22.7 1.0 SG A:CYS992 4.7 26.7 1.0 N A:ALA946 4.7 21.3 1.0 C A:THR987 4.8 24.6 1.0 SG A:CYS963 4.8 23.0 1.0 CA A:THR987 4.9 20.5 1.0 N A:CYS986 4.9 22.0 1.0 C A:GLY988 4.9 24.0 1.0 SG A:CYS989 5.0 23.8 1.0

Iron binding site 9 out of 64 in the Dihydropyrimidine Dehydrogenase (Dpd) C671S Mutant Soaked with Dihydrothymine and Nadph Quasi-Anaerobically


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) C671S Mutant Soaked with Dihydrothymine and Nadph Quasi-Anaerobically within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1103 b:21.2 occ:1.00 FE1 A:SF41103 0.0 21.2 1.0 SG A:CYS79 2.2 19.5 1.0 S2 A:SF41103 2.3 20.7 1.0 S3 A:SF41103 2.3 21.2 1.0 S4 A:SF41103 2.3 22.8 1.0 FE4 A:SF41103 2.7 20.2 1.0 FE2 A:SF41103 2.8 20.8 1.0 FE3 A:SF41103 2.8 22.6 1.0 CB A:CYS79 3.3 19.3 1.0 S1 A:SF41103 3.9 19.8 1.0 CA A:CYS79 3.9 21.0 1.0 N A:LEU80 3.9 18.4 1.0 N A:LYS81 4.0 20.2 1.0 CG1 A:ILE150 4.0 22.1 1.0 C A:CYS79 4.3 21.5 1.0 CB A:ILE150 4.6 21.1 1.0 CA A:LYS81 4.6 19.3 1.0 CD1 A:ILE101 4.7 20.4 1.0 SG A:CYS82 4.7 23.4 1.0 SG A:CYS140 4.8 22.9 1.0 N A:CYS82 4.9 20.0 1.0 SG A:CYS87 4.9 24.2 1.0 CA A:LEU80 4.9 18.2 1.0 C A:LEU80 4.9 20.8 1.0 CG2 A:ILE150 4.9 20.6 1.0

Iron binding site 10 out of 64 in the Dihydropyrimidine Dehydrogenase (Dpd) C671S Mutant Soaked with Dihydrothymine and Nadph Quasi-Anaerobically


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) C671S Mutant Soaked with Dihydrothymine and Nadph Quasi-Anaerobically within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1103 b:20.8 occ:1.00 FE2 A:SF41103 0.0 20.8 1.0 S1 A:SF41103 2.3 19.8 1.0 SG A:CYS82 2.3 23.4 1.0 S4 A:SF41103 2.3 22.8 1.0 S3 A:SF41103 2.3 21.2 1.0 FE3 A:SF41103 2.7 22.6 1.0 FE1 A:SF41103 2.8 21.2 1.0 FE4 A:SF41103 2.8 20.2 1.0 CB A:CYS82 3.3 21.0 1.0 N A:CYS82 3.7 20.0 1.0 S2 A:SF41103 3.9 20.7 1.0 CA A:CYS82 4.1 22.7 1.0 ND2 A:ASN141 4.2 18.5 1.0 N A:LYS81 4.3 20.2 1.0 SG A:CYS79 4.5 19.5 1.0 CB A:LEU80 4.6 22.4 1.0 N A:LEU80 4.6 18.4 1.0 CB A:ASN141 4.7 23.5 1.0 SG A:CYS87 4.7 24.2 1.0 N A:ASN141 4.7 20.3 1.0 CB A:ALA85 4.8 23.0 1.0 C A:LYS81 4.8 23.4 1.0 C A:LEU80 4.8 20.8 1.0 CA A:LYS81 4.8 19.3 1.0 SG A:CYS140 4.8 22.9 1.0 CG A:ASN141 4.9 22.7 1.0 CA A:LEU80 4.9 18.2 1.0

M.M.Smith, D.C.Forouzesh, N.E.Kaley, D.Liu, G.R.Moran. Mammalian Dihydropyrimidine Dehydrogenase: Added Mechanistic Details From Transient-State Analysis of Charge Transfer Complexes. Arch.Biochem.Biophys. 09517 2023.
ISSN: ESSN 1096-0384
PubMed: 36681231
DOI: 10.1016/J.ABB.2023.109517