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Iron in PDB 7m31: Dihydropyrimidine Dehydrogenase (Dpd) C671S Mutant Soaked with Thymine and Nadph Anaerobically

Enzymatic activity of Dihydropyrimidine Dehydrogenase (Dpd) C671S Mutant Soaked with Thymine and Nadph Anaerobically

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

Protein crystallography data

The structure of Dihydropyrimidine Dehydrogenase (Dpd) C671S Mutant Soaked with Thymine and Nadph Anaerobically, PDB code: 7m31 was solved by A.Butrin, B.Beaupre, 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) 36.15 / 1.69
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 82.04, 159.56, 162.95, 90, 95.75, 90
R / Rfree (%) 17.7 / 20

Iron Binding Sites:

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 Thymine and Nadph Anaerobically (pdb code 7m31). 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 Thymine and Nadph Anaerobically, PDB code: 7m31:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 64 in 7m31

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Iron binding site 1 out of 64 in the Dihydropyrimidine Dehydrogenase (Dpd) C671S Mutant Soaked with Thymine and Nadph 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 Thymine and Nadph Anaerobically within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1101

b:18.1
occ:1.00
 FE1 A:SF41101 0.0 18.1 1.0
S3 A:SF41101 2.3 18.8 1.0
S4 A:SF41101 2.3 17.7 1.0
SG A:CYS130 2.3 18.4 1.0
S2 A:SF41101 2.3 17.6 1.0
FE3 A:SF41101 2.7 17.4 1.0
FE2 A:SF41101 2.7 18.1 1.0
FE4 A:SF41101 2.7 17.3 1.0
CB A:CYS130 3.1 16.6 1.0
S1 A:SF41101 3.9 18.0 1.0
CG2 A:VAL490 4.3 17.4 1.0
CB A:CYS126 4.3 18.3 1.0
O A:CYS126 4.3 15.9 1.0
OE1 A:GLN156 4.4 14.8 1.0
CB A:VAL490 4.4 16.4 1.0
CA A:CYS130 4.6 19.9 1.0
CG1 A:VAL490 4.6 22.9 1.0
C A:CYS126 4.7 19.6 1.0
NE2 A:GLN156 4.7 18.0 1.0
SG A:CYS136 4.8 18.2 1.0
SG A:CYS91 4.9 16.0 1.0
CD1 A:LEU135 4.9 17.9 1.0
CG2 A:THR132 4.9 17.8 1.0
CD A:GLN156 4.9 17.4 1.0

Iron binding site 2 out of 64 in 7m31

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Iron binding site 2 out of 64 in the Dihydropyrimidine Dehydrogenase (Dpd) C671S Mutant Soaked with Thymine and Nadph 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 Thymine and Nadph Anaerobically within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1101

b:18.1
occ:1.00
 FE2 A:SF41101 0.0 18.1 1.0
SG A:CYS136 2.3 18.2 1.0
S3 A:SF41101 2.3 18.8 1.0
S4 A:SF41101 2.3 17.7 1.0
S1 A:SF41101 2.3 18.0 1.0
FE3 A:SF41101 2.7 17.4 1.0
FE1 A:SF41101 2.7 18.1 1.0
FE4 A:SF41101 2.7 17.3 1.0
CB A:CYS136 3.2 19.3 1.0
S2 A:SF41101 3.9 17.6 1.0
CG2 A:THR132 4.2 17.8 1.0
CG2 A:ILE152 4.3 17.0 1.0
N A:CYS136 4.4 16.5 1.0
CA A:CYS136 4.4 18.5 1.0
OE1 A:GLN156 4.5 14.8 1.0
CB A:CYS91 4.7 17.0 1.0
SG A:CYS91 4.7 16.0 1.0
SG A:CYS130 4.7 18.4 1.0
CB A:CYS130 4.8 16.6 1.0
CB A:ILE152 4.9 17.4 1.0
CB A:THR132 4.9 17.1 1.0
CD1 A:ILE97 5.0 21.2 1.0

Iron binding site 3 out of 64 in 7m31

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Iron binding site 3 out of 64 in the Dihydropyrimidine Dehydrogenase (Dpd) C671S Mutant Soaked with Thymine and Nadph 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 Thymine and Nadph Anaerobically within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1101

b:17.4
occ:1.00
 FE3 A:SF41101 0.0 17.4 1.0
OE1 A:GLN156 1.9 14.8 1.0
S1 A:SF41101 2.3 18.0 1.0
S4 A:SF41101 2.3 17.7 1.0
S2 A:SF41101 2.3 17.6 1.0
FE1 A:SF41101 2.7 18.1 1.0
FE2 A:SF41101 2.7 18.1 1.0
FE4 A:SF41101 2.7 17.3 1.0
CD A:GLN156 2.9 17.4 1.0
NE2 A:GLN156 3.3 18.0 1.0
CD2 A:LEU95 3.7 21.0 1.0
S3 A:SF41101 3.9 18.8 1.0
CG A:GLN156 4.3 17.6 1.0
CB A:GLN156 4.5 17.0 1.0
SG A:CYS130 4.7 18.4 1.0
CG2 A:ILE152 4.8 17.0 1.0
SG A:CYS91 4.8 16.0 1.0
SG A:CYS136 4.8 18.2 1.0
CG A:LEU95 4.9 20.4 1.0

Iron binding site 4 out of 64 in 7m31

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Iron binding site 4 out of 64 in the Dihydropyrimidine Dehydrogenase (Dpd) C671S Mutant Soaked with Thymine and Nadph 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 Thymine and Nadph Anaerobically within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1101

b:17.3
occ:1.00
 FE4 A:SF41101 0.0 17.3 1.0
S2 A:SF41101 2.3 17.6 1.0
S1 A:SF41101 2.3 18.0 1.0
SG A:CYS91 2.3 16.0 1.0
S3 A:SF41101 2.3 18.8 1.0
FE2 A:SF41101 2.7 18.1 1.0
FE3 A:SF41101 2.7 17.4 1.0
FE1 A:SF41101 2.7 18.1 1.0
CB A:CYS91 3.1 17.0 1.0
S4 A:SF41101 3.9 17.7 1.0
CA A:CYS91 4.0 17.3 1.0
OG1 A:THR93 4.2 17.5 1.0
CG2 A:VAL490 4.4 17.4 1.0
CD2 A:LEU95 4.5 21.0 1.0
OE1 A:GLN156 4.5 14.8 1.0
CD A:PRO92 4.6 17.8 1.0
CB A:LEU95 4.6 18.5 1.0
C A:CYS91 4.6 19.8 1.0
SG A:CYS136 4.7 18.2 1.0
CB A:CYS136 4.7 19.3 1.0
N A:PRO92 4.8 17.5 1.0
CD1 A:LEU95 4.8 27.5 1.0
SG A:CYS130 4.9 18.4 1.0
CG A:LEU95 4.9 20.4 1.0

Iron binding site 5 out of 64 in 7m31

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Iron binding site 5 out of 64 in the Dihydropyrimidine Dehydrogenase (Dpd) C671S Mutant Soaked with Thymine and Nadph 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 Thymine and Nadph Anaerobically within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1102

b:17.0
occ:1.00
 FE1 A:SF41102 0.0 17.0 1.0
S4 A:SF41102 2.3 16.2 1.0
S2 A:SF41102 2.3 16.5 1.0
SG A:CYS140 2.3 15.9 1.0
S3 A:SF41102 2.3 16.0 1.0
FE4 A:SF41102 2.7 17.4 1.0
FE3 A:SF41102 2.7 16.4 1.0
FE2 A:SF41102 2.8 16.4 1.0
CB A:CYS140 3.3 16.1 1.0
CA A:CYS140 3.7 16.0 1.0
N A:ASN141 3.8 16.1 1.0
S1 A:SF41102 3.9 17.6 1.0
CG1 A:ILE150 4.1 17.0 1.0
C A:CYS140 4.1 19.7 1.0
N A:LEU142 4.4 15.5 1.0
CB A:ILE150 4.5 16.7 1.0
SG A:CYS87 4.7 17.2 1.0
SG A:CYS82 4.8 15.2 1.0
CB A:LEU142 4.8 18.9 1.0
CB A:CYS87 4.9 19.1 1.0
CA A:ASN141 4.9 14.3 1.0
SG A:CYS79 4.9 15.5 1.0
N A:ILE150 5.0 17.5 1.0

Iron binding site 6 out of 64 in 7m31

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Iron binding site 6 out of 64 in the Dihydropyrimidine Dehydrogenase (Dpd) C671S Mutant Soaked with Thymine and Nadph 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 Thymine and Nadph Anaerobically within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1102

b:16.4
occ:1.00
 FE2 A:SF41102 0.0 16.4 1.0
S3 A:SF41102 2.3 16.0 1.0
SG A:CYS82 2.3 15.2 1.0
S4 A:SF41102 2.3 16.2 1.0
S1 A:SF41102 2.3 17.6 1.0
FE4 A:SF41102 2.7 17.4 1.0
FE3 A:SF41102 2.7 16.4 1.0
FE1 A:SF41102 2.8 17.0 1.0
CB A:CYS82 3.3 15.6 1.0
N A:CYS82 3.8 15.1 1.0
S2 A:SF41102 3.9 16.5 1.0
CA A:CYS82 4.2 15.8 1.0
ND2 A:ASN141 4.3 16.3 1.0
N A:LYS81 4.3 15.7 1.0
CB A:LEU80 4.5 13.7 1.0
SG A:CYS79 4.5 15.5 1.0
N A:LEU80 4.6 16.1 1.0
CB A:ASN141 4.7 16.6 1.0
N A:ASN141 4.7 16.1 1.0
SG A:CYS87 4.7 17.2 1.0
CB A:ALA85 4.8 18.9 1.0
C A:LEU80 4.8 14.6 1.0
SG A:CYS140 4.8 15.9 1.0
C A:LYS81 4.9 16.4 1.0
CA A:LYS81 4.9 16.8 1.0
CG A:ASN141 4.9 16.0 1.0
CA A:LEU80 4.9 14.3 1.0

Iron binding site 7 out of 64 in 7m31

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Iron binding site 7 out of 64 in the Dihydropyrimidine Dehydrogenase (Dpd) C671S Mutant Soaked with Thymine and Nadph 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 Thymine and Nadph Anaerobically within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1102

b:16.4
occ:1.00
 FE3 A:SF41102 0.0 16.4 1.0
S2 A:SF41102 2.3 16.5 1.0
SG A:CYS79 2.3 15.5 1.0
S1 A:SF41102 2.3 17.6 1.0
S4 A:SF41102 2.3 16.2 1.0
FE4 A:SF41102 2.7 17.4 1.0
FE2 A:SF41102 2.7 16.4 1.0
FE1 A:SF41102 2.7 17.0 1.0
CB A:CYS79 3.5 17.6 1.0
S3 A:SF41102 3.9 16.0 1.0
N A:LEU80 4.0 16.1 1.0
CA A:CYS79 4.0 17.0 1.0
N A:LYS81 4.0 15.7 1.0
CG1 A:ILE150 4.1 17.0 1.0
C A:CYS79 4.4 16.7 1.0
CB A:ILE150 4.6 16.7 1.0
CD1 A:ILE101 4.7 19.7 1.0
CA A:LYS81 4.7 16.8 1.0
SG A:CYS82 4.7 15.2 1.0
SG A:CYS140 4.8 15.9 1.0
SG A:CYS87 4.9 17.2 1.0
CA A:LEU80 4.9 14.3 1.0
CG2 A:ILE150 4.9 16.1 1.0
C A:LEU80 4.9 14.6 1.0
N A:CYS82 5.0 15.1 1.0

Iron binding site 8 out of 64 in 7m31

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Iron binding site 8 out of 64 in the Dihydropyrimidine Dehydrogenase (Dpd) C671S Mutant Soaked with Thymine and Nadph 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 Thymine and Nadph Anaerobically within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1102

b:17.4
occ:1.00
 FE4 A:SF41102 0.0 17.4 1.0
S1 A:SF41102 2.3 17.6 1.0
SG A:CYS87 2.3 17.2 1.0
S3 A:SF41102 2.3 16.0 1.0
S2 A:SF41102 2.3 16.5 1.0
FE1 A:SF41102 2.7 17.0 1.0
FE2 A:SF41102 2.7 16.4 1.0
FE3 A:SF41102 2.7 16.4 1.0
CB A:CYS87 3.3 19.1 1.0
S4 A:SF41102 3.9 16.2 1.0
CG2 A:ILE97 4.2 18.8 1.0
CB A:ALA85 4.2 18.9 1.0
N A:CYS87 4.4 18.4 1.0
CA A:CYS87 4.5 18.1 1.0
SG A:CYS79 4.7 15.5 1.0
CD1 A:ILE152 4.7 17.5 1.0
SG A:CYS140 4.8 15.9 1.0
SG A:CYS82 4.8 15.2 1.0
CB A:ILE97 4.9 15.5 1.0

Iron binding site 9 out of 64 in 7m31

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Iron binding site 9 out of 64 in the Dihydropyrimidine Dehydrogenase (Dpd) C671S Mutant Soaked with Thymine and Nadph 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 Thymine and Nadph Anaerobically within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1103

b:18.8
occ:1.00
 FE1 A:SF41103 0.0 18.8 1.0
S2 A:SF41103 2.3 19.1 1.0
S3 A:SF41103 2.3 17.9 1.0
S4 A:SF41103 2.3 18.4 1.0
SG A:CYS953 2.3 18.3 1.0
FE3 A:SF41103 2.7 18.5 1.0
FE2 A:SF41103 2.7 17.8 1.0
FE4 A:SF41103 2.7 18.1 1.0
CB A:CYS953 3.3 20.4 1.0
CA A:CYS953 3.7 16.7 1.0
S1 A:SF41103 3.9 17.9 1.0
N A:ILE954 3.9 14.1 1.0
N A:ASN955 3.9 15.5 1.0
CG A:PRO980 4.1 16.0 1.0
C A:CYS953 4.2 18.2 1.0
SG A:CYS1001 4.4 18.9 1.0
CD A:PRO980 4.4 17.9 1.0
CA A:ASN955 4.6 14.2 1.0
N A:CYS956 4.7 16.3 1.0
C A:ILE954 4.8 15.9 1.0
SG A:CYS959 4.8 17.9 1.0
SG A:CYS996 4.8 17.7 1.0
CA A:ILE954 4.9 16.9 1.0
CG2 A:ILE948 5.0 23.2 1.0
N A:CYS953 5.0 20.9 1.0
SG A:CYS956 5.0 15.7 1.0

Iron binding site 10 out of 64 in 7m31

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Iron binding site 10 out of 64 in the Dihydropyrimidine Dehydrogenase (Dpd) C671S Mutant Soaked with Thymine and Nadph 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 Thymine and Nadph Anaerobically within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1103

b:17.8
occ:1.00
 FE2 A:SF41103 0.0 17.8 1.0
S4 A:SF41103 2.3 18.4 1.0
S1 A:SF41103 2.3 17.9 1.0
S3 A:SF41103 2.3 17.9 1.0
SG A:CYS956 2.3 15.7 1.0
FE3 A:SF41103 2.7 18.5 1.0
FE1 A:SF41103 2.7 18.8 1.0
FE4 A:SF41103 2.8 18.1 1.0
N A:CYS956 3.5 16.3 1.0
CB A:CYS956 3.6 15.4 1.0
N A:GLY957 3.8 13.9 1.0
S2 A:SF41103 3.9 19.1 1.0
CA A:CYS956 4.0 14.3 1.0
CD A:PRO997 4.0 14.5 1.0
N A:LYS958 4.1 16.4 1.0
C A:CYS956 4.2 16.3 1.0
N A:ASN955 4.3 15.5 1.0
CG A:PRO997 4.5 17.7 1.0
C A:ASN955 4.6 17.1 1.0
SG A:CYS953 4.6 18.3 1.0
CA A:GLY957 4.7 14.3 1.0
SG A:CYS996 4.7 17.7 1.0
CB A:LYS958 4.7 13.8 1.0
SG A:CYS959 4.8 17.9 1.0
CA A:ASN955 4.8 14.2 1.0
N A:CYS959 4.9 15.5 1.0
C A:GLY957 4.9 16.3 1.0
CG1 A:ILE954 4.9 17.3 1.0
N A:ILE954 4.9 14.1 1.0
C A:ILE954 5.0 15.9 1.0
CA A:LYS958 5.0 14.6 1.0

Reference:

B.A.Beaupre, D.C.Forouzesh, A.Butrin, D.Liu, G.R.Moran. Perturbing the Movement of Hydrogens to Delineate and Assign Events in the Reductive Activation and Turnover of Porcine Dihydropyrimidine Dehydrogenase. Biochemistry 2021.
ISSN: ISSN 0006-2960
PubMed: 34032117
DOI: 10.1021/ACS.BIOCHEM.1C00243
Page generated: Thu Aug 8 08:10:53 2024

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