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

Go back to Iron Binding Sites List in 7m31
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

Go back to Iron Binding Sites List in 7m31
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

Go back to Iron Binding Sites List in 7m31
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

Go back to Iron Binding Sites List in 7m31
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

Go back to Iron Binding Sites List in 7m31
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

Go back to Iron Binding Sites List in 7m31
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

Go back to Iron Binding Sites List in 7m31
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

Go back to Iron Binding Sites List in 7m31
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

Go back to Iron Binding Sites List in 7m31
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

Go back to Iron Binding Sites List in 7m31
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: Sat Jul 10 15:31:41 2021

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy