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Fluorine in PDB 3i8d: The Pairing Geometry of the Hydrophobic Thymine Analog 2,4- Difluorotoluene in Duplex Dna As Analyzed By X-Ray Crystallography

Enzymatic activity of The Pairing Geometry of the Hydrophobic Thymine Analog 2,4- Difluorotoluene in Duplex Dna As Analyzed By X-Ray Crystallography

All present enzymatic activity of The Pairing Geometry of the Hydrophobic Thymine Analog 2,4- Difluorotoluene in Duplex Dna As Analyzed By X-Ray Crystallography:
3.1.26.4;

Protein crystallography data

The structure of The Pairing Geometry of the Hydrophobic Thymine Analog 2,4- Difluorotoluene in Duplex Dna As Analyzed By X-Ray Crystallography, PDB code: 3i8d was solved by M.Egli, P.S.Pallan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.39 / 1.61
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 96.178, 66.714, 77.571, 90.00, 121.04, 90.00
R / Rfree (%) 19.7 / 23.8

Fluorine Binding Sites:

The binding sites of Fluorine atom in the The Pairing Geometry of the Hydrophobic Thymine Analog 2,4- Difluorotoluene in Duplex Dna As Analyzed By X-Ray Crystallography (pdb code 3i8d). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the The Pairing Geometry of the Hydrophobic Thymine Analog 2,4- Difluorotoluene in Duplex Dna As Analyzed By X-Ray Crystallography, PDB code: 3i8d:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 3i8d

Go back to Fluorine Binding Sites List in 3i8d
Fluorine binding site 1 out of 4 in the The Pairing Geometry of the Hydrophobic Thymine Analog 2,4- Difluorotoluene in Duplex Dna As Analyzed By X-Ray Crystallography


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of The Pairing Geometry of the Hydrophobic Thymine Analog 2,4- Difluorotoluene in Duplex Dna As Analyzed By X-Ray Crystallography within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F8

b:16.5
occ:1.00
 F4 B:DFT8 0.0 16.5 1.0
C4 B:DFT8 1.3 13.9 1.0
C3 B:DFT8 2.3 16.3 1.0
C5 B:DFT8 2.3 12.8 1.0
C5M B:DFT8 2.8 14.9 1.0
C4 B:DT7 3.1 13.4 1.0
O4 B:DT7 3.2 14.1 1.0
C5 B:DT7 3.4 13.9 1.0
C2 B:DFT8 3.5 15.6 1.0
N3 B:DT7 3.5 14.3 1.0
N4 B:DC9 3.5 11.0 1.0
C6 B:DFT8 3.6 14.6 1.0
C7 B:DT7 3.8 13.4 1.0
C4 B:DC9 3.9 14.3 1.0
C6 B:DT7 4.0 14.7 1.0
C1 B:DFT8 4.0 14.8 1.0
N3 B:DC9 4.2 13.2 1.0
C2 B:DT7 4.2 13.2 1.0
N1 B:DT7 4.4 13.8 1.0
F2 B:DFT8 4.6 15.7 1.0
C5 B:DC9 4.7 12.4 1.0

Fluorine binding site 2 out of 4 in 3i8d

Go back to Fluorine Binding Sites List in 3i8d
Fluorine binding site 2 out of 4 in the The Pairing Geometry of the Hydrophobic Thymine Analog 2,4- Difluorotoluene in Duplex Dna As Analyzed By X-Ray Crystallography


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of The Pairing Geometry of the Hydrophobic Thymine Analog 2,4- Difluorotoluene in Duplex Dna As Analyzed By X-Ray Crystallography within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F8

b:15.7
occ:1.00
 F2 B:DFT8 0.0 15.7 1.0
C2 B:DFT8 1.3 15.6 1.0
C3 B:DFT8 2.2 16.3 1.0
C1 B:DFT8 2.3 14.8 1.0
C1' B:DFT8 2.8 17.8 1.0
O4' B:DC9 3.3 15.9 1.0
C4 B:DFT8 3.5 13.9 1.0
C6 B:DFT8 3.5 14.6 1.0
O4' B:DFT8 3.6 18.9 1.0
N1 B:DC9 3.6 12.6 1.0
C6 B:DC9 3.8 12.6 1.0
C1' B:DC9 3.8 15.3 1.0
C5 B:DFT8 4.0 12.8 1.0
O2 B:DT7 4.0 18.1 1.0
C2' B:DFT8 4.1 20.3 1.0
C2 B:DC9 4.1 11.6 1.0
C5 B:DC9 4.3 12.4 1.0
C2 B:DT7 4.4 13.2 1.0
C4' B:DC9 4.5 15.3 1.0
N3 B:DC9 4.5 13.2 1.0
F4 B:DFT8 4.6 16.5 1.0
C4 B:DC9 4.6 14.3 1.0
N3 B:DT7 4.6 14.3 1.0
O2 B:DC9 4.6 14.8 1.0
O B:HOH176 4.7 11.9 0.5
C4' B:DFT8 4.8 18.4 1.0
C5' B:DC9 4.8 16.2 1.0
C3' B:DFT8 5.0 19.2 1.0

Fluorine binding site 3 out of 4 in 3i8d

Go back to Fluorine Binding Sites List in 3i8d
Fluorine binding site 3 out of 4 in the The Pairing Geometry of the Hydrophobic Thymine Analog 2,4- Difluorotoluene in Duplex Dna As Analyzed By X-Ray Crystallography


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of The Pairing Geometry of the Hydrophobic Thymine Analog 2,4- Difluorotoluene in Duplex Dna As Analyzed By X-Ray Crystallography within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F8

b:17.7
occ:1.00
 F4 D:DFT8 0.0 17.7 1.0
C4 D:DFT8 1.3 13.1 1.0
C3 D:DFT8 2.3 15.7 1.0
C5 D:DFT8 2.3 16.3 1.0
C5M D:DFT8 2.7 13.6 1.0
C4 D:DT7 3.1 16.4 1.0
O4 D:DT7 3.2 13.4 1.0
C5 D:DT7 3.4 13.2 1.0
C2 D:DFT8 3.5 15.6 1.0
C6 D:DFT8 3.5 14.6 1.0
N3 D:DT7 3.6 15.9 1.0
N4 D:DC9 3.6 11.5 1.0
C7 D:DT7 3.8 17.1 1.0
C6 D:DT7 4.0 13.6 1.0
C1 D:DFT8 4.0 12.3 1.0
C4 D:DC9 4.0 14.7 1.0
C2 D:DT7 4.2 12.7 1.0
N3 D:DC9 4.4 11.8 1.0
N1 D:DT7 4.4 14.6 1.0
F2 D:DFT8 4.6 15.6 1.0
C5 D:DC9 4.8 12.8 1.0

Fluorine binding site 4 out of 4 in 3i8d

Go back to Fluorine Binding Sites List in 3i8d
Fluorine binding site 4 out of 4 in the The Pairing Geometry of the Hydrophobic Thymine Analog 2,4- Difluorotoluene in Duplex Dna As Analyzed By X-Ray Crystallography


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of The Pairing Geometry of the Hydrophobic Thymine Analog 2,4- Difluorotoluene in Duplex Dna As Analyzed By X-Ray Crystallography within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F8

b:15.6
occ:1.00
 F2 D:DFT8 0.0 15.6 1.0
C2 D:DFT8 1.3 15.6 1.0
C3 D:DFT8 2.3 15.7 1.0
C1 D:DFT8 2.3 12.3 1.0
C1' D:DFT8 2.8 16.1 1.0
O4' D:DC9 3.3 15.5 1.0
C4 D:DFT8 3.5 13.1 1.0
C6 D:DFT8 3.5 14.6 1.0
O4' D:DFT8 3.5 15.7 1.0
N1 D:DC9 3.6 13.1 1.0
C6 D:DC9 3.7 10.7 1.0
O D:HOH226 3.8 12.1 0.6
C1' D:DC9 3.9 14.9 1.0
C5 D:DFT8 3.9 16.3 1.0
C2 D:DC9 4.1 11.4 1.0
C5 D:DC9 4.1 12.8 1.0
C2' D:DFT8 4.1 17.1 1.0
O2 D:DT7 4.1 18.3 1.0
N3 D:DC9 4.4 11.8 1.0
C4 D:DC9 4.4 14.7 1.0
C2 D:DT7 4.5 12.7 1.0
F4 D:DFT8 4.6 17.7 1.0
C4' D:DC9 4.6 13.5 1.0
O2 D:DC9 4.6 13.8 1.0
C4' D:DFT8 4.7 17.6 1.0
N3 D:DT7 4.7 15.9 1.0
C5' D:DC9 4.9 15.1 1.0
O D:HOH227 4.9 22.6 0.6
C3' D:DFT8 5.0 18.5 1.0

Reference:

P.S.Pallan, M.Egli. Pairing Geometry of the Hydrophobic Thymine Analogue 2,4-Difluorotoluene in Duplex Dna As Analyzed By X-Ray Crystallography. J.Am.Chem.Soc. V. 131 12548 2009.
ISSN: ISSN 0002-7863
PubMed: 19685868
DOI: 10.1021/JA905739J
Page generated: Mon Jul 14 16:58:36 2025

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