Atomistry » Fluorine » PDB 3hky-3ig6 » 3i8d
Atomistry »
  Fluorine »
    PDB 3hky-3ig6 »
      3i8d »

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: Wed Jul 31 19:26:38 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy