Fluorine in PDB 3qep: RB69 Dna Polymerase (L561A/S565G/Y567A) Ternary Complex with Dttp Opposite Difluorotoluene Nucleoside

All present enzymatic activity of RB69 Dna Polymerase (L561A/S565G/Y567A) Ternary Complex with Dttp Opposite Difluorotoluene Nucleoside:
2.7.7.7;

The structure of RB69 Dna Polymerase (L561A/S565G/Y567A) Ternary Complex with Dttp Opposite Difluorotoluene Nucleoside, PDB code: 3qep was solved by S.Xia, W.H.Konigsberg, J.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 1.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	75.133, 119.774, 130.481, 90.00, 90.00, 90.00
R / Rfree (%)	16.7 / 20.4

The structure of RB69 Dna Polymerase (L561A/S565G/Y567A) Ternary Complex with Dttp Opposite Difluorotoluene Nucleoside also contains other interesting chemical elements:

Calcium

(Ca)

7 atoms

The binding sites of Fluorine atom in the RB69 Dna Polymerase (L561A/S565G/Y567A) Ternary Complex with Dttp Opposite Difluorotoluene Nucleoside (pdb code 3qep). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the RB69 Dna Polymerase (L561A/S565G/Y567A) Ternary Complex with Dttp Opposite Difluorotoluene Nucleoside, PDB code: 3qep:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in the RB69 Dna Polymerase (L561A/S565G/Y567A) Ternary Complex with Dttp Opposite Difluorotoluene Nucleoside


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of RB69 Dna Polymerase (L561A/S565G/Y567A) Ternary Complex with Dttp Opposite Difluorotoluene Nucleoside within 5.0Å range: probe atom residue distance (Å) B Occ T:F4 b:11.2 occ:1.00 F4 T:DFT4 0.0 11.2 1.0 C4 T:DFT4 1.4 10.9 1.0 C3 T:DFT4 2.3 9.0 1.0 C5 T:DFT4 2.4 7.8 1.0 O A:HOH1795 2.9 21.0 1.0 C5M T:DFT4 2.9 9.6 1.0 N3 A:TTP904 3.0 16.4 1.0 O6 T:DG5 3.1 3.2 1.0 O A:HOH1779 3.3 20.8 1.0 C6 T:DG5 3.3 3.7 1.0 O A:HOH1801 3.3 19.4 1.0 C2 T:DFT4 3.5 4.4 1.0 C5 T:DG5 3.5 2.6 1.0 O4 A:TTP904 3.6 17.2 1.0 O T:HOH687 3.7 18.3 1.0 N7 T:DG5 3.7 4.3 1.0 C6 T:DFT4 3.7 7.5 1.0 C4 A:TTP904 3.7 15.9 1.0 O2 A:TTP904 3.9 17.3 1.0 C2 A:TTP904 3.9 15.9 1.0 N1 T:DG5 4.1 2.4 1.0 C1 T:DFT4 4.1 4.0 1.0 C4 T:DG5 4.4 2.0 1.0 N4 P:DOC115 4.5 2.1 1.0 O T:HOH290 4.6 12.5 1.0 C8 T:DG5 4.6 2.5 1.0 F2 T:DFT4 4.6 10.5 1.0 C2 T:DG5 4.9 3.5 1.0 O A:HOH1311 5.0 9.1 1.0 N9 T:DG5 5.0 2.0 1.0

Fluorine binding site 2 out of 2 in the RB69 Dna Polymerase (L561A/S565G/Y567A) Ternary Complex with Dttp Opposite Difluorotoluene Nucleoside


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of RB69 Dna Polymerase (L561A/S565G/Y567A) Ternary Complex with Dttp Opposite Difluorotoluene Nucleoside within 5.0Å range: probe atom residue distance (Å) B Occ T:F4 b:10.5 occ:1.00 F2 T:DFT4 0.0 10.5 1.0 C2 T:DFT4 1.3 4.4 1.0 C3 T:DFT4 2.3 9.0 1.0 C1 T:DFT4 2.4 4.0 1.0 C1' T:DFT4 2.9 2.9 1.0 CA A:GLY568 3.0 7.3 1.0 C2' T:DFT4 3.2 4.5 1.0 N A:GLY568 3.2 7.7 1.0 O A:ASN564 3.3 8.6 1.0 C4 T:DFT4 3.5 10.9 1.0 CA A:GLY565 3.6 8.0 1.0 C6 T:DFT4 3.7 7.5 1.0 O4' T:DG5 3.7 2.0 1.0 O A:GLY565 3.7 7.6 1.0 O A:HOH1326 3.7 9.0 1.0 N9 T:DG5 3.8 2.0 1.0 C A:GLY568 3.8 5.9 1.0 C8 T:DG5 3.9 2.5 1.0 C1' T:DG5 3.9 2.0 1.0 C A:GLY565 4.0 8.5 1.0 C A:ASN564 4.0 7.7 1.0 C5 T:DFT4 4.1 7.8 1.0 N A:ALA569 4.1 5.1 1.0 O T:HOH35 4.1 14.9 1.0 N A:GLY565 4.2 7.4 1.0 O4' T:DFT4 4.3 5.4 1.0 C4 T:DG5 4.3 2.0 1.0 N7 T:DG5 4.5 4.3 1.0 C A:ALA567 4.6 7.6 1.0 O A:GLY568 4.6 7.4 1.0 C3' T:DFT4 4.6 2.6 1.0 F4 T:DFT4 4.6 11.2 1.0 C5 T:DG5 4.7 2.6 1.0 O2 A:TTP904 4.7 17.3 1.0 N3 T:DG5 4.9 2.1 1.0

S.Xia, W.H.Konigsberg, J.Wang. Hydrogen-Bonding Capability of A Templating Difluorotoluene Nucleotide Residue in An RB69 Dna Polymerase Ternary Complex. J.Am.Chem.Soc. V. 133 10003 2011.
ISSN: ISSN 0002-7863
PubMed: 21667997
DOI: 10.1021/JA2021735