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

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

The structure of RB69 Dna Polymerase (L561A/S565G/Y567A) Ternary Complex with Dgtp Opposite Difluorotoluene Nucleoside, PDB code: 3qes 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)	46.81 / 1.98
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	74.824, 119.979, 130.068, 90.00, 90.00, 90.00
R / Rfree (%)	17.7 / 21.8

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

Calcium

(Ca)

5 atoms

The binding sites of Fluorine atom in the RB69 Dna Polymerase (L561A/S565G/Y567A) Ternary Complex with Dgtp Opposite Difluorotoluene Nucleoside (pdb code 3qes). 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 Dgtp Opposite Difluorotoluene Nucleoside, PDB code: 3qes:
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 Dgtp 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 Dgtp Opposite Difluorotoluene Nucleoside within 5.0Å range: probe atom residue distance (Å) B Occ T:F4 b:58.7 occ:1.00 F4 T:DFT4 0.0 58.7 1.0 C4 T:DFT4 1.3 55.9 1.0 C3 T:DFT4 2.4 50.7 1.0 C5 T:DFT4 2.4 55.4 1.0 C5M T:DFT4 2.9 54.4 1.0 O A:HOH1594 3.1 42.3 1.0 O T:HOH249 3.3 45.5 1.0 O A:HOH1356 3.4 31.4 1.0 C2 T:DFT4 3.6 49.6 1.0 C6 T:DFT4 3.6 53.0 1.0 N1 A:DGT904 4.0 19.6 1.0 C1 T:DFT4 4.1 50.8 1.0 O6 A:DGT904 4.2 21.2 1.0 O A:HOH1357 4.3 33.0 1.0 O T:HOH227 4.3 41.1 1.0 N7 T:DG5 4.5 20.5 1.0 C6 A:DGT904 4.6 20.8 1.0 O6 T:DG5 4.7 21.4 1.0 F2 T:DFT4 4.7 40.6 1.0

Fluorine binding site 2 out of 2 in the RB69 Dna Polymerase (L561A/S565G/Y567A) Ternary Complex with Dgtp 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 Dgtp Opposite Difluorotoluene Nucleoside within 5.0Å range: probe atom residue distance (Å) B Occ T:F4 b:40.6 occ:1.00 F2 T:DFT4 0.0 40.6 1.0 C2 T:DFT4 1.3 49.6 1.0 C1 T:DFT4 2.4 50.8 1.0 C3 T:DFT4 2.4 50.7 1.0 N2 A:DGT904 2.5 21.8 1.0 C1' T:DFT4 2.8 48.3 1.0 C2' T:DFT4 3.0 46.4 1.0 C8 T:DG5 3.3 18.7 1.0 CA A:GLY565 3.6 17.5 1.0 CA A:GLY568 3.6 17.8 1.0 C6 T:DFT4 3.6 53.0 1.0 C4 T:DFT4 3.6 55.9 1.0 N9 T:DG5 3.6 17.5 1.0 C2 A:DGT904 3.7 20.3 1.0 N7 T:DG5 3.7 20.5 1.0 O4' T:DG5 3.8 15.7 1.0 O A:ASN564 3.9 16.7 1.0 O A:GLY565 4.0 19.7 1.0 C1' T:DG5 4.1 16.2 1.0 C5 T:DFT4 4.1 55.4 1.0 N1 A:DGT904 4.1 19.6 1.0 N A:GLY568 4.1 16.2 1.0 C3' T:DFT4 4.2 42.7 1.0 O4' T:DFT4 4.2 46.2 1.0 C A:GLY565 4.2 18.1 1.0 C4 T:DG5 4.2 15.2 1.0 O A:HOH1356 4.3 31.4 1.0 C5 T:DG5 4.3 19.4 1.0 N A:GLY565 4.3 16.4 1.0 C A:GLY568 4.3 17.3 1.0 C A:ASN564 4.4 17.2 1.0 O A:HOH991 4.6 28.1 1.0 N A:ALA569 4.6 15.8 1.0 F4 T:DFT4 4.7 58.7 1.0 N3 A:DGT904 4.9 20.1 1.0 O T:HOH220 4.9 37.4 1.0 C4' T:DFT4 4.9 45.5 1.0 O A:GLY568 5.0 17.3 1.0

S.Xia, S.H.Eom, W.H.Konigsberg, J.Wang. Structural Basis For Differential Insertion Kinetics of Dnmps Opposite A Difluorotoluene Nucleotide Residue. Biochemistry V. 51 1476 2012.
ISSN: ISSN 0006-2960
PubMed: 22304682
DOI: 10.1021/BI2016487