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

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

The structure of RB69 Dna Polymerase (L561A/S565G/Y567A) Ternary Complex with Dctp Opposite Difluorotoluene Nucleoside, PDB code: 3qei 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 / 2.18
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	78.345, 118.231, 130.854, 90.00, 90.00, 90.00
R / Rfree (%)	19 / 23.8

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

Calcium

(Ca)

4 atoms

The binding sites of Fluorine atom in the RB69 Dna Polymerase (L561A/S565G/Y567A) Ternary Complex with Dctp Opposite Difluorotoluene Nucleoside (pdb code 3qei). 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 Dctp Opposite Difluorotoluene Nucleoside, PDB code: 3qei:
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 Dctp 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 Dctp Opposite Difluorotoluene Nucleoside within 5.0Å range: probe atom residue distance (Å) B Occ T:F4 b:34.3 occ:1.00 F4 T:DFT4 0.0 34.3 1.0 C4 T:DFT4 1.3 30.0 1.0 C3 T:DFT4 2.4 29.1 1.0 C5 T:DFT4 2.5 28.9 1.0 O A:HOH1176 2.7 18.6 1.0 O A:HOH1018 2.8 24.1 1.0 C5M T:DFT4 3.0 28.8 1.0 O A:HOH1351 3.1 29.1 1.0 O T:HOH485 3.2 36.2 1.0 O6 T:DG5 3.6 5.6 1.0 C2 T:DFT4 3.6 25.8 1.0 C6 T:DFT4 3.7 26.8 1.0 N4 A:DCP904 3.8 13.6 1.0 N7 T:DG5 3.8 6.8 1.0 O T:HOH467 3.9 25.3 1.0 C6 T:DG5 4.0 7.6 1.0 N3 A:DCP904 4.0 9.8 1.0 C5 T:DG5 4.1 7.2 1.0 C1 T:DFT4 4.2 23.2 1.0 C4 A:DCP904 4.4 11.1 1.0 F2 T:DFT4 4.7 28.2 1.0 C8 T:DG5 4.7 6.3 1.0 N4 P:DOC115 5.0 2.3 1.0 O A:HOH981 5.0 9.2 0.5 N1 T:DG5 5.0 7.5 1.0

Fluorine binding site 2 out of 2 in the RB69 Dna Polymerase (L561A/S565G/Y567A) Ternary Complex with Dctp 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 Dctp Opposite Difluorotoluene Nucleoside within 5.0Å range: probe atom residue distance (Å) B Occ T:F4 b:28.2 occ:1.00 F2 T:DFT4 0.0 28.2 1.0 C2 T:DFT4 1.3 25.8 1.0 C3 T:DFT4 2.3 29.1 1.0 C1 T:DFT4 2.4 23.2 1.0 C1' T:DFT4 2.9 19.1 1.0 CA A:GLY568 3.1 12.4 1.0 C2' T:DFT4 3.2 12.3 1.0 O A:ASN564 3.4 14.1 1.0 N A:GLY568 3.5 12.6 1.0 CA A:GLY565 3.6 17.6 1.0 C8 T:DG5 3.6 6.3 1.0 C4 T:DFT4 3.6 30.0 1.0 O4' T:DG5 3.6 3.5 1.0 N9 T:DG5 3.6 6.4 1.0 O A:HOH1349 3.7 33.0 1.0 C6 T:DFT4 3.7 26.8 1.0 O A:GLY565 3.7 18.8 1.0 C1' T:DG5 3.8 3.9 1.0 C A:GLY568 3.9 13.7 1.0 C A:GLY565 4.0 18.0 1.0 C A:ASN564 4.0 14.1 1.0 N A:GLY565 4.1 16.9 1.0 N7 T:DG5 4.2 6.8 1.0 C5 T:DFT4 4.2 28.9 1.0 C4 T:DG5 4.2 4.2 1.0 O4' T:DFT4 4.3 17.8 1.0 N A:ALA569 4.3 13.7 1.0 C5 T:DG5 4.5 7.2 1.0 C3' T:DFT4 4.6 10.9 1.0 F4 T:DFT4 4.7 34.3 1.0 O A:GLY568 4.7 12.3 1.0 C A:ALA567 4.8 13.5 1.0 O2 A:DCP904 4.8 14.7 1.0 O A:HOH1018 4.9 24.1 1.0 N3 T:DG5 4.9 4.7 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