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

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

The structure of RB69 Dna Polymerase (L561A/S565G/Y567A) Ternary Complex with Datp Opposite Difluorotoluene Nucleoside, PDB code: 3qer 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 / 1.96
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	78.269, 118.705, 130.523, 90.00, 90.00, 90.00
R / Rfree (%)	17.8 / 21.7

The structure of RB69 Dna Polymerase (L561A/S565G/Y567A) Ternary Complex with Datp 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 Datp Opposite Difluorotoluene Nucleoside (pdb code 3qer). 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 Datp Opposite Difluorotoluene Nucleoside, PDB code: 3qer:
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 Datp 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 Datp Opposite Difluorotoluene Nucleoside within 5.0Å range: probe atom residue distance (Å) B Occ T:F4 b:19.5 occ:1.00 F4 T:DFT4 0.0 19.5 1.0 C4 T:DFT4 1.3 14.8 1.0 C3 T:DFT4 2.4 11.7 1.0 C5 T:DFT4 2.4 11.7 1.0 O A:HOH1281 2.7 29.1 1.0 C5M T:DFT4 2.9 13.7 1.0 O A:HOH1298 2.9 18.5 1.0 O A:HOH1383 3.1 31.5 1.0 O T:HOH109 3.2 18.3 1.0 O T:HOH252 3.6 17.4 1.0 C2 T:DFT4 3.6 9.7 1.0 N1 A:DTP904 3.6 4.8 1.0 C6 T:DFT4 3.7 10.4 1.0 N6 A:DTP904 4.0 3.3 1.0 C1 T:DFT4 4.2 9.2 1.0 C6 A:DTP904 4.3 6.8 1.0 O A:HOH1263 4.3 21.5 1.0 N7 T:DG5 4.5 8.4 1.0 O6 T:DG5 4.5 8.6 1.0 C2 A:DTP904 4.6 3.6 1.0 F2 T:DFT4 4.7 10.9 1.0 O T:HOH476 4.9 33.2 1.0 C5 T:DG5 5.0 6.2 1.0 C6 T:DG5 5.0 8.0 1.0

Fluorine binding site 2 out of 2 in the RB69 Dna Polymerase (L561A/S565G/Y567A) Ternary Complex with Datp 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 Datp Opposite Difluorotoluene Nucleoside within 5.0Å range: probe atom residue distance (Å) B Occ T:F4 b:10.9 occ:1.00 F2 T:DFT4 0.0 10.9 1.0 C2 T:DFT4 1.3 9.7 1.0 C3 T:DFT4 2.4 11.7 1.0 C1 T:DFT4 2.5 9.2 1.0 C1' T:DFT4 2.9 8.9 1.0 C2' T:DFT4 3.1 5.4 1.0 C8 T:DG5 3.2 7.8 1.0 CA A:GLY568 3.4 13.3 1.0 N9 T:DG5 3.4 6.5 1.0 C4 T:DFT4 3.6 14.8 1.0 O4' T:DG5 3.6 4.0 1.0 N7 T:DG5 3.7 8.4 1.0 C6 T:DFT4 3.7 10.4 1.0 C2 A:DTP904 3.7 3.6 1.0 O A:ASN564 3.7 11.7 1.0 CA A:GLY565 3.8 13.4 1.0 C1' T:DG5 3.9 4.1 1.0 O A:GLY565 3.9 13.5 1.0 N A:GLY568 4.0 13.3 1.0 C4 T:DG5 4.0 4.8 1.0 C5 T:DG5 4.1 6.2 1.0 C A:GLY568 4.2 12.7 1.0 C5 T:DFT4 4.2 11.7 1.0 C A:GLY565 4.3 14.1 1.0 N1 A:DTP904 4.3 4.8 1.0 O4' T:DFT4 4.3 6.8 1.0 C3' T:DFT4 4.4 6.4 1.0 C A:ASN564 4.4 10.5 1.0 N A:GLY565 4.4 12.2 1.0 O A:HOH947 4.4 11.0 1.0 N A:ALA569 4.5 12.1 1.0 F4 T:DFT4 4.7 19.5 1.0 O T:HOH395 4.7 26.1 1.0 N3 A:DTP904 4.7 4.2 1.0 N3 T:DG5 4.8 4.3 1.0 O A:HOH1383 4.9 31.5 1.0 O A:GLY568 4.9 11.9 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