Fluorine in PDB 3rwu: RB69 Dna Polymerase (Y567A) Ternary Complex with Datp Opposite Difluorotoluene Nucleoside

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

The structure of RB69 Dna Polymerase (Y567A) Ternary Complex with Datp Opposite Difluorotoluene Nucleoside, PDB code: 3rwu 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 / 2.33
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	74.913, 120.103, 130.596, 90.00, 90.00, 90.00
R / Rfree (%)	22.2 / 27.6

The structure of RB69 Dna Polymerase (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 (Y567A) Ternary Complex with Datp Opposite Difluorotoluene Nucleoside (pdb code 3rwu). 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 (Y567A) Ternary Complex with Datp Opposite Difluorotoluene Nucleoside, PDB code: 3rwu:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in the RB69 Dna Polymerase (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 (Y567A) Ternary Complex with Datp Opposite Difluorotoluene Nucleoside within 5.0Å range: probe atom residue distance (Å) B Occ T:F4 b:28.2 occ:1.00 F4 T:DFT4 0.0 28.2 1.0 C4 T:DFT4 1.3 29.4 1.0 C5 T:DFT4 2.3 31.8 1.0 C3 T:DFT4 2.4 26.9 1.0 C5M T:DFT4 2.8 28.3 1.0 CD1 A:LEU561 3.3 31.2 1.0 C2 T:DFT4 3.6 27.8 1.0 C6 T:DFT4 3.6 32.7 1.0 N1 A:ATP902 3.8 32.7 1.0 C1 T:DFT4 4.1 28.5 1.0 N6 A:ATP902 4.3 24.9 1.0 C6 A:ATP902 4.5 24.6 1.0 OG A:SER565 4.5 33.2 1.0 O6 T:DG5 4.6 30.6 1.0 N7 T:DG5 4.6 26.4 1.0 CG A:LEU561 4.6 27.5 1.0 F2 T:DFT4 4.7 24.1 1.0 C2 A:ATP902 4.8 32.3 1.0

Fluorine binding site 2 out of 2 in the RB69 Dna Polymerase (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 (Y567A) Ternary Complex with Datp Opposite Difluorotoluene Nucleoside within 5.0Å range: probe atom residue distance (Å) B Occ T:F4 b:24.1 occ:1.00 F2 T:DFT4 0.0 24.1 1.0 C2 T:DFT4 1.3 27.8 1.0 C3 T:DFT4 2.3 26.9 1.0 C1 T:DFT4 2.4 28.5 1.0 C1' T:DFT4 2.8 32.4 1.0 C2' T:DFT4 3.0 32.4 1.0 C8 T:DG5 3.4 31.8 1.0 CA A:GLY568 3.4 25.1 1.0 CA A:SER565 3.5 25.7 1.0 C4 T:DFT4 3.6 29.4 1.0 C6 T:DFT4 3.6 32.7 1.0 N9 T:DG5 3.6 27.8 1.0 N7 T:DG5 3.8 26.4 1.0 O4' T:DG5 3.9 29.5 1.0 C2 A:ATP902 3.9 32.3 1.0 O A:ASN564 3.9 26.4 1.0 O A:SER565 3.9 26.5 1.0 N A:GLY568 4.1 26.5 1.0 C1' T:DG5 4.1 30.6 1.0 C5 T:DFT4 4.1 31.8 1.0 C4 T:DG5 4.1 27.7 1.0 C A:SER565 4.1 25.1 1.0 C5 T:DG5 4.2 26.0 1.0 O4' T:DFT4 4.2 28.3 1.0 C A:GLY568 4.2 26.1 1.0 CB A:SER565 4.2 27.1 1.0 N A:SER565 4.2 23.9 1.0 C3' T:DFT4 4.3 30.9 1.0 OG A:SER565 4.3 33.2 1.0 C A:ASN564 4.4 25.2 1.0 N1 A:ATP902 4.4 32.7 1.0 N A:ALA569 4.5 26.4 1.0 F4 T:DFT4 4.7 28.2 1.0 N3 A:ATP902 4.9 28.4 1.0 C4' T:DFT4 5.0 34.1 1.0 N3 T:DG5 5.0 26.2 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