Fluorine in PDB 5t2w: Structure of Thymine Dna Glycosylase Bound to Substrate Analog 2'-F-5- Formyl-Dc

All present enzymatic activity of Structure of Thymine Dna Glycosylase Bound to Substrate Analog 2'-F-5- Formyl-Dc:
3.2.2.29;

The structure of Structure of Thymine Dna Glycosylase Bound to Substrate Analog 2'-F-5- Formyl-Dc, PDB code: 5t2w was solved by L.S.Pidugu, E.Pozharski, A.C.Drohat, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	21.37 / 2.20
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	83.530, 51.900, 82.030, 90.00, 101.52, 90.00
R / Rfree (%)	18 / 22.6

The binding sites of Fluorine atom in the Structure of Thymine Dna Glycosylase Bound to Substrate Analog 2'-F-5- Formyl-Dc (pdb code 5t2w). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total only one binding site of Fluorine was determined in the Structure of Thymine Dna Glycosylase Bound to Substrate Analog 2'-F-5- Formyl-Dc, PDB code: 5t2w:

Fluorine binding site 1 out of 1 in the Structure of Thymine Dna Glycosylase Bound to Substrate Analog 2'-F-5- Formyl-Dc


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Structure of Thymine Dna Glycosylase Bound to Substrate Analog 2'-F-5- Formyl-Dc within 5.0Å range: probe atom residue distance (Å) B Occ D:F17 b:34.3 occ:1.00 F2' D:XFC17 0.0 34.3 1.0 C2' D:XFC17 1.4 28.6 1.0 C1' D:XFC17 2.4 27.8 1.0 C3' D:XFC17 2.4 26.8 1.0 N1 D:XFC17 2.8 23.8 1.0 O4' D:XFC17 3.0 30.3 1.0 C4' D:XFC17 3.3 28.1 1.0 CB A:SER273 3.3 20.3 1.0 O5' D:XFC17 3.3 28.1 1.0 C6 D:XFC17 3.4 23.1 1.0 ND2 A:ASN157 3.5 20.0 1.0 C2 D:XFC17 3.6 23.2 1.0 O3' D:XFC17 3.6 28.5 1.0 O A:HOH405 3.6 21.9 1.0 OG A:SER271 3.8 18.7 1.0 O2 D:XFC17 3.8 24.2 1.0 CA A:SER273 3.9 21.4 1.0 C5' D:XFC17 3.9 25.2 1.0 N A:SER273 4.0 21.7 1.0 OG A:SER273 4.1 21.8 1.0 OP1 D:XFC17 4.1 25.7 1.0 P D:XFC17 4.4 27.5 1.0 C5 D:XFC17 4.4 25.9 1.0 O5' D:DG18 4.4 28.4 1.0 P D:DG18 4.5 29.3 1.0 N3 D:XFC17 4.6 23.4 1.0 OP2 D:DG18 4.7 27.2 1.0 CG A:ASN157 4.8 29.0 1.0 OG A:SER272 4.8 30.4 1.0 C A:SER272 4.9 24.6 1.0 C4 D:XFC17 4.9 26.7 1.0

L.S.Pidugu, J.W.Flowers, C.T.Coey, E.Pozharski, M.M.Greenberg, A.C.Drohat. Structural Basis For Excision of 5-Formylcytosine By Thymine Dna Glycosylase. Biochemistry V. 55 6205 2016.
ISSN: ISSN 1520-4995
PubMed: 27805810
DOI: 10.1021/ACS.BIOCHEM.6B00982