Fluorine in PDB 6u17: Human Thymine Dna Glycosylase Bound to Dna with 2'-F-5-Carboxyl-Dc Substrate Analog

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

The structure of Human Thymine Dna Glycosylase Bound to Dna with 2'-F-5-Carboxyl-Dc Substrate Analog, PDB code: 6u17 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)	43.25 / 1.55
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	96.870, 52.760, 81.620, 90.00, 95.25, 90.00
R / Rfree (%)	18.9 / 22.4

The binding sites of Fluorine atom in the Human Thymine Dna Glycosylase Bound to Dna with 2'-F-5-Carboxyl-Dc Substrate Analog (pdb code 6u17). 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 Human Thymine Dna Glycosylase Bound to Dna with 2'-F-5-Carboxyl-Dc Substrate Analog, PDB code: 6u17:

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


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Human Thymine Dna Glycosylase Bound to Dna with 2'-F-5-Carboxyl-Dc Substrate Analog within 5.0Å range: probe atom residue distance (Å) B Occ D:F17 b:37.5 occ:1.00 F24 D:1FC17 0.0 37.5 1.0 C2' D:1FC17 1.4 30.7 1.0 C1' D:1FC17 2.4 28.8 1.0 C3' D:1FC17 2.4 31.4 1.0 N1 D:1FC17 2.7 27.8 1.0 O4' D:1FC17 3.0 29.2 1.0 O A:HOH550 3.2 31.3 1.0 C2 D:1FC17 3.3 29.0 1.0 C4' D:1FC17 3.3 30.2 1.0 O2 D:1FC17 3.3 29.2 1.0 CB A:SER273 3.4 29.9 1.0 C6 D:1FC17 3.4 26.1 1.0 O3' D:1FC17 3.5 32.3 1.0 O5' D:1FC17 3.6 30.7 1.0 OG A:SER271 3.6 29.2 1.0 ND2 A:ASN157 4.0 30.1 1.0 C5' D:1FC17 4.1 30.8 1.0 CA A:SER273 4.1 28.0 1.0 N A:SER273 4.1 29.4 1.0 OG A:SER273 4.3 29.2 1.0 O5' D:DG18 4.3 30.6 1.0 N3 D:1FC17 4.4 29.6 1.0 C5 D:1FC17 4.5 28.9 1.0 P D:DG18 4.5 31.5 1.0 OP1 D:1FC17 4.7 28.4 1.0 OP2 D:DG18 4.8 30.1 1.0 P D:1FC17 4.8 31.4 1.0 C5' D:DG18 4.8 31.3 1.0 O A:HOH546 4.8 40.6 1.0 CE1 A:TYR152 4.9 27.8 1.0 C4 D:1FC17 4.9 29.2 1.0 CB A:SER271 5.0 30.8 1.0

L.S.Pidugu, Q.Dai, S.S.Malik, E.Pozharski, A.C.Drohat. Excision of 5-Carboxylcytosine By Thymine Dna Glycosylase. J.Am.Chem.Soc. 2019.
ISSN: ESSN 1520-5126
PubMed: 31693361
DOI: 10.1021/JACS.9B10376