Fluorine in PDB 6tc8: 2'-F-Arabinoguanosine and 2'-F-Riboguanosine Modified Hybrid Type G- Quadruplex with V-Loop

The binding sites of Fluorine atom in the 2'-F-Arabinoguanosine and 2'-F-Riboguanosine Modified Hybrid Type G- Quadruplex with V-Loop (pdb code 6tc8). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the 2'-F-Arabinoguanosine and 2'-F-Riboguanosine Modified Hybrid Type G- Quadruplex with V-Loop, PDB code: 6tc8:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in the 2'-F-Arabinoguanosine and 2'-F-Riboguanosine Modified Hybrid Type G- Quadruplex with V-Loop


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of 2'-F-Arabinoguanosine and 2'-F-Riboguanosine Modified Hybrid Type G- Quadruplex with V-Loop within 5.0Å range: probe atom residue distance (Å) B Occ A:F14 b:0.0 occ:1.00 F A:GFL14 0.0 0.0 1.0 C2' A:GFL14 1.4 0.0 1.0 H2' A:GFL14 2.0 0.0 1.0 H22 A:DG1 2.3 0.0 1.0 C3' A:GFL14 2.4 0.0 1.0 C1' A:GFL14 2.5 0.0 1.0 H3' A:GFL14 2.5 0.0 1.0 H5' A:GF215 2.8 0.0 1.0 N9 A:GFL14 2.8 0.0 1.0 H1' A:GFL14 3.0 0.0 1.0 N2 A:DG1 3.0 0.0 1.0 O3' A:GFL14 3.1 0.0 1.0 C4 A:GFL14 3.2 0.0 1.0 H21 A:DG1 3.2 0.0 1.0 N3 A:GFL14 3.2 0.0 1.0 O5' A:DG1 3.3 0.0 1.0 H8 A:DG16 3.4 0.0 1.0 O5' A:GF215 3.4 0.0 1.0 C5' A:GF215 3.5 0.0 1.0 HO5' A:DG1 3.5 0.0 1.0 O4' A:GFL14 3.6 0.0 1.0 C4' A:GFL14 3.6 0.0 1.0 O4' A:GF215 3.8 0.0 1.0 C8 A:GFL14 3.8 0.0 1.0 N7 A:DG16 3.9 0.0 1.0 P A:GF215 4.0 0.0 1.0 C2 A:DG1 4.0 0.0 1.0 C8 A:DG16 4.0 0.0 1.0 H4' A:GFL14 4.2 0.0 1.0 C4' A:GF215 4.2 0.0 1.0 C5 A:GFL14 4.2 0.0 1.0 H8 A:GFL14 4.3 0.0 1.0 N3 A:DG1 4.3 0.0 1.0 C2 A:GFL14 4.3 0.0 1.0 H5' A:DG1 4.3 0.0 1.0 H5'A A:GF215 4.4 0.0 1.0 C5' A:DG1 4.4 0.0 1.0 H5'2 A:GFL14 4.6 0.0 1.0 OP2 A:GF215 4.6 0.0 1.0 N7 A:GFL14 4.6 0.0 1.0 C5' A:GFL14 4.7 0.0 1.0 HN22 A:GFL14 4.7 0.0 1.0 H5'' A:DG1 4.8 0.0 1.0 H4' A:GF215 4.8 0.0 1.0 N2 A:GFL14 4.9 0.0 1.0

Fluorine binding site 2 out of 2 in the 2'-F-Arabinoguanosine and 2'-F-Riboguanosine Modified Hybrid Type G- Quadruplex with V-Loop


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of 2'-F-Arabinoguanosine and 2'-F-Riboguanosine Modified Hybrid Type G- Quadruplex with V-Loop within 5.0Å range: probe atom residue distance (Å) B Occ A:F15 b:0.0 occ:1.00 F A:GF215 0.0 0.0 1.0 C2' A:GF215 1.4 0.0 1.0 H2' A:GF215 2.0 0.0 1.0 H1' A:GF215 2.3 0.0 1.0 C1' A:GF215 2.4 0.0 1.0 C3' A:GF215 2.4 0.0 1.0 O3' A:GF215 2.8 0.0 1.0 H4' A:GF215 2.9 0.0 1.0 OP1 A:DG16 3.0 0.0 1.0 C4' A:GF215 3.1 0.0 1.0 H3' A:GF215 3.3 0.0 1.0 O4' A:GF215 3.4 0.0 1.0 N9 A:GF215 3.4 0.0 1.0 P A:DG16 3.5 0.0 1.0 H8 A:GF215 3.7 0.0 1.0 C8 A:GF215 3.9 0.0 1.0 H5' A:DG16 4.0 0.0 1.0 O5' A:DG16 4.3 0.0 1.0 C4 A:GF215 4.5 0.0 1.0 C5' A:GF215 4.6 0.0 1.0 C5' A:DG16 4.7 0.0 1.0 OP2 A:DG16 4.8 0.0 1.0 O4' A:DG16 4.8 0.0 1.0 H5'A A:GF215 4.8 0.0 1.0

L.Haase, K.Weisz. Switching the Type of V-Loop in Sugar-Modified G-Quadruplexes Through Altered Fluorine Interactions Chem.Commun.(Camb.) 2020.
ISSN: ESSN 1364-548X
DOI: 10.1039/D0CC01285H