Fluorine in PDB 8qdu: Formation of Left-Handed Helices By C2'-Fluorinated Nucleic Acids Under Physiological Salt Conditions

The binding sites of Fluorine atom in the Formation of Left-Handed Helices By C2'-Fluorinated Nucleic Acids Under Physiological Salt Conditions (pdb code 8qdu). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Formation of Left-Handed Helices By C2'-Fluorinated Nucleic Acids Under Physiological Salt Conditions, PDB code: 8qdu:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in the Formation of Left-Handed Helices By C2'-Fluorinated Nucleic Acids Under Physiological Salt Conditions


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Formation of Left-Handed Helices By C2'-Fluorinated Nucleic Acids Under Physiological Salt Conditions within 5.0Å range: probe atom residue distance (Å) B Occ A:F1 b:0.0 occ:1.00 F A:CFL1 0.0 0.0 1.0 C2' A:CFL1 1.4 0.0 1.0 H2' A:CFL1 2.1 0.0 1.0 C3' A:CFL1 2.4 0.0 1.0 C1' A:CFL1 2.4 0.0 1.0 H3' A:CFL1 2.4 0.0 1.0 HO5' A:CFL1 2.8 0.0 1.0 N1 A:CFL1 2.8 0.0 1.0 O4' A:CFL1 2.9 0.0 1.0 C4' A:CFL1 3.1 0.0 1.0 O5' A:CFL1 3.2 0.0 1.0 H1' A:CFL1 3.3 0.0 1.0 C6 A:CFL1 3.4 0.0 1.0 C2 A:CFL1 3.5 0.0 1.0 H6 A:CFL1 3.6 0.0 1.0 O3' A:CFL1 3.6 0.0 1.0 C5' A:CFL1 3.7 0.0 1.0 O2 A:CFL1 3.8 0.0 1.0 H4' A:CFL1 4.1 0.0 1.0 H5'2 A:CFL1 4.4 0.0 1.0 C5 A:CFL1 4.4 0.0 1.0 N3 A:CFL1 4.5 0.0 1.0 H5'1 A:CFL1 4.5 0.0 1.0 OP1 A:DG2 4.8 0.0 1.0 C4 A:CFL1 4.8 0.0 1.0 P A:DG2 4.9 0.0 1.0

Fluorine binding site 2 out of 6 in the Formation of Left-Handed Helices By C2'-Fluorinated Nucleic Acids Under Physiological Salt Conditions


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Formation of Left-Handed Helices By C2'-Fluorinated Nucleic Acids Under Physiological Salt Conditions within 5.0Å range: probe atom residue distance (Å) B Occ A:F3 b:0.0 occ:1.00 F A:CFL3 0.0 0.0 1.0 C2' A:CFL3 1.4 0.0 1.0 H2' A:CFL3 2.0 0.0 1.0 C3' A:CFL3 2.4 0.0 1.0 H3' A:CFL3 2.4 0.0 1.0 C1' A:CFL3 2.4 0.0 1.0 H2' A:DG2 2.5 0.0 1.0 H3' A:DG2 2.7 0.0 1.0 N1 A:CFL3 2.8 0.0 1.0 O4' A:CFL3 3.1 0.0 1.0 H22 A:DG2 3.1 0.0 1.0 C4' A:CFL3 3.2 0.0 1.0 H1' A:CFL3 3.3 0.0 1.0 C2 A:CFL3 3.3 0.0 1.0 C2' A:DG2 3.4 0.0 1.0 O5' A:CFL3 3.4 0.0 1.0 C6 A:CFL3 3.5 0.0 1.0 C3' A:DG2 3.5 0.0 1.0 O2 A:CFL3 3.5 0.0 1.0 O3' A:CFL3 3.5 0.0 1.0 N3 A:DG2 3.5 0.0 1.0 H6 A:CFL3 3.7 0.0 1.0 H5'' A:DG2 3.8 0.0 1.0 H2'' A:DG2 3.8 0.0 1.0 N2 A:DG2 3.8 0.0 1.0 C5' A:CFL3 3.9 0.0 1.0 C2 A:DG2 4.0 0.0 1.0 H4' A:CFL3 4.2 0.0 1.0 N3 A:CFL3 4.3 0.0 1.0 H5' A:DG2 4.4 0.0 1.0 C5' A:DG2 4.4 0.0 1.0 H5'2 A:CFL3 4.4 0.0 1.0 C5 A:CFL3 4.4 0.0 1.0 C4 A:DG2 4.4 0.0 1.0 O3' A:DG2 4.5 0.0 1.0 C4' A:DG2 4.5 0.0 1.0 P A:CFL3 4.5 0.0 1.0 C1' A:DG2 4.6 0.0 1.0 H21 A:DG2 4.6 0.0 1.0 O2P A:CFL3 4.7 0.0 1.0 H21 B:DG10 4.7 0.0 1.0 OP1 A:DG4 4.7 0.0 1.0 H5'1 A:CFL3 4.8 0.0 1.0 C4 A:CFL3 4.8 0.0 1.0 P A:DG4 4.8 0.0 1.0 N9 A:DG2 4.8 0.0 1.0 O4' A:DG2 4.9 0.0 1.0

Fluorine binding site 3 out of 6 in the Formation of Left-Handed Helices By C2'-Fluorinated Nucleic Acids Under Physiological Salt Conditions


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Formation of Left-Handed Helices By C2'-Fluorinated Nucleic Acids Under Physiological Salt Conditions within 5.0Å range: probe atom residue distance (Å) B Occ A:F5 b:0.0 occ:1.00 F A:CFL5 0.0 0.0 1.0 C2' A:CFL5 1.4 0.0 1.0 H2' A:CFL5 2.0 0.0 1.0 C3' A:CFL5 2.4 0.0 1.0 H3' A:CFL5 2.4 0.0 1.0 C1' A:CFL5 2.4 0.0 1.0 H2' A:DG4 2.5 0.0 1.0 H3' A:DG4 2.8 0.0 1.0 N1 A:CFL5 2.8 0.0 1.0 H22 A:DG4 3.0 0.0 1.0 O4' A:CFL5 3.1 0.0 1.0 C4' A:CFL5 3.2 0.0 1.0 H1' A:CFL5 3.3 0.0 1.0 O5' A:CFL5 3.3 0.0 1.0 C2 A:CFL5 3.4 0.0 1.0 C2' A:DG4 3.4 0.0 1.0 O3' A:CFL5 3.5 0.0 1.0 O2 A:CFL5 3.5 0.0 1.0 C6 A:CFL5 3.5 0.0 1.0 C3' A:DG4 3.5 0.0 1.0 N3 A:DG4 3.6 0.0 1.0 H6 A:CFL5 3.7 0.0 1.0 H2'' A:DG4 3.8 0.0 1.0 N2 A:DG4 3.8 0.0 1.0 H5'' A:DG4 3.8 0.0 1.0 C5' A:CFL5 3.9 0.0 1.0 C2 A:DG4 4.2 0.0 1.0 H4' A:CFL5 4.2 0.0 1.0 N3 A:CFL5 4.4 0.0 1.0 H5'2 A:CFL5 4.4 0.0 1.0 C5 A:CFL5 4.5 0.0 1.0 O3' A:DG4 4.5 0.0 1.0 C5' A:DG4 4.5 0.0 1.0 P A:CFL5 4.5 0.0 1.0 C4' A:DG4 4.6 0.0 1.0 H5' A:DG4 4.6 0.0 1.0 H21 A:DG4 4.6 0.0 1.0 C1' A:DG4 4.6 0.0 1.0 C4 A:DG4 4.6 0.0 1.0 OP1 A:DG6 4.7 0.0 1.0 H5'1 A:CFL5 4.7 0.0 1.0 O2P A:CFL5 4.8 0.0 1.0 C4 A:CFL5 4.8 0.0 1.0 P A:DG6 4.8 0.0 1.0 H21 B:DG8 4.8 0.0 1.0 O4' A:DG4 4.9 0.0 1.0

Fluorine binding site 4 out of 6 in the Formation of Left-Handed Helices By C2'-Fluorinated Nucleic Acids Under Physiological Salt Conditions


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Formation of Left-Handed Helices By C2'-Fluorinated Nucleic Acids Under Physiological Salt Conditions within 5.0Å range: probe atom residue distance (Å) B Occ B:F7 b:0.0 occ:1.00 F B:CFL7 0.0 0.0 1.0 C2' B:CFL7 1.4 0.0 1.0 H2' B:CFL7 2.1 0.0 1.0 C3' B:CFL7 2.4 0.0 1.0 C1' B:CFL7 2.4 0.0 1.0 H3' B:CFL7 2.4 0.0 1.0 HO5' B:CFL7 2.6 0.0 1.0 N1 B:CFL7 2.8 0.0 1.0 O4' B:CFL7 2.9 0.0 1.0 C4' B:CFL7 3.1 0.0 1.0 O5' B:CFL7 3.2 0.0 1.0 H1' B:CFL7 3.3 0.0 1.0 C6 B:CFL7 3.4 0.0 1.0 H6 B:CFL7 3.5 0.0 1.0 C2 B:CFL7 3.5 0.0 1.0 O3' B:CFL7 3.6 0.0 1.0 C5' B:CFL7 3.7 0.0 1.0 O2 B:CFL7 3.8 0.0 1.0 H4' B:CFL7 4.0 0.0 1.0 H5'2 B:CFL7 4.3 0.0 1.0 C5 B:CFL7 4.4 0.0 1.0 N3 B:CFL7 4.5 0.0 1.0 H5'1 B:CFL7 4.5 0.0 1.0 C4 B:CFL7 4.8 0.0 1.0 OP1 B:DG8 4.8 0.0 1.0 P B:DG8 4.9 0.0 1.0

Fluorine binding site 5 out of 6 in the Formation of Left-Handed Helices By C2'-Fluorinated Nucleic Acids Under Physiological Salt Conditions


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Formation of Left-Handed Helices By C2'-Fluorinated Nucleic Acids Under Physiological Salt Conditions within 5.0Å range: probe atom residue distance (Å) B Occ B:F9 b:0.0 occ:1.00 F B:CFL9 0.0 0.0 1.0 C2' B:CFL9 1.4 0.0 1.0 H2' B:CFL9 2.0 0.0 1.0 C3' B:CFL9 2.4 0.0 1.0 H3' B:CFL9 2.4 0.0 1.0 C1' B:CFL9 2.4 0.0 1.0 H2' B:DG8 2.6 0.0 1.0 H3' B:DG8 2.7 0.0 1.0 N1 B:CFL9 2.8 0.0 1.0 O4' B:CFL9 3.1 0.0 1.0 H22 B:DG8 3.1 0.0 1.0 C4' B:CFL9 3.2 0.0 1.0 H1' B:CFL9 3.3 0.0 1.0 C2 B:CFL9 3.3 0.0 1.0 O5' B:CFL9 3.3 0.0 1.0 C2' B:DG8 3.4 0.0 1.0 O2 B:CFL9 3.5 0.0 1.0 C3' B:DG8 3.5 0.0 1.0 C6 B:CFL9 3.5 0.0 1.0 O3' B:CFL9 3.5 0.0 1.0 N3 B:DG8 3.6 0.0 1.0 H6 B:CFL9 3.7 0.0 1.0 H5'' B:DG8 3.8 0.0 1.0 N2 B:DG8 3.8 0.0 1.0 C5' B:CFL9 3.9 0.0 1.0 H2'' B:DG8 3.9 0.0 1.0 C2 B:DG8 4.1 0.0 1.0 H4' B:CFL9 4.2 0.0 1.0 N3 B:CFL9 4.3 0.0 1.0 H5' B:DG8 4.4 0.0 1.0 C5' B:DG8 4.4 0.0 1.0 H5'2 B:CFL9 4.4 0.0 1.0 O3' B:DG8 4.4 0.0 1.0 C5 B:CFL9 4.4 0.0 1.0 C4' B:DG8 4.5 0.0 1.0 P B:CFL9 4.5 0.0 1.0 C4 B:DG8 4.5 0.0 1.0 H21 B:DG8 4.6 0.0 1.0 C1' B:DG8 4.6 0.0 1.0 O1P B:CFL9 4.7 0.0 1.0 H21 A:DG4 4.7 0.0 1.0 OP1 B:DG10 4.7 0.0 1.0 H5'1 B:CFL9 4.7 0.0 1.0 C4 B:CFL9 4.8 0.0 1.0 P B:DG10 4.8 0.0 1.0 N9 B:DG8 4.9 0.0 1.0 O4' B:DG8 5.0 0.0 1.0

Fluorine binding site 6 out of 6 in the Formation of Left-Handed Helices By C2'-Fluorinated Nucleic Acids Under Physiological Salt Conditions


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Formation of Left-Handed Helices By C2'-Fluorinated Nucleic Acids Under Physiological Salt Conditions within 5.0Å range: probe atom residue distance (Å) B Occ B:F11 b:0.0 occ:1.00 F B:CFL11 0.0 0.0 1.0 C2' B:CFL11 1.4 0.0 1.0 H2' B:CFL11 2.0 0.0 1.0 H3' B:CFL11 2.4 0.0 1.0 C3' B:CFL11 2.4 0.0 1.0 C1' B:CFL11 2.4 0.0 1.0 H2' B:DG10 2.5 0.0 1.0 N1 B:CFL11 2.8 0.0 1.0 H3' B:DG10 2.8 0.0 1.0 H22 B:DG10 3.1 0.0 1.0 O4' B:CFL11 3.1 0.0 1.0 C4' B:CFL11 3.2 0.0 1.0 H1' B:CFL11 3.3 0.0 1.0 C2' B:DG10 3.3 0.0 1.0 C2 B:CFL11 3.3 0.0 1.0 C6 B:CFL11 3.5 0.0 1.0 O3' B:CFL11 3.5 0.0 1.0 O5' B:CFL11 3.5 0.0 1.0 O2 B:CFL11 3.5 0.0 1.0 C3' B:DG10 3.5 0.0 1.0 N3 B:DG10 3.6 0.0 1.0 H6 B:CFL11 3.7 0.0 1.0 H2'' B:DG10 3.7 0.0 1.0 H5'' B:DG10 3.8 0.0 1.0 N2 B:DG10 3.9 0.0 1.0 C5' B:CFL11 3.9 0.0 1.0 H4' B:CFL11 4.2 0.0 1.0 C2 B:DG10 4.2 0.0 1.0 N3 B:CFL11 4.3 0.0 1.0 C5 B:CFL11 4.4 0.0 1.0 H5'2 B:CFL11 4.4 0.0 1.0 C5' B:DG10 4.5 0.0 1.0 H5' B:DG10 4.5 0.0 1.0 O3' B:DG10 4.5 0.0 1.0 C4' B:DG10 4.5 0.0 1.0 P B:CFL11 4.6 0.0 1.0 C1' B:DG10 4.6 0.0 1.0 C4 B:DG10 4.6 0.0 1.0 OP1 B:DG12 4.7 0.0 1.0 H21 B:DG10 4.7 0.0 1.0 C4 B:CFL11 4.7 0.0 1.0 O1P B:CFL11 4.8 0.0 1.0 P B:DG12 4.8 0.0 1.0 H21 A:DG2 4.8 0.0 1.0 H5'1 B:CFL11 4.9 0.0 1.0 O4' B:DG10 4.9 0.0 1.0 N9 B:DG10 5.0 0.0 1.0

R.El-Khoury, C.Cabrero, S.Movilla, H.Kaur, D.Friedland, A.Dominguez, J.D.Thorpe, M.Roman, M.Orozco, C.Gonzalez, M.J.Damha. Formation of Left-Handed Helices By C2'-Fluorinated Nucleic Acids Under Physiological Salt Conditions. Nucleic Acids Res. 2024.
ISSN: ESSN 1362-4962
PubMed: 38874502
DOI: 10.1093/NAR/GKAE508