Fluorine in PDB 4f2y: Structure of 3'-Fluoro Cyclohexenyl Nucleic Acid Decamer

The structure of Structure of 3'-Fluoro Cyclohexenyl Nucleic Acid Decamer, PDB code: 4f2y was solved by P.S.Pallan, M.Egli, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.88 / 1.59
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	24.775, 38.299, 47.746, 90.00, 90.00, 90.00
R / Rfree (%)	18.2 / 25.3

The structure of Structure of 3'-Fluoro Cyclohexenyl Nucleic Acid Decamer also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Fluorine atom in the Structure of 3'-Fluoro Cyclohexenyl Nucleic Acid Decamer (pdb code 4f2y). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the Structure of 3'-Fluoro Cyclohexenyl Nucleic Acid Decamer, PDB code: 4f2y:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in the Structure of 3'-Fluoro Cyclohexenyl Nucleic Acid Decamer


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Structure of 3'-Fluoro Cyclohexenyl Nucleic Acid Decamer within 5.0Å range: probe atom residue distance (Å) B Occ A:F106 b:18.5 occ:1.00 F A:XTF106 0.0 18.5 1.0 C2' A:XTF106 1.4 18.8 1.0 C3' A:XTF106 2.3 19.8 1.0 C1' A:XTF106 2.3 18.8 1.0 O3' A:XTF106 2.7 21.5 1.0 C4' A:XTF106 2.9 16.7 1.0 C7' A:XTF106 3.1 18.6 1.0 C6' A:XTF106 3.3 18.8 1.0 N1 A:XTF106 3.6 16.0 1.0 O4' A:DA107 3.6 21.9 1.0 O5' A:DA107 3.8 26.9 1.0 C5' A:DA107 3.8 24.6 1.0 P A:DA107 3.9 25.5 1.0 O2 A:XTF106 4.1 17.3 1.0 C4' A:DA107 4.2 21.3 1.0 C2 A:XTF106 4.3 15.8 1.0 C5' A:XTF106 4.4 19.8 1.0 C6 A:XTF106 4.5 15.9 1.0 OP2 A:DA107 4.7 24.6 1.0 OP1 A:DA107 4.9 28.8 1.0 C1' A:DA107 4.9 18.2 1.0 O B:HOH401 4.9 25.6 1.0

Fluorine binding site 2 out of 2 in the Structure of 3'-Fluoro Cyclohexenyl Nucleic Acid Decamer


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Structure of 3'-Fluoro Cyclohexenyl Nucleic Acid Decamer within 5.0Å range: probe atom residue distance (Å) B Occ B:F206 b:20.4 occ:1.00 F B:XTF206 0.0 20.4 1.0 C2' B:XTF206 1.4 16.9 1.0 C1' B:XTF206 2.4 15.7 1.0 C3' B:XTF206 2.4 17.2 1.0 O3' B:XTF206 2.8 20.7 1.0 C4' B:XTF206 3.0 17.1 1.0 C7' B:XTF206 3.1 14.8 1.0 C6' B:XTF206 3.3 15.6 1.0 N1 B:XTF206 3.7 13.0 1.0 C5' B:DA207 3.7 19.7 1.0 O4' B:DA207 3.7 17.9 1.0 O5' B:DA207 3.8 20.1 1.0 P B:DA207 4.0 20.7 1.0 O2 B:XTF206 4.2 15.8 1.0 C4' B:DA207 4.2 19.2 1.0 C2 B:XTF206 4.3 14.1 1.0 C5' B:XTF206 4.4 18.4 1.0 O B:HOH401 4.5 25.6 1.0 C6 B:XTF206 4.5 12.6 1.0 OP2 B:DA207 4.9 20.1 1.0 OP1 B:DA207 4.9 23.2 1.0 C1' B:DA207 5.0 15.9 1.0

P.P.Seth, J.Yu, A.Jazayeri, P.S.Pallan, C.R.Allerson, M.E.Ostergaard, F.Liu, P.Herdewijn, M.Egli, E.E.Swayze. Synthesis and Antisense Properties of Fluoro Cyclohexenyl Nucleic Acid (F-Cena), A Nuclease Stable Mimic of 2'-Fluoro Rna. J.Org.Chem. V. 77 5074 2012.
ISSN: ISSN 0022-3263
PubMed: 22591005
DOI: 10.1021/JO300594B