Fluorine in PDB 4f2x: Structure of 3'-Fluoro Cyclohexenyl Nucleic Acid Heptamer

The structure of Structure of 3'-Fluoro Cyclohexenyl Nucleic Acid Heptamer, PDB code: 4f2x 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)	40.08 / 1.57
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	26.700, 33.862, 80.165, 90.00, 90.00, 90.00
R / Rfree (%)	18.5 / 25.1

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

Cobalt

(Co)

8 atoms

The binding sites of Fluorine atom in the Structure of 3'-Fluoro Cyclohexenyl Nucleic Acid Heptamer (pdb code 4f2x). 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 Heptamer, PDB code: 4f2x:
Jump to Fluorine binding site number: 1; 2;

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


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 Heptamer within 5.0Å range: probe atom residue distance (Å) B Occ A:F4 b:30.4 occ:1.00 F A:XTF4 0.0 30.4 1.0 C2' A:XTF4 1.4 28.9 1.0 C1' A:XTF4 2.2 25.4 1.0 C3' A:XTF4 2.3 32.1 1.0 O3' A:XTF4 2.7 37.3 1.0 N1 A:XTF4 2.9 23.6 1.0 C8 A:DG5 2.9 23.4 1.0 OP2 A:DG5 3.1 42.9 1.0 O5' A:DG5 3.2 41.0 1.0 P A:DG5 3.2 44.9 1.0 N7 A:DG5 3.3 21.6 1.0 C6 A:XTF4 3.5 22.1 1.0 O A:HOH211 3.5 34.4 1.0 C7' A:XTF4 3.6 26.9 1.0 O A:HOH203 3.7 29.9 1.0 C4' A:XTF4 3.7 32.1 1.0 C2 A:XTF4 3.7 21.0 1.0 O2 A:XTF4 4.0 22.6 1.0 C6' A:XTF4 4.1 29.3 1.0 N9 A:DG5 4.1 24.0 1.0 O5' A:XTF4 4.1 32.8 1.0 C5' A:DG5 4.2 36.4 1.0 O4' A:DG5 4.5 29.1 1.0 C5' A:XTF4 4.6 33.2 1.0 C5 A:DG5 4.6 20.8 1.0 C5 A:XTF4 4.6 22.5 1.0 OP1 A:DG5 4.6 43.2 1.0 C1' A:DG5 4.7 26.8 1.0 N3 A:XTF4 4.8 20.6 1.0 C2' A:DG5 4.8 27.9 1.0 C4' A:DG5 4.9 31.1 1.0 C4 A:DG5 5.0 21.3 1.0

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


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 Heptamer within 5.0Å range: probe atom residue distance (Å) B Occ C:F4 b:30.1 occ:1.00 F C:XTF4 0.0 30.1 1.0 C2' C:XTF4 1.4 30.0 1.0 C1' C:XTF4 2.3 29.1 1.0 C3' C:XTF4 2.4 31.5 1.0 O3' C:XTF4 2.7 32.6 1.0 C4' C:XTF4 2.8 33.5 1.0 C7' C:XTF4 2.9 29.7 1.0 C6' C:XTF4 3.1 32.4 1.0 C5' C:DG5 3.4 28.8 1.0 O C:HOH202 3.4 35.2 1.0 N1 C:XTF4 3.7 27.3 1.0 O4' C:DG5 3.8 25.7 1.0 O5' C:DG5 3.8 29.4 1.0 P C:DG5 3.9 31.4 1.0 C4' C:DG5 4.1 26.6 1.0 O2 C:XTF4 4.1 26.9 1.0 C5' C:XTF4 4.3 35.4 1.0 C2 C:XTF4 4.4 25.1 1.0 C6 C:XTF4 4.6 27.5 1.0 OP1 C:DG5 4.8 34.3 1.0 OP2 C:DG5 4.9 31.9 1.0 O5' C:XTF4 5.0 37.4 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