Fluorine in PDB 3v06: Crystal Structure of S-6'-Me-3'-Fluoro Hexitol Nucleic Acid

The structure of Crystal Structure of S-6'-Me-3'-Fluoro Hexitol Nucleic Acid, PDB code: 3v06 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)	32.45 / 1.53
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	24.879, 45.222, 46.598, 90.00, 90.00, 90.00
R / Rfree (%)	16.7 / 22.7

The structure of Crystal Structure of S-6'-Me-3'-Fluoro Hexitol Nucleic Acid also contains other interesting chemical elements:

Strontium

(Sr)

1 atom

The binding sites of Fluorine atom in the Crystal Structure of S-6'-Me-3'-Fluoro Hexitol Nucleic Acid (pdb code 3v06). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the Crystal Structure of S-6'-Me-3'-Fluoro Hexitol Nucleic Acid, PDB code: 3v06:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in the Crystal Structure of S-6'-Me-3'-Fluoro Hexitol Nucleic Acid


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure of S-6'-Me-3'-Fluoro Hexitol Nucleic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:F106 b:18.0 occ:1.00 F3' A:F5H106 0.0 18.0 1.0 C3' A:F5H106 1.4 15.6 1.0 C2' A:F5H106 2.3 15.1 1.0 C4' A:F5H106 2.4 17.0 1.0 O4' A:F5H106 2.7 18.8 1.0 C5' A:F5H106 2.9 17.9 1.0 C1' A:F5H106 2.9 16.9 1.0 O5' A:F5H106 3.4 17.4 1.0 C5' A:DA107 3.4 16.9 1.0 O4' A:DA107 3.5 15.1 1.0 N1 A:F5H106 3.6 14.9 1.0 O A:HOH331 3.7 35.5 1.0 O5' A:DA107 3.7 16.4 1.0 P A:DA107 3.9 17.8 1.0 C4' A:DA107 4.1 16.2 1.0 O2 A:F5H106 4.2 15.0 1.0 C2 A:F5H106 4.3 14.7 1.0 C6' A:F5H106 4.3 18.2 1.0 C6 A:F5H106 4.4 12.9 1.0 OP1 A:DA107 4.8 20.1 1.0 C1' A:DA107 4.8 15.8 1.0 OP2 A:DA107 4.9 18.3 1.0 C8 A:DA107 4.9 14.3 1.0 O A:HOH304 4.9 22.3 1.0

Fluorine binding site 2 out of 2 in the Crystal Structure of S-6'-Me-3'-Fluoro Hexitol Nucleic Acid


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structure of S-6'-Me-3'-Fluoro Hexitol Nucleic Acid within 5.0Å range: probe atom residue distance (Å) B Occ B:F206 b:21.1 occ:1.00 F3' B:F5H206 0.0 21.1 1.0 C3' B:F5H206 1.4 18.0 1.0 C2' B:F5H206 2.3 16.2 1.0 C4' B:F5H206 2.4 17.7 1.0 O4' B:F5H206 2.7 18.8 1.0 C5' B:F5H206 2.9 16.7 1.0 C1' B:F5H206 2.9 16.1 1.0 O5' B:F5H206 3.3 16.0 1.0 N1 B:F5H206 3.6 15.1 1.0 O4' B:DA207 3.7 20.4 1.0 C5' B:DA207 3.7 22.0 1.0 O5' B:DA207 3.7 21.7 1.0 P B:DA207 3.9 22.4 1.0 C4' B:DA207 4.2 21.9 1.0 C6' B:F5H206 4.3 16.6 1.0 O2 B:F5H206 4.3 16.9 1.0 C2 B:F5H206 4.4 15.5 1.0 C6 B:F5H206 4.5 14.2 1.0 O A:HOH304 4.7 22.3 1.0 OP2 B:DA207 4.7 24.6 1.0 OP1 B:DA207 4.8 24.7 1.0 C1' B:DA207 4.9 18.7 1.0 C8 B:DA207 4.9 14.6 1.0

P.S.Pallan, J.Yu, C.R.Allerson, E.E.Swayze, P.Seth, M.Egli. Insights From Crystal Structures Into the Opposite Effects on Rna Affinity Caused By the S- and R-6'-Methyl Backbone Modifications of 3'-Fluoro Hexitol Nucleic Acid. Biochemistry V. 51 7 2012.
ISSN: ISSN 0006-2960
PubMed: 22229409
DOI: 10.1021/BI201810R