Fluorine in PDB 3q61: 3'-Fluoro Hexitol Nucleic Acid Dna Structure

The structure of 3'-Fluoro Hexitol Nucleic Acid Dna Structure, PDB code: 3q61 was solved by P.R.Seth, C.R.Allerson, T.P.Prakash, A.Siwkowski, A.Berdeja, J.Yu, P.S.Pallan, A.T.Watt, H.Gaus, B.Bhat, M.Egli, E.E.Swayze, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	31.31 / 1.56
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	28.014, 43.134, 45.507, 90.00, 90.00, 90.00
R / Rfree (%)	16.4 / 20.9

The binding sites of Fluorine atom in the 3'-Fluoro Hexitol Nucleic Acid Dna Structure (pdb code 3q61). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the 3'-Fluoro Hexitol Nucleic Acid Dna Structure, PDB code: 3q61:
Jump to Fluorine binding site number: 1; 2;

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


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of 3'-Fluoro Hexitol Nucleic Acid Dna Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:F106 b:18.3 occ:1.00 F2' A:F3H106 0.0 18.3 1.0 C2' A:F3H106 1.4 15.9 1.0 C1' A:F3H106 2.3 15.7 1.0 C3' A:F3H106 2.3 17.4 1.0 O3' A:F3H106 2.7 19.0 1.0 C6' A:F3H106 2.8 15.1 1.0 C4' A:F3H106 2.9 16.1 1.0 O4' A:F3H106 3.3 17.0 1.0 C5' A:DA107 3.5 16.3 1.0 N1 A:F3H106 3.6 14.7 1.0 O4' A:DA107 3.6 16.7 1.0 O5' A:DA107 3.7 19.5 1.0 O A:HOH5 3.8 25.6 1.0 P A:DA107 3.9 19.8 1.0 C4' A:DA107 4.1 18.1 1.0 O2 A:F3H106 4.2 14.7 1.0 C5' A:F3H106 4.3 17.7 1.0 C2 A:F3H106 4.3 12.4 1.0 C6 A:F3H106 4.4 13.8 1.0 OP1 A:DA107 4.7 23.8 1.0 C1' A:DA107 4.9 13.5 1.0 OP2 A:DA107 4.9 20.4 1.0 O5' A:F3H106 5.0 17.0 1.0 C8 A:DA107 5.0 13.0 1.0

Fluorine binding site 2 out of 2 in the 3'-Fluoro Hexitol Nucleic Acid Dna Structure


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of 3'-Fluoro Hexitol Nucleic Acid Dna Structure within 5.0Å range: probe atom residue distance (Å) B Occ B:F206 b:17.5 occ:1.00 F2' B:F3H206 0.0 17.5 1.0 C2' B:F3H206 1.4 15.8 1.0 C1' B:F3H206 2.3 14.6 1.0 C3' B:F3H206 2.4 13.4 1.0 O3' B:F3H206 2.8 17.0 1.0 C6' B:F3H206 2.9 14.1 1.0 C4' B:F3H206 2.9 14.4 1.0 O4' B:F3H206 3.4 15.5 1.0 O B:HOH16 3.5 35.5 1.0 O4' B:DA207 3.5 15.6 1.0 O A:HOH9 3.6 28.6 1.0 C5' B:DA207 3.6 16.6 1.0 N1 B:F3H206 3.6 13.3 1.0 O5' B:DA207 3.7 15.6 1.0 P B:DA207 4.0 17.7 1.0 C4' B:DA207 4.1 17.6 1.0 O2 B:F3H206 4.3 15.6 1.0 C5' B:F3H206 4.3 17.4 1.0 C2 B:F3H206 4.4 13.9 1.0 C6 B:F3H206 4.5 14.2 1.0 C1' B:DA207 4.7 15.4 1.0 OP1 B:DA207 4.9 20.7 1.0 C8 B:DA207 4.9 12.8 1.0 OP2 B:DA207 4.9 19.7 1.0

M.Egli, P.S.Pallan, C.R.Allerson, T.P.Prakash, A.Berdeja, J.Yu, S.Lee, A.Watt, H.Gaus, B.Bhat, E.E.Swayze, P.P.Seth. Synthesis, Improved Antisense Activity and Structural Rationale For the Divergent Rna Affinities of 3'-Fluoro Hexitol Nucleic Acid (Fhna and Ara-Fhna) Modified Oligonucleotides. J.Am.Chem.Soc. V. 133 16642 2011.
ISSN: ISSN 0002-7863
PubMed: 21919455
DOI: 10.1021/JA207086X