Fluorine in PDB 389d: Crystal Structure of B-Dna with Incorporated 2'-Deoxy-2'- Fluoro-Arabino-Furanosyl Thymines: Implications of Conformational Preorganization For Duplex Stability

The structure of Crystal Structure of B-Dna with Incorporated 2'-Deoxy-2'- Fluoro-Arabino-Furanosyl Thymines: Implications of Conformational Preorganization For Duplex Stability, PDB code: 389d was solved by I.Berger, V.Tereshko, H.Ikeda, V.E.Marquez, M.Egli, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	8.00 / 1.55
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	25.200, 39.710, 65.680, 90.00, 90.00, 90.00
R / Rfree (%)	21.8 / n/a

The structure of Crystal Structure of B-Dna with Incorporated 2'-Deoxy-2'- Fluoro-Arabino-Furanosyl Thymines: Implications of Conformational Preorganization For Duplex Stability also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Fluorine atom in the Crystal Structure of B-Dna with Incorporated 2'-Deoxy-2'- Fluoro-Arabino-Furanosyl Thymines: Implications of Conformational Preorganization For Duplex Stability (pdb code 389d). 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 B-Dna with Incorporated 2'-Deoxy-2'- Fluoro-Arabino-Furanosyl Thymines: Implications of Conformational Preorganization For Duplex Stability, PDB code: 389d:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in the Crystal Structure of B-Dna with Incorporated 2'-Deoxy-2'- Fluoro-Arabino-Furanosyl Thymines: Implications of Conformational Preorganization For Duplex Stability


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 B-Dna with Incorporated 2'-Deoxy-2'- Fluoro-Arabino-Furanosyl Thymines: Implications of Conformational Preorganization For Duplex Stability within 5.0Å range: probe atom residue distance (Å) B Occ A:F7 b:15.4 occ:1.00 F2' A:TAF7 0.0 15.4 1.0 C2' A:TAF7 1.4 15.7 1.0 C3' A:TAF7 2.4 14.0 1.0 C1' A:TAF7 2.5 17.1 1.0 O A:HOH127 2.9 22.1 1.0 N1 A:TAF7 2.9 16.0 1.0 C7 A:DT8 2.9 10.7 1.0 C6 A:TAF7 3.1 11.8 1.0 O4' A:TAF7 3.2 14.2 1.0 C6 A:DT8 3.3 15.8 1.0 C5 A:DT8 3.3 12.9 1.0 O A:HOH128 3.4 20.6 1.0 C4' A:TAF7 3.4 14.4 1.0 O3' A:TAF7 3.4 16.0 1.0 OP2 A:DT8 3.5 18.5 1.0 O A:HOH164 3.7 13.9 1.0 O5' A:DT8 3.7 16.8 1.0 P A:DT8 3.8 19.6 1.0 C2 A:TAF7 3.9 12.2 1.0 O5' A:TAF7 4.1 16.9 1.0 O4' A:DT8 4.1 16.8 1.0 C5 A:TAF7 4.2 11.9 1.0 N1 A:DT8 4.3 13.3 1.0 O A:HOH137 4.3 24.8 1.0 O2 A:TAF7 4.4 14.4 1.0 C5' A:TAF7 4.4 15.4 1.0 C4 A:DT8 4.5 7.7 1.0 C5' A:DT8 4.6 17.0 1.0 N3 A:TAF7 4.8 11.7 1.0 C1' A:DT8 4.8 17.8 1.0 C4' A:DT8 4.9 16.4 1.0

Fluorine binding site 2 out of 2 in the Crystal Structure of B-Dna with Incorporated 2'-Deoxy-2'- Fluoro-Arabino-Furanosyl Thymines: Implications of Conformational Preorganization For Duplex Stability


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 B-Dna with Incorporated 2'-Deoxy-2'- Fluoro-Arabino-Furanosyl Thymines: Implications of Conformational Preorganization For Duplex Stability within 5.0Å range: probe atom residue distance (Å) B Occ B:F19 b:17.0 occ:1.00 F2' B:TAF19 0.0 17.0 1.0 C2' B:TAF19 1.4 19.7 1.0 C1' B:TAF19 2.3 19.9 1.0 C3' B:TAF19 2.4 14.7 1.0 N1 B:TAF19 2.7 13.4 1.0 O4' B:TAF19 2.9 16.2 1.0 C6 B:TAF19 2.9 10.1 1.0 C7 B:DT20 3.1 13.0 1.0 C4' B:TAF19 3.2 15.1 1.0 O B:HOH107 3.4 24.7 1.0 O B:HOH169 3.4 21.5 1.0 C6 B:DT20 3.4 12.2 1.0 C5 B:DT20 3.6 12.1 1.0 O3' B:TAF19 3.6 26.2 1.0 OP2 B:DT20 3.7 18.5 1.0 O5' B:TAF19 3.7 17.3 1.0 C2 B:TAF19 3.8 11.0 1.0 C5 B:TAF19 4.0 13.6 1.0 P B:DT20 4.1 22.9 1.0 C5' B:TAF19 4.1 15.7 1.0 O5' B:DT20 4.1 19.9 1.0 O2 B:TAF19 4.3 14.0 1.0 O4' B:DT20 4.4 15.1 1.0 N1 B:DT20 4.6 15.8 1.0 O B:HOH279 4.6 42.8 1.0 N3 B:TAF19 4.7 11.4 1.0 C4 B:DT20 4.8 9.8 1.0 O B:HOH275 4.8 44.2 1.0 C5M B:TAF19 4.8 15.7 1.0 C4 B:TAF19 4.9 8.6 1.0

I.Berger, V.Tereshko, H.Ikeda, V.E.Marquez, M.Egli. Crystal Structures of B-Dna with Incorporated 2'-Deoxy-2'-Fluoro-Arabino-Furanosyl Thymines: Implications of Conformational Preorganization For Duplex Stability. Nucleic Acids Res. V. 26 2473 1998.
ISSN: ISSN 0305-1048
PubMed: 9580702
DOI: 10.1093/NAR/26.10.2473