Fluorine in PDB 388d: 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: 388d 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 (°)	24.930, 39.820, 65.620, 90.00, 90.00, 90.00
R / Rfree (%)	20.8 / 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 388d). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 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: 388d:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 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:18.0 occ:1.00 F2' A:TAF7 0.0 18.0 1.0 C2' A:TAF7 1.4 18.3 1.0 C1' A:TAF7 2.4 18.1 1.0 C3' A:TAF7 2.5 17.5 1.0 N1 A:TAF7 2.7 16.7 1.0 C6 A:TAF7 2.9 14.2 1.0 C5M A:TAF8 3.0 13.8 1.0 O A:HOH181 3.1 24.4 1.0 O4' A:TAF7 3.1 15.7 1.0 C6 A:TAF8 3.3 16.9 1.0 O A:HOH183 3.3 19.2 1.0 O A:HOH141 3.4 15.1 1.0 C5 A:TAF8 3.4 12.0 1.0 C4' A:TAF7 3.4 15.4 1.0 O3' A:TAF7 3.6 17.2 1.0 C2 A:TAF7 3.7 15.2 1.0 OP2 A:TAF8 3.8 21.9 1.0 O5' A:TAF7 3.9 17.2 1.0 O5' A:TAF8 4.0 17.8 1.0 C5 A:TAF7 4.0 12.8 1.0 P A:TAF8 4.1 19.3 1.0 O4' A:TAF8 4.1 17.1 1.0 O2 A:TAF7 4.2 16.9 1.0 C5' A:TAF7 4.3 15.6 1.0 N1 A:TAF8 4.4 14.7 1.0 C4 A:TAF8 4.6 10.6 1.0 N3 A:TAF7 4.6 14.0 1.0 C4 A:TAF7 4.8 10.2 1.0 C5' A:TAF8 4.9 16.6 1.0 C1' A:TAF8 4.9 18.6 1.0 C5M A:TAF7 4.9 12.7 1.0

Fluorine binding site 2 out of 4 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 A:F8 b:22.6 occ:1.00 F2' A:TAF8 0.0 22.6 1.0 C2' A:TAF8 1.4 17.6 1.0 C3' A:TAF8 2.3 20.8 1.0 C1' A:TAF8 2.5 18.6 1.0 N1 A:TAF8 2.8 14.7 1.0 C6 A:TAF8 2.9 16.9 1.0 O4' A:TAF8 3.1 17.1 1.0 C4' A:TAF8 3.3 17.9 1.0 C5 A:DC9 3.4 15.3 1.0 O3' A:TAF8 3.4 25.8 1.0 OP2 A:DC9 3.4 31.5 1.0 O A:HOH189 3.4 48.4 0.0 O A:HOH184 3.4 35.9 1.0 C6 A:DC9 3.5 16.1 1.0 O5' A:TAF8 3.8 17.8 1.0 P A:DC9 3.8 26.1 1.0 C2 A:TAF8 3.9 13.3 1.0 C5 A:TAF8 4.0 12.0 1.0 O5' A:DC9 4.1 23.2 1.0 C5' A:TAF8 4.1 16.6 1.0 O A:HOH148 4.2 21.1 1.0 O2 A:TAF8 4.4 17.0 1.0 C4 A:DC9 4.6 16.8 1.0 O A:HOH181 4.6 24.4 1.0 N1 A:DC9 4.7 17.5 1.0 N3 A:TAF8 4.8 13.9 1.0 C5M A:TAF8 4.9 13.8 1.0 C5' A:DC9 4.9 22.6 1.0 O4' A:DC9 4.9 20.0 1.0 C4 A:TAF8 5.0 10.6 1.0

Fluorine binding site 3 out of 4 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 3 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:16.6 occ:1.00 F2' B:TAF19 0.0 16.6 1.0 C2' B:TAF19 1.4 13.8 1.0 C1' B:TAF19 2.3 15.9 1.0 C3' B:TAF19 2.4 17.7 1.0 N1 B:TAF19 2.7 13.6 1.0 C6 B:TAF19 2.9 11.9 1.0 O4' B:TAF19 2.9 18.0 1.0 O B:HOH110 3.1 24.0 1.0 C4' B:TAF19 3.2 21.5 1.0 C5M B:TAF20 3.2 15.8 1.0 O B:HOH157 3.3 37.0 1.0 C6 B:TAF20 3.5 11.1 1.0 O3' B:TAF19 3.6 23.0 1.0 C5 B:TAF20 3.7 13.3 1.0 OP2 B:TAF20 3.7 19.4 1.0 O5' B:TAF19 3.7 22.1 1.0 O B:HOH121 3.8 26.3 1.0 C2 B:TAF19 3.8 13.7 1.0 C5' B:TAF19 4.0 22.1 1.0 C5 B:TAF19 4.1 12.2 1.0 P B:TAF20 4.1 23.7 1.0 O4' B:TAF20 4.2 15.1 1.0 O5' B:TAF20 4.3 23.3 1.0 O2 B:TAF19 4.3 15.9 1.0 N1 B:TAF20 4.6 13.5 1.0 O B:HOH158 4.6 31.2 1.0 N3 B:TAF19 4.8 12.3 1.0 C4 B:TAF20 4.9 13.7 1.0 C1' B:TAF20 5.0 13.8 1.0 C5M B:TAF19 5.0 14.2 1.0

Fluorine binding site 4 out of 4 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 4 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:F20 b:20.9 occ:1.00 F2' B:TAF20 0.0 20.9 1.0 C2' B:TAF20 1.4 17.0 1.0 C1' B:TAF20 2.2 13.8 1.0 C3' B:TAF20 2.5 16.1 1.0 N1 B:TAF20 2.6 13.5 1.0 C6 B:TAF20 2.8 11.1 1.0 O4' B:TAF20 2.9 15.1 1.0 O B:HOH154 3.0 23.1 1.0 O B:HOH110 3.1 24.0 1.0 O B:HOH156 3.1 19.3 1.0 C5 B:DC21 3.2 17.1 1.0 C4' B:TAF20 3.3 16.2 1.0 C6 B:DC21 3.4 20.0 1.0 O3' B:TAF20 3.7 20.5 1.0 C2 B:TAF20 3.7 14.5 1.0 OP2 B:DC21 3.8 30.8 1.0 O5' B:TAF20 3.9 23.3 1.0 C5 B:TAF20 4.0 13.3 1.0 O2 B:TAF20 4.2 16.7 1.0 P B:DC21 4.2 25.7 1.0 O5' B:DC21 4.2 28.1 1.0 O B:HOH107 4.3 14.9 1.0 C5' B:TAF20 4.3 22.1 1.0 C4 B:DC21 4.4 14.9 1.0 O B:HOH219 4.4 44.9 1.0 N1 B:DC21 4.5 20.0 1.0 O4' B:DC21 4.6 20.8 1.0 N3 B:TAF20 4.6 15.6 1.0 C5M B:TAF20 4.8 15.8 1.0 C4 B:TAF20 4.8 13.7 1.0 C2' B:TAF19 4.8 13.8 1.0 N4 B:DC21 4.9 13.2 1.0 OP2 B:TAF20 5.0 19.4 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