Fluorine in PDB 478d: Crystal Structure of the B-Dna Dodecamer 5'-D(Cgcgaa(Taf)Tcgcg), Where Taf Is 2'-Deoxy-2'-Fluoro-Arabino-Furanosyl Thymine

The structure of Crystal Structure of the B-Dna Dodecamer 5'-D(Cgcgaa(Taf)Tcgcg), Where Taf Is 2'-Deoxy-2'-Fluoro-Arabino-Furanosyl Thymine, PDB code: 478d was solved by G.Minasov, V.Tereshko, M.Egli, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	8.00 / 2.20
Space group	H 3
Cell size a, b, c (Å), α, β, γ (°)	42.310, 42.310, 99.680, 90.00, 90.00, 120.00
R / Rfree (%)	19.7 / 26.2

The structure of Crystal Structure of the B-Dna Dodecamer 5'-D(Cgcgaa(Taf)Tcgcg), Where Taf Is 2'-Deoxy-2'-Fluoro-Arabino-Furanosyl Thymine also contains other interesting chemical elements:

Calcium

(Ca)

3 atoms

The binding sites of Fluorine atom in the Crystal Structure of the B-Dna Dodecamer 5'-D(Cgcgaa(Taf)Tcgcg), Where Taf Is 2'-Deoxy-2'-Fluoro-Arabino-Furanosyl Thymine (pdb code 478d). 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 the B-Dna Dodecamer 5'-D(Cgcgaa(Taf)Tcgcg), Where Taf Is 2'-Deoxy-2'-Fluoro-Arabino-Furanosyl Thymine, PDB code: 478d:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in the Crystal Structure of the B-Dna Dodecamer 5'-D(Cgcgaa(Taf)Tcgcg), Where Taf Is 2'-Deoxy-2'-Fluoro-Arabino-Furanosyl Thymine


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 the B-Dna Dodecamer 5'-D(Cgcgaa(Taf)Tcgcg), Where Taf Is 2'-Deoxy-2'-Fluoro-Arabino-Furanosyl Thymine within 5.0Å range: probe atom residue distance (Å) B Occ A:F7 b:37.2 occ:1.00 F2' A:TAF7 0.0 37.2 1.0 C2' A:TAF7 1.4 31.7 1.0 C1' A:TAF7 2.5 29.9 1.0 C3' A:TAF7 2.5 33.9 1.0 C6 A:TAF7 2.7 26.5 1.0 N1 A:TAF7 2.8 27.2 1.0 O4' A:TAF7 3.2 31.9 1.0 C7 A:DT8 3.2 32.1 1.0 C4' A:TAF7 3.4 33.5 1.0 O5' A:TAF7 3.4 35.4 1.0 OP2 A:DT8 3.4 39.8 1.0 O3' A:TAF7 3.6 38.3 1.0 C5 A:DT8 3.8 31.7 1.0 C5 A:TAF7 3.8 26.8 1.0 C6 A:DT8 3.8 32.4 1.0 C5' A:TAF7 4.0 33.5 1.0 P A:DT8 4.1 41.6 1.0 C2 A:TAF7 4.1 27.7 1.0 O5' A:DT8 4.5 41.0 1.0 C5M A:TAF7 4.5 25.8 1.0 O A:HOH221 4.6 41.0 0.5 OP2 A:TAF7 4.7 33.2 1.0 P A:TAF7 4.7 33.1 1.0 O2 A:TAF7 4.7 27.9 1.0 C4 A:DT8 4.9 31.8 1.0 N3 A:TAF7 4.9 26.8 1.0 C4 A:TAF7 4.9 25.1 1.0 N1 A:DT8 4.9 35.5 1.0

Fluorine binding site 2 out of 2 in the Crystal Structure of the B-Dna Dodecamer 5'-D(Cgcgaa(Taf)Tcgcg), Where Taf Is 2'-Deoxy-2'-Fluoro-Arabino-Furanosyl Thymine


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 the B-Dna Dodecamer 5'-D(Cgcgaa(Taf)Tcgcg), Where Taf Is 2'-Deoxy-2'-Fluoro-Arabino-Furanosyl Thymine within 5.0Å range: probe atom residue distance (Å) B Occ B:F19 b:42.1 occ:1.00 F2' B:TAF19 0.0 42.1 1.0 C2' B:TAF19 1.4 40.4 1.0 C3' B:TAF19 2.5 41.8 1.0 C1' B:TAF19 2.6 39.1 1.0 C7 B:DT20 2.8 32.5 1.0 N1 B:TAF19 3.0 36.6 1.0 C6 B:TAF19 3.1 35.9 1.0 C5 B:DT20 3.4 34.0 1.0 O4' B:TAF19 3.4 40.7 1.0 C6 B:DT20 3.4 33.9 1.0 OP2 B:DT20 3.4 44.8 1.0 O3' B:TAF19 3.5 43.2 1.0 C4' B:TAF19 3.5 43.1 1.0 O B:HOH232 3.8 44.3 0.5 O5' B:DT20 3.8 44.5 1.0 P B:DT20 3.8 43.7 1.0 O5' B:TAF19 3.9 43.3 1.0 C2 B:TAF19 4.0 35.8 1.0 C5 B:TAF19 4.2 35.2 1.0 C5' B:TAF19 4.4 44.2 1.0 O B:HOH231 4.5 35.0 1.0 O2 B:TAF19 4.5 34.6 1.0 N1 B:DT20 4.6 36.4 1.0 C4 B:DT20 4.6 33.6 1.0 C5' B:DT20 4.6 40.4 1.0 O4' B:DT20 4.9 39.5 1.0 N3 B:TAF19 4.9 35.3 1.0 C5M B:TAF19 5.0 32.7 1.0

G.Minasov, V.Tereshko, M.Egli. Atomic-Resolution Crystal Structures of B-Dna Reveal Specific Influences of Divalent Metal Ions on Conformation and Packing. J.Mol.Biol. V. 291 83 1999.
ISSN: ISSN 0022-2836
PubMed: 10438608
DOI: 10.1006/JMBI.1999.2934