Fluorine in PDB 1dpn: B-Dodecamer Cgcgaa(Taf)Tcgcg with Incorporated 2'-Deoxy-2'- Fluoro-Arabino-Furanosyl Thymine

The structure of B-Dodecamer Cgcgaa(Taf)Tcgcg with Incorporated 2'-Deoxy-2'- Fluoro-Arabino-Furanosyl Thymine, PDB code: 1dpn was solved by M.Egli, V.Tereshko, M.Teplova, G.Minasov, A.Joachimiak, R.Sanishvili, C.M.Weeks, R.Miller, M.A.Maier, H.An, P.Dan Cook, M.Manoharan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 0.95
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	24.623, 39.732, 65.737, 90.00, 90.00, 90.00
R / Rfree (%)	16 / 15.9

The structure of B-Dodecamer Cgcgaa(Taf)Tcgcg with Incorporated 2'-Deoxy-2'- Fluoro-Arabino-Furanosyl Thymine also contains other interesting chemical elements:

Magnesium

(Mg)

4 atoms

The binding sites of Fluorine atom in the B-Dodecamer Cgcgaa(Taf)Tcgcg with Incorporated 2'-Deoxy-2'- Fluoro-Arabino-Furanosyl Thymine (pdb code 1dpn). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the B-Dodecamer Cgcgaa(Taf)Tcgcg with Incorporated 2'-Deoxy-2'- Fluoro-Arabino-Furanosyl Thymine, PDB code: 1dpn:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in the B-Dodecamer Cgcgaa(Taf)Tcgcg with Incorporated 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 B-Dodecamer Cgcgaa(Taf)Tcgcg with Incorporated 2'-Deoxy-2'- Fluoro-Arabino-Furanosyl Thymine within 5.0Å range: probe atom residue distance (Å) B Occ A:F7 b:14.6 occ:1.00 F2' A:TAF7 0.0 14.6 1.0 C2' A:TAF7 1.4 13.9 1.0 C1' A:TAF7 2.2 14.2 1.0 C3' A:TAF7 2.4 13.8 1.0 N1 A:TAF7 2.7 13.0 1.0 C6 A:TAF7 2.9 12.8 1.0 C7 A:DT8 2.9 15.7 1.0 O4' A:TAF7 3.0 13.9 1.0 C4' A:TAF7 3.3 13.7 1.0 O A:HOH113 3.3 17.4 1.0 C6 A:DT8 3.3 13.6 1.0 O A:HOH118 3.3 19.5 1.0 C5 A:DT8 3.4 13.5 1.0 O3' A:TAF7 3.5 15.4 1.0 O A:HOH106 3.5 16.4 1.0 OP2 A:DT8 3.7 17.9 1.0 C2 A:TAF7 3.7 12.5 1.0 O5' A:TAF7 3.8 13.8 1.0 C5 A:TAF7 4.0 12.6 1.0 O5' A:DT8 4.0 16.9 1.0 P A:DT8 4.0 16.4 1.0 C5' A:TAF7 4.2 15.5 1.0 O2 A:TAF7 4.2 14.3 1.0 O4' A:DT8 4.3 15.6 1.0 N1 A:DT8 4.4 14.1 1.0 C4 A:DT8 4.5 12.5 1.0 N3 A:TAF7 4.6 12.4 1.0 O A:HOH142 4.6 23.2 1.0 C4 A:TAF7 4.8 12.1 1.0 C5' A:DT8 4.8 16.6 1.0 C5M A:TAF7 4.9 13.2 1.0

Fluorine binding site 2 out of 2 in the B-Dodecamer Cgcgaa(Taf)Tcgcg with Incorporated 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 B-Dodecamer Cgcgaa(Taf)Tcgcg with Incorporated 2'-Deoxy-2'- Fluoro-Arabino-Furanosyl Thymine within 5.0Å range: probe atom residue distance (Å) B Occ B:F19 b:16.5 occ:1.00 F2' B:TAF19 0.0 16.5 1.0 C2' B:TAF19 1.3 15.1 1.0 C1' B:TAF19 2.3 16.6 1.0 C3' B:TAF19 2.4 15.4 1.0 N1 B:TAF19 2.8 13.7 1.0 C6 B:TAF19 2.9 14.7 1.0 O4' B:TAF19 2.9 15.9 1.0 C7 B:DT20 3.1 19.8 1.0 O B:HOH132 3.3 20.8 1.0 C4' B:TAF19 3.3 15.2 1.0 O B:HOH137 3.4 26.7 1.0 C6 B:DT20 3.5 17.4 1.0 O3' B:TAF19 3.5 16.5 1.0 C5 B:DT20 3.6 15.0 1.0 O B:HOH163 3.7 35.7 1.0 OP2 B:DT20 3.8 18.3 1.0 O5' B:TAF19 3.8 16.4 1.0 C2 B:TAF19 3.8 12.5 1.0 C5 B:TAF19 4.0 14.6 1.0 P B:DT20 4.1 17.4 1.0 O5' B:DT20 4.1 17.9 1.0 C5' B:TAF19 4.2 17.0 1.0 O2 B:TAF19 4.4 14.2 1.0 O4' B:DT20 4.5 15.7 1.0 N1 B:DT20 4.6 16.5 1.0 O A:HOH184 4.7 38.7 1.0 N3 B:TAF19 4.7 13.7 1.0 C4 B:DT20 4.8 16.9 1.0 C5M B:TAF19 4.9 17.6 1.0 C4 B:TAF19 4.9 13.0 1.0 C5' B:DT20 4.9 17.2 1.0

M.Egli, V.Tereshko, M.Teplova, G.Minasov, A.Joachimiak, R.Sanishvili, C.M.Weeks, R.Miller, M.A.Maier, H.An, P.Dan Cook, M.Manoharan. X-Ray Crystallographic Analysis of the Hydration of A- and B-Form Dna at Atomic Resolution. Biopolymers V. 48 234 1998.
ISSN: ISSN 0006-3525
PubMed: 10699842
DOI: 10.1002/(SICI)1097-0282(1998)48:4<234::AID-BIP4>3.0.CO;2-H