Fluorine in PDB 436d: The Dickerson-Drew B-Dna Dodecamer Revisited-at Atomic Resolution

The structure of The Dickerson-Drew B-Dna Dodecamer Revisited-at Atomic Resolution, PDB code: 436d was solved by V.Tereshko, G.Minasov, M.Egli, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 1.10
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	24.640, 39.630, 65.530, 90.00, 90.00, 90.00
R / Rfree (%)	16.2 / n/a

The structure of The Dickerson-Drew B-Dna Dodecamer Revisited-at Atomic Resolution also contains other interesting chemical elements:

Magnesium

(Mg)

5 atoms

The binding sites of Fluorine atom in the The Dickerson-Drew B-Dna Dodecamer Revisited-at Atomic Resolution (pdb code 436d). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the The Dickerson-Drew B-Dna Dodecamer Revisited-at Atomic Resolution, PDB code: 436d:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in the The Dickerson-Drew B-Dna Dodecamer Revisited-at Atomic Resolution


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of The Dickerson-Drew B-Dna Dodecamer Revisited-at Atomic Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:F7 b:13.7 occ:1.00 F2' A:TAF7 0.0 13.7 1.0 C2' A:TAF7 1.3 12.9 1.0 C1' A:TAF7 2.3 12.7 1.0 C3' A:TAF7 2.4 12.9 1.0 N1 A:TAF7 2.7 11.8 1.0 C7 A:DT8 2.9 15.0 1.0 C6 A:TAF7 2.9 12.1 1.0 O4' A:TAF7 3.0 13.0 1.0 O A:HOH118 3.2 18.3 1.0 O A:HOH113 3.3 16.5 1.0 C4' A:TAF7 3.3 13.3 1.0 C6 A:DT8 3.3 12.5 1.0 C5 A:DT8 3.3 12.3 1.0 O A:HOH106 3.4 15.0 1.0 O3' A:TAF7 3.5 14.0 1.0 OP2 A:DT8 3.7 15.6 1.0 C2 A:TAF7 3.8 11.8 1.0 O5' A:TAF7 3.8 13.0 1.0 O5' A:DT8 4.0 14.4 1.0 P A:DT8 4.0 14.6 1.0 C5 A:TAF7 4.0 11.6 1.0 C5' A:TAF7 4.2 13.1 1.0 O2 A:TAF7 4.3 13.3 1.0 O4' A:DT8 4.3 14.6 1.0 N1 A:DT8 4.4 12.3 1.0 C4 A:DT8 4.5 12.1 1.0 N3 A:TAF7 4.6 11.2 1.0 O A:HOH142 4.6 22.7 1.0 C5' A:DT8 4.8 14.2 1.0 C4 A:TAF7 4.8 11.3 1.0 C5M A:TAF7 4.9 12.7 1.0

Fluorine binding site 2 out of 2 in the The Dickerson-Drew B-Dna Dodecamer Revisited-at Atomic Resolution


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of The Dickerson-Drew B-Dna Dodecamer Revisited-at Atomic Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:F19 b:15.3 occ:1.00 F2' B:TAF19 0.0 15.3 1.0 C2' B:TAF19 1.3 13.9 1.0 C1' B:TAF19 2.3 13.7 1.0 C3' B:TAF19 2.4 13.3 1.0 N1 B:TAF19 2.8 12.6 1.0 C6 B:TAF19 2.9 13.2 1.0 O4' B:TAF19 3.0 14.0 1.0 C7 B:DT20 3.0 14.8 1.0 O B:HOH137 3.3 26.4 1.0 O B:HOH132 3.3 18.6 1.0 C4' B:TAF19 3.3 13.3 1.0 C6 B:DT20 3.5 13.8 1.0 O3' B:TAF19 3.5 14.2 1.0 C5 B:DT20 3.5 13.5 1.0 O B:HOH163 3.8 24.2 1.0 OP2 B:DT20 3.8 17.1 1.0 O5' B:TAF19 3.8 14.3 1.0 C2 B:TAF19 3.8 12.3 1.0 C5 B:TAF19 4.0 13.2 1.0 P B:DT20 4.1 15.0 1.0 O5' B:DT20 4.2 15.1 1.0 C5' B:TAF19 4.2 15.0 1.0 O2 B:TAF19 4.4 13.4 1.0 O4' B:DT20 4.5 14.2 1.0 N1 B:DT20 4.6 13.7 1.0 N3 B:TAF19 4.7 12.1 1.0 C4 B:DT20 4.8 13.6 1.0 O A:HOH184 4.8 37.5 1.0 C5M B:TAF19 4.9 16.0 1.0 C4 B:TAF19 4.9 12.1 1.0 C5' B:DT20 5.0 14.3 1.0

V.Tereshko, G.Minasov, M.Egli. The Dickerson-Drew B-Dna Dodecamer Revisited-at Atomic Resolution J.Am.Chem.Soc. V. 121 470 1999.
ISSN: ISSN 0002-7863