Fluorine in PDB 1i0m: 1.05 A Structure of the A-Decamer Gcgtatacgc with A Single 2'-O-Fluoroethyl Thymine in Place of T6, High Rb-Salt

The structure of 1.05 A Structure of the A-Decamer Gcgtatacgc with A Single 2'-O-Fluoroethyl Thymine in Place of T6, High Rb-Salt, PDB code: 1i0m was solved by V.Tereshko, C.J.Wilds, G.Minasov, T.P.Prakash, M.A.Maier, A.Howard, Z.Wawrzak, M.Manoharan, M.Egli, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 1.05
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	24.820, 45.260, 43.970, 90.00, 90.00, 90.00
R / Rfree (%)	15.4 / 17

The structure of 1.05 A Structure of the A-Decamer Gcgtatacgc with A Single 2'-O-Fluoroethyl Thymine in Place of T6, High Rb-Salt also contains other interesting chemical elements:

Rubidium

(Rb)

3 atoms

The binding sites of Fluorine atom in the 1.05 A Structure of the A-Decamer Gcgtatacgc with A Single 2'-O-Fluoroethyl Thymine in Place of T6, High Rb-Salt (pdb code 1i0m). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the 1.05 A Structure of the A-Decamer Gcgtatacgc with A Single 2'-O-Fluoroethyl Thymine in Place of T6, High Rb-Salt, PDB code: 1i0m:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in the 1.05 A Structure of the A-Decamer Gcgtatacgc with A Single 2'-O-Fluoroethyl Thymine in Place of T6, High Rb-Salt


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of 1.05 A Structure of the A-Decamer Gcgtatacgc with A Single 2'-O-Fluoroethyl Thymine in Place of T6, High Rb-Salt within 5.0Å range: probe atom residue distance (Å) B Occ A:F6 b:21.4 occ:1.00 FC' A:1256 0.0 21.4 1.0 CB' A:1256 1.4 20.0 1.0 CA' A:1256 2.4 15.8 1.0 O2' A:1256 2.7 14.1 1.0 O A:HOH228 2.9 34.0 1.0 O A:HOH123 3.1 19.1 1.0 O A:HOH294 3.3 33.0 1.0 C5' A:DA7 3.5 14.5 1.0 O A:HOH251 3.9 34.2 1.0 C4' A:DA7 3.9 12.8 1.0 O4' A:DA7 4.0 11.6 1.0 C2' A:1256 4.0 12.6 1.0 O3' A:1256 4.3 14.1 1.0 O5' A:DA7 4.5 12.8 1.0 C3' A:1256 4.8 14.1 1.0 O A:HOH154 4.8 21.7 1.0 O A:HOH242 4.9 29.5 1.0 O A:HOH116 5.0 16.5 1.0

Fluorine binding site 2 out of 2 in the 1.05 A Structure of the A-Decamer Gcgtatacgc with A Single 2'-O-Fluoroethyl Thymine in Place of T6, High Rb-Salt


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of 1.05 A Structure of the A-Decamer Gcgtatacgc with A Single 2'-O-Fluoroethyl Thymine in Place of T6, High Rb-Salt within 5.0Å range: probe atom residue distance (Å) B Occ B:F16 b:20.7 occ:1.00 FC' B:12516 0.0 20.7 1.0 CB' B:12516 1.4 18.2 1.0 CA' B:12516 2.4 16.6 1.0 O B:HOH221 2.5 31.4 1.0 O2' B:12516 2.8 13.7 1.0 O B:HOH192 3.0 26.7 1.0 O B:HOH170 3.1 28.0 1.0 O B:HOH120 3.3 20.5 1.0 O B:HOH240 3.3 27.9 1.0 O B:HOH344 3.5 27.8 1.0 O B:HOH163 3.6 24.1 1.0 O B:HOH321 3.6 29.0 1.0 C5' B:DA17 3.8 15.7 1.0 O4' B:DA17 3.9 14.4 1.0 C4' B:DA17 4.0 16.0 1.0 C2' B:12516 4.1 12.1 1.0 O B:HOH158 4.2 30.6 1.0 O3' B:12516 4.6 12.8 1.0 O5' B:DA17 4.8 15.0 1.0 C3' B:12516 4.9 13.2 1.0 O B:HOH178 5.0 19.9 1.0

V.Tereshko, C.J.Wilds, G.Minasov, T.P.Prakash, M.A.Maier, A.Howard, Z.Wawrzak, M.Manoharan, M.Egli. Detection of Alkali Metal Ions in Dna Crystals Using State-of-the-Art X-Ray Diffraction Experiments. Nucleic Acids Res. V. 29 1208 2001.
ISSN: ISSN 0305-1048
PubMed: 11222771
DOI: 10.1093/NAR/29.5.1208