Fluorine in PDB 5ob3: Ispinach Aptamer

The structure of Ispinach Aptamer, PDB code: 5ob3 was solved by P.Fernandez-Millan, A.Autour, E.Westhof, M.Ryckelynck, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.17 / 2.00
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	150.700, 48.500, 30.100, 90.00, 91.86, 90.00
R / Rfree (%)	19.8 / 22.3

The structure of Ispinach Aptamer also contains other interesting chemical elements:

Potassium

(K)

2 atoms

The binding sites of Fluorine atom in the Ispinach Aptamer (pdb code 5ob3). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the Ispinach Aptamer, PDB code: 5ob3:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in the Ispinach Aptamer


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Ispinach Aptamer within 5.0Å range: probe atom residue distance (Å) B Occ A:F101 b:36.8 occ:1.00 F8 A:1TU101 0.0 36.8 1.0 C6 A:1TU101 1.3 38.8 1.0 C5 A:1TU101 2.4 34.1 1.0 C1 A:1TU101 2.4 33.0 1.0 H1 A:1TU101 2.6 39.7 1.0 O9 A:1TU101 2.8 34.0 1.0 O A:HOH220 3.0 37.5 1.0 O A:HOH219 3.2 34.9 1.0 O2' A:A45 3.2 39.0 1.0 C2' A:A45 3.3 40.6 1.0 C8 A:A45 3.4 35.8 1.0 C2 A:1TU101 3.6 34.4 1.0 H12 A:1TU101 3.7 40.8 1.0 C4 A:1TU101 3.7 33.0 1.0 N2 A:G46 3.8 32.4 1.0 C8 A:G16 3.9 36.3 1.0 N9 A:A45 3.9 40.6 1.0 N7 A:G16 3.9 30.3 1.0 O2 A:U42 4.0 44.2 1.0 N7 A:A45 4.0 31.0 1.0 OP2 A:A45 4.2 33.1 1.0 C3 A:1TU101 4.2 33.1 1.0 C1' A:A45 4.2 39.5 1.0 O5' A:A45 4.3 44.7 1.0 O2' A:G15 4.3 40.9 1.0 C3' A:A45 4.6 37.9 1.0 C2 A:U42 4.6 36.6 1.0 C4 A:A45 4.7 37.0 1.0 C5 A:A45 4.7 37.2 1.0 N9 A:G16 4.7 42.4 1.0 N12 A:1TU101 4.8 36.1 1.0 N3 A:U42 4.8 34.4 1.0 C2 A:G46 4.8 39.7 1.0 C5 A:G16 4.8 29.6 1.0 F7 A:1TU101 4.8 42.1 1.0 C10 A:1TU101 4.9 32.9 1.0 P A:A45 4.9 41.3 1.0

Fluorine binding site 2 out of 2 in the Ispinach Aptamer


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Ispinach Aptamer within 5.0Å range: probe atom residue distance (Å) B Occ A:F101 b:42.1 occ:1.00 F7 A:1TU101 0.0 42.1 1.0 C4 A:1TU101 1.3 33.0 1.0 C3 A:1TU101 2.3 33.1 1.0 H12 A:1TU101 2.3 40.8 1.0 C5 A:1TU101 2.5 34.1 1.0 H2 A:1TU101 2.5 39.7 1.0 O9 A:1TU101 2.8 34.0 1.0 O2' A:G16 3.2 30.7 1.0 C4 A:U42 3.2 33.6 1.0 O4 A:U42 3.3 37.3 1.0 N3 A:U42 3.4 34.4 1.0 N3 A:G16 3.4 29.7 1.0 C4 A:G16 3.4 32.7 1.0 C6 A:1TU101 3.7 38.8 1.0 N9 A:G16 3.7 42.4 1.0 C2 A:1TU101 3.7 34.4 1.0 C5 A:U42 3.9 33.2 1.0 C2 A:G16 3.9 25.6 1.0 C5 A:G16 4.0 29.6 1.0 C2' A:G16 4.1 34.2 1.0 C1' A:G16 4.1 31.8 1.0 C2 A:U42 4.1 36.6 1.0 C1 A:1TU101 4.2 33.0 1.0 N6 A:A45 4.3 38.8 1.0 C8 A:G16 4.4 36.3 1.0 N1 A:G16 4.4 27.7 1.0 C6 A:U42 4.4 32.6 1.0 N7 A:A45 4.5 31.0 1.0 C6 A:G16 4.5 30.5 1.0 N7 A:G16 4.5 30.3 1.0 N2 A:G16 4.6 24.0 1.0 N1 A:U42 4.6 46.9 1.0 O2 A:U42 4.8 44.2 1.0 F8 A:1TU101 4.8 36.8 1.0 C6 A:A45 4.9 37.4 1.0 C10 A:1TU101 4.9 32.9 1.0 H3 A:1TU101 4.9 39.5 1.0 C5 A:A45 4.9 37.2 1.0 O6 A:G21 5.0 35.1 1.0

P.Fernandez-Millan, A.Autour, E.Ennifar, E.Westhof, M.Ryckelynck. Crystal Structure and Fluorescence Properties of the Ispinach Aptamer in Complex with Dfhbi. Rna V. 23 1788 2017.
ISSN: ESSN 1469-9001
PubMed: 28939697
DOI: 10.1261/RNA.063008.117