Potassium 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:

Fluorine

(F)

2 atoms

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

Potassium binding site 1 out of 2 in the Ispinach Aptamer


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Ispinach Aptamer within 5.0Å range: probe atom residue distance (Å) B Occ A:K102 b:32.1 occ:1.00 O6 A:G15 2.8 23.6 1.0 O A:HOH236 2.8 24.9 1.0 O2 A:U54 2.8 27.1 1.0 O6 A:G55 2.9 26.5 1.0 O2' A:U54 3.0 39.1 1.0 O6 A:G49 3.0 32.6 1.0 O6 A:G53 3.1 31.2 1.0 O6 A:G19 3.2 27.5 1.0 N7 A:G55 3.3 26.6 1.0 C6 A:G55 3.5 25.0 1.0 C6 A:G53 3.6 34.4 1.0 C5 A:G55 3.7 22.7 1.0 C6 A:G49 3.7 33.0 1.0 K A:K103 3.8 30.4 1.0 N1 A:G49 3.9 30.9 1.0 C6 A:G15 3.9 26.0 1.0 C6 A:G19 3.9 27.9 1.0 N1 A:G53 3.9 29.1 1.0 C2' A:U54 3.9 39.9 1.0 N1 A:G19 4.0 26.2 1.0 C2 A:U54 4.0 32.5 1.0 N1 A:G15 4.3 30.4 1.0 C1' A:U54 4.3 35.5 1.0 C8 A:G55 4.4 36.2 1.0 C5 A:G53 4.6 26.2 1.0 N4 A:C18 4.7 33.0 1.0 N1 A:U54 4.7 36.8 1.0 O A:HOH212 4.8 37.5 1.0 C5 A:G49 4.9 24.2 1.0 N1 A:G55 4.9 30.1 1.0 N3 A:U47 4.9 32.3 1.0 C2 A:G53 4.9 35.3 1.0 C4 A:G55 5.0 23.6 1.0

Potassium binding site 2 out of 2 in the Ispinach Aptamer


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Ispinach Aptamer within 5.0Å range: probe atom residue distance (Å) B Occ A:K103 b:30.4 occ:1.00 O6 A:G16 2.7 29.5 1.0 O6 A:G49 2.7 32.6 1.0 O6 A:G51 2.8 27.1 1.0 O6 A:G46 2.8 28.7 1.0 O6 A:G20 2.8 25.3 1.0 O6 A:G19 3.0 27.5 1.0 O6 A:G15 3.1 23.6 1.0 O6 A:G53 3.1 31.2 1.0 C6 A:G49 3.5 33.0 1.0 C6 A:G20 3.5 25.7 1.0 C6 A:G16 3.5 30.5 1.0 C6 A:G51 3.6 32.6 1.0 C6 A:G46 3.7 32.2 1.0 N1 A:G49 3.7 30.9 1.0 N1 A:G20 3.7 29.1 1.0 N1 A:G16 3.7 27.7 1.0 C6 A:G15 3.7 26.0 1.0 K A:K102 3.8 32.1 1.0 N1 A:G46 3.9 30.6 1.0 N1 A:G51 3.9 27.5 1.0 C6 A:G19 3.9 27.9 1.0 H4 A:1TU101 3.9 39.5 1.0 C6 A:G53 4.0 34.4 1.0 N1 A:G15 4.1 30.4 1.0 N1 A:G53 4.2 29.1 1.0 N1 A:G19 4.3 26.2 1.0 H5 A:1TU101 4.4 46.9 1.0 C5 A:G49 4.7 24.2 1.0 C5 A:G15 4.7 25.0 1.0 C5 A:G20 4.7 24.2 1.0 C5 A:G51 4.8 37.5 1.0 C5 A:G16 4.8 29.6 1.0 N1 A:G21 4.8 35.4 1.0 C10 A:1TU101 4.9 32.9 1.0 C5 A:G46 4.9 25.7 1.0 C2 A:G49 4.9 35.9 1.0 C2 A:G20 4.9 34.3 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