Potassium in PDB 6e8s: Structure of the Imango-III Aptamer Bound to TO1-Biotin

The structure of Structure of the Imango-III Aptamer Bound to TO1-Biotin, PDB code: 6e8s was solved by R.J.Trachman, A.R.Ferre-D'amare, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.33 / 2.35
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	63.031, 67.585, 76.667, 90.00, 90.00, 90.00
R / Rfree (%)	18.2 / 20.8

The structure of Structure of the Imango-III Aptamer Bound to TO1-Biotin also contains other interesting chemical elements:

Magnesium	(Mg)	2 atoms
Sodium	(Na)	4 atoms

The binding sites of Potassium atom in the Structure of the Imango-III Aptamer Bound to TO1-Biotin (pdb code 6e8s). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 2 binding sites of Potassium where determined in the Structure of the Imango-III Aptamer Bound to TO1-Biotin, PDB code: 6e8s:
Jump to Potassium binding site number: 1; 2;

Potassium binding site 1 out of 2 in the Structure of the Imango-III Aptamer Bound to TO1-Biotin


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Structure of the Imango-III Aptamer Bound to TO1-Biotin within 5.0Å range: probe atom residue distance (Å) B Occ A:K102 b:56.5 occ:1.00 O6 A:G23 2.7 59.4 1.0 O6 A:G19 2.7 67.5 1.0 O6 A:G14 2.7 65.8 1.0 O6 A:G10 2.8 69.3 1.0 O6 A:G9 2.8 66.8 1.0 O6 A:G18 2.9 66.9 1.0 O6 A:G13 2.9 65.1 1.0 O6 A:G25 2.9 56.1 1.0 C6 A:G23 3.5 66.5 1.0 C6 A:G19 3.6 69.5 1.0 C6 A:G9 3.6 67.5 1.0 N1 A:G19 3.6 67.8 1.0 C6 A:G13 3.6 65.7 1.0 C6 A:G10 3.7 66.4 1.0 N1 A:G13 3.7 64.0 1.0 C6 A:G14 3.7 65.2 1.0 C6 A:G18 3.7 68.8 1.0 C6 A:G25 3.8 61.0 1.0 N1 A:G25 3.9 57.4 1.0 N1 A:G10 3.9 67.2 1.0 N1 A:G23 3.9 63.0 1.0 N1 A:G9 3.9 64.2 1.0 N1 A:G18 3.9 70.3 1.0 N1 A:G14 4.0 67.4 1.0 O A:HOH205 4.5 57.2 1.0 S23 A:EKJ101 4.5 63.9 1.0 C5 A:G23 4.8 65.7 1.0 C5 A:G9 4.8 68.1 1.0 C10 A:EKJ101 4.8 65.6 1.0 C2 A:G19 4.9 64.6 1.0 C2 A:G13 4.9 69.6 1.0 C5 A:G13 4.9 66.8 1.0 C5 A:G19 4.9 69.3 1.0 C5 A:G10 4.9 62.9 1.0 C5 A:G14 5.0 67.8 1.0

Potassium binding site 2 out of 2 in the Structure of the Imango-III Aptamer Bound to TO1-Biotin


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Structure of the Imango-III Aptamer Bound to TO1-Biotin within 5.0Å range: probe atom residue distance (Å) B Occ B:K103 b:59.9 occ:1.00 O6 B:G19 2.7 66.9 1.0 O6 B:G23 2.7 66.3 1.0 O6 B:G14 2.7 65.1 1.0 O6 B:G13 2.7 65.5 1.0 O6 B:G10 2.7 65.0 1.0 O6 B:G9 2.7 68.8 1.0 O6 B:G25 2.8 67.0 1.0 O6 B:G18 2.8 68.0 1.0 C6 B:G9 3.5 70.2 1.0 C6 B:G13 3.5 68.2 1.0 C6 B:G23 3.6 69.8 1.0 C6 B:G10 3.6 65.5 1.0 C6 B:G19 3.6 69.5 1.0 C6 B:G14 3.7 66.3 1.0 C6 B:G25 3.7 69.3 1.0 N1 B:G13 3.7 69.7 1.0 C6 B:G18 3.8 69.6 1.0 N1 B:G19 3.8 70.4 1.0 N1 B:G10 3.8 69.8 1.0 N1 B:G9 3.8 68.6 1.0 N1 B:G23 3.9 69.2 1.0 N1 B:G25 3.9 64.7 1.0 N1 B:G14 4.0 68.9 1.0 N1 B:G18 4.1 71.9 1.0 S23 B:EKJ101 4.4 61.6 1.0 O B:HOH204 4.4 62.0 1.0 C5 B:G9 4.7 72.5 1.0 C5 B:G23 4.8 68.4 1.0 C10 B:EKJ101 4.8 68.7 1.0 C5 B:G10 4.8 65.6 1.0 C5 B:G13 4.9 67.1 1.0 C5 B:G14 4.9 68.4 1.0 C5 B:G19 5.0 68.7 1.0

R.J.Trachman 3Rd., A.Autour, S.C.Y.Jeng, A.Abdolahzadeh, A.Andreoni, R.Cojocaru, R.Garipov, E.V.Dolgosheina, J.R.Knutson, M.Ryckelynck, P.J.Unrau, A.R.Ferre-D'amare. Structure and Functional Reselection of the Mango-III Fluorogenic Rna Aptamer. Nat. Chem. Biol. V. 15 472 2019.
ISSN: ESSN 1552-4469
PubMed: 30992561
DOI: 10.1038/S41589-019-0267-9