Magnesium 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:

Potassium	(K)	2 atoms
Sodium	(Na)	4 atoms

The binding sites of Magnesium 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 Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Structure of the Imango-III Aptamer Bound to TO1-Biotin, PDB code: 6e8s:
Jump to Magnesium binding site number: 1; 2;

Magnesium 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 Magnesium with other atoms in the Mg 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:Mg103 b:89.8 occ:1.00 O4 A:U31 3.3 69.5 1.0 N6 A:A7 3.6 72.0 1.0 O6 A:G6 4.2 76.8 1.0 C4 A:U31 4.3 65.5 1.0 O4 A:U32 4.4 67.8 1.0 N6 A:A8 4.6 65.7 1.0 C6 A:A7 4.8 71.8 1.0 C5 A:U31 4.9 68.1 1.0

Magnesium 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 Magnesium with other atoms in the Mg 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:Mg104 b:95.8 occ:1.00 O6 B:G6 3.7 75.0 1.0 N7 B:G6 3.7 73.8 1.0 N6 B:A7 4.0 67.1 1.0 C6 B:G6 4.4 73.7 1.0 C5 B:G6 4.4 74.6 1.0 N4 B:C5 4.5 68.6 1.0 C5 B:C5 4.6 69.2 1.0 C4 B:C5 4.7 74.8 1.0 C8 B:G6 4.8 76.2 1.0 O4 B:U31 5.0 67.5 1.0 N7 B:A7 5.0 73.3 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