Sodium in PDB 6e8u: Structure of the Mango-III (A10U) Aptamer Bound to TO1-Biotin

The structure of Structure of the Mango-III (A10U) Aptamer Bound to TO1-Biotin, PDB code: 6e8u 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)	40.59 / 1.55
Space group	I 41 2 2
Cell size a, b, c (Å), α, β, γ (°)	53.270, 53.270, 188.036, 90.00, 90.00, 90.00
R / Rfree (%)	17.7 / 20.6

The structure of Structure of the Mango-III (A10U) Aptamer Bound to TO1-Biotin also contains other interesting chemical elements:

Magnesium	(Mg)	5 atoms
Potassium	(K)	1 atom

The binding sites of Sodium atom in the Structure of the Mango-III (A10U) Aptamer Bound to TO1-Biotin (pdb code 6e8u). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Structure of the Mango-III (A10U) Aptamer Bound to TO1-Biotin, PDB code: 6e8u:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Structure of the Mango-III (A10U) Aptamer Bound to TO1-Biotin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of the Mango-III (A10U) Aptamer Bound to TO1-Biotin within 5.0Å range: probe atom residue distance (Å) B Occ B:Na107 b:36.3 occ:1.00 O B:HOH315 2.2 42.6 1.0 OP1 B:U15 2.2 36.9 1.0 OP1 B:U14 2.2 29.0 1.0 O B:HOH303 2.2 42.0 1.0 O B:HOH314 2.2 39.3 1.0 O B:HOH276 2.6 60.4 1.0 P B:U15 3.7 30.1 1.0 P B:U14 3.7 27.5 1.0 O B:HOH333 3.8 65.0 1.0 C5' B:U14 4.1 26.3 1.0 O B:HOH235 4.1 35.4 1.0 C5' B:U15 4.3 39.5 1.0 O B:HOH205 4.3 52.7 1.0 O5' B:U14 4.3 24.9 1.0 O3' B:G13 4.4 28.1 1.0 OP2 B:U15 4.4 38.5 1.0 O B:HOH318 4.4 43.8 1.0 C3' B:U14 4.4 27.4 1.0 O5' B:U15 4.4 31.8 1.0 O B:HOH225 4.5 39.7 1.0 O3' B:U14 4.6 30.4 1.0 C4' B:U14 4.7 24.1 1.0 OP2 B:U14 4.7 27.2 1.0 O B:HOH336 4.9 56.4 1.0

Sodium binding site 2 out of 2 in the Structure of the Mango-III (A10U) Aptamer Bound to TO1-Biotin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of the Mango-III (A10U) Aptamer Bound to TO1-Biotin within 5.0Å range: probe atom residue distance (Å) B Occ B:Na108 b:43.8 occ:1.00 O B:HOH218 2.3 47.8 1.0 O B:HOH320 2.3 45.9 1.0 O B:HOH325 2.3 45.7 1.0 O B:HOH341 2.4 63.0 1.0 O B:HOH236 2.4 35.7 1.0 O B:HOH343 2.4 44.2 1.0 O B:HOH252 3.9 44.2 1.0 O6 B:G5 4.0 31.1 0.8 O6 B:G5 4.0 31.2 0.3 O B:HOH283 4.3 39.5 1.0 N4 B:C4 4.4 33.3 1.0 O B:HOH219 4.4 43.7 1.0 N7 B:G5 4.5 31.7 0.3 N7 B:G5 4.6 31.7 0.8 O B:HOH245 4.6 44.0 1.0 O B:HOH216 4.7 43.1 1.0 O B:HOH319 4.8 48.1 1.0 N6 B:A6 4.8 32.5 1.0 C6 B:G5 4.9 30.6 0.8 C6 B:G5 4.9 30.6 0.3 C5 B:C4 5.0 34.0 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