Sodium in PDB 6e8t: 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: 6e8t 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)	45.97 / 2.90
Space group	H 3
Cell size a, b, c (Å), α, β, γ (°)	91.945, 91.945, 161.691, 90.00, 90.00, 120.00
R / Rfree (%)	19.5 / 23.7

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

Potassium

(K)

4 atoms

The binding sites of Sodium atom in the Structure of the Mango-III (A10U) Aptamer Bound to TO1-Biotin (pdb code 6e8t). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Structure of the Mango-III (A10U) Aptamer Bound to TO1-Biotin, PDB code: 6e8t:

Sodium binding site 1 out of 1 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 C:Na103 b:51.9 occ:0.33 O2' C:C4 2.8 46.6 1.0 O3' C:C4 3.1 44.1 1.0 C5' C:G5 3.5 43.7 1.0 O C:HOH202 3.7 43.3 0.3 C2' C:C4 3.8 41.7 1.0 C3' C:C4 3.9 45.1 1.0 OP1 C:G5 3.9 47.1 1.0 P C:G5 4.0 47.4 1.0 O5' C:G5 4.2 43.8 1.0 C4' C:C4 4.3 46.1 1.0 C4' C:G5 4.5 44.4 1.0 O4' C:G5 4.9 47.0 1.0 C1' C:C4 5.0 41.5 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