Sodium in PDB 8d29: Crystal Structure of Theophylline Aptamer - Apo Form

The structure of Crystal Structure of Theophylline Aptamer - Apo Form, PDB code: 8d29 was solved by E.Menichelli, G.Spraggon, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	68.66 / 1.81
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	76.151, 92.849, 93.639, 97.34, 90.32, 106.92
R / Rfree (%)	17.6 / 21.1

The structure of Crystal Structure of Theophylline Aptamer - Apo Form also contains other interesting chemical elements:

Potassium

(K)

5 atoms

The binding sites of Sodium atom in the Crystal Structure of Theophylline Aptamer - Apo Form (pdb code 8d29). 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 Crystal Structure of Theophylline Aptamer - Apo Form, PDB code: 8d29:

Sodium binding site 1 out of 1 in the Crystal Structure of Theophylline Aptamer - Apo Form


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Theophylline Aptamer - Apo Form within 5.0Å range: probe atom residue distance (Å) B Occ G:Na301 b:31.3 occ:0.62 O G:HOH590 2.2 35.1 1.0 O G:HOH622 2.6 37.1 1.0 O G:VAL123 2.7 13.1 1.0 O G:HOH600 3.0 44.4 1.0 OG1 G:THR94 3.4 15.3 1.0 C G:VAL123 3.8 13.4 1.0 O G:ALA91 3.9 17.6 1.0 CB G:ALA91 4.0 17.9 1.0 O G:HOH427 4.0 39.2 1.0 CB G:SER124 4.0 17.7 1.0 CA G:ALA91 4.1 19.2 1.0 O G:HOH658 4.2 38.5 1.0 CB G:THR94 4.3 13.0 1.0 C G:ALA91 4.4 18.3 1.0 CA G:SER124 4.4 14.6 1.0 N G:SER124 4.5 12.9 1.0 N G:VAL123 4.6 13.5 1.0 CG2 G:THR94 4.7 11.2 1.0 OG G:SER124 4.7 18.1 1.0 CA G:VAL123 4.7 12.6 1.0 CG2 G:THR122 4.9 19.2 1.0

E.Menichelli, B.J.Lam, Y.Wang, V.S.Wang, J.Shaffer, K.F.Tjhung, B.Bursulaya, T.N.Nguyen, T.Vo, P.B.Alper, C.S.Mcallister, D.H.Jones, G.Spraggon, P.Y.Michellys, J.Joslin, G.F.Joyce, J.Rogers. Discovery of Small Molecules That Target A Tertiary-Structured Rna. Proc.Natl.Acad.Sci.Usa V. 119 17119 2022.
ISSN: ESSN 1091-6490
PubMed: 36413497
DOI: 10.1073/PNAS.2213117119