Sodium in PDB 8d2a: Crystal Structure of Theophylline Aptamer in Complex with TAL3

The structure of Crystal Structure of Theophylline Aptamer in Complex with TAL3, PDB code: 8d2a 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)	27.91 / 2.17
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	23.075, 29.662, 80.291, 95.39, 89.99, 109.01
R / Rfree (%)	18.7 / 25.2

The structure of Crystal Structure of Theophylline Aptamer in Complex with TAL3 also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Sodium atom in the Crystal Structure of Theophylline Aptamer in Complex with TAL3 (pdb code 8d2a). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Crystal Structure of Theophylline Aptamer in Complex with TAL3, PDB code: 8d2a:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Crystal Structure of Theophylline Aptamer in Complex with TAL3


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 in Complex with TAL3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na102 b:32.1 occ:1.00 HO2' A:C22 2.1 29.5 1.0 N7 A:A5 2.4 22.3 1.0 O4 A:U6 2.4 17.6 1.0 O2' A:C22 2.5 24.7 1.0 O A:HOH214 2.5 28.0 1.0 O A:HOH230 2.6 22.5 1.0 O A:HOH256 2.8 27.3 1.0 H62 A:A5 3.0 22.8 1.0 H5 A:U6 3.1 28.0 1.0 C4 A:U6 3.1 22.5 1.0 C8 A:A5 3.3 19.8 1.0 C5 A:A5 3.4 20.8 1.0 H8 A:A5 3.4 23.6 1.0 C5 A:U6 3.5 23.5 1.0 H5 A:U23 3.7 29.7 1.0 N6 A:A5 3.7 19.1 1.0 C2' A:C22 3.7 27.7 1.0 H6 A:C22 3.9 25.0 1.0 C6 A:A5 3.9 22.1 1.0 H1' A:C22 4.0 29.3 1.0 C6 A:C22 4.0 21.0 1.0 H2' A:C22 4.1 33.1 1.0 N1 A:C22 4.1 24.6 1.0 C1' A:C22 4.2 24.6 1.0 OP2 A:A5 4.2 23.5 1.0 O A:HOH232 4.3 29.3 1.0 OP2 A:U23 4.3 24.9 1.0 N3 A:U6 4.3 26.0 1.0 H61 A:A5 4.4 22.8 1.0 N9 A:A5 4.4 23.8 1.0 C4 A:A5 4.5 23.2 1.0 H3 A:U6 4.5 31.1 1.0 C5 A:U23 4.6 24.9 1.0 C5 A:C22 4.7 17.7 1.0 C6 A:U6 4.7 24.2 1.0 H6 A:U23 4.7 27.6 1.0 C2 A:C22 4.8 25.7 1.0 N7 A:G4 4.9 18.8 1.0 O3' A:C22 4.9 28.5 1.0 H3' A:G4 4.9 29.6 1.0 C3' A:C22 4.9 23.5 1.0 H5 A:C22 5.0 21.0 1.0 H2' A:G4 5.0 26.6 1.0

Sodium binding site 2 out of 4 in the Crystal Structure of Theophylline Aptamer in Complex with TAL3


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Theophylline Aptamer in Complex with TAL3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na104 b:19.6 occ:1.00 O2' A:U23 2.4 21.6 1.0 O A:HOH238 2.4 26.8 1.0 O A:HOH218 2.5 15.5 1.0 O A:HOH259 2.5 20.4 1.0 O2 A:U23 2.6 25.7 1.0 O A:HOH217 2.8 19.7 1.0 H1' A:U23 3.0 32.1 1.0 C2 A:U23 3.1 24.8 1.0 C2' A:U23 3.4 26.1 1.0 C1' A:U23 3.4 26.9 1.0 N1 A:U23 3.6 26.4 1.0 O A:HOH249 3.7 22.6 1.0 H5'' A:A28 3.8 29.5 1.0 O3' A:U23 4.0 29.0 1.0 N3 A:U23 4.1 23.8 1.0 H8 A:A28 4.1 26.4 1.0 H2' A:U23 4.1 31.1 1.0 H3 A:U23 4.2 28.4 1.0 O A:HOH203 4.3 18.4 1.0 C3' A:U23 4.4 27.8 1.0 O4' A:U24 4.5 24.6 1.0 N7 A:G29 4.6 18.5 1.0 C6 A:U23 4.7 23.2 1.0 C8 A:A28 4.8 22.2 1.0 C5' A:A28 4.8 24.7 1.0 O4' A:U23 4.8 25.8 1.0 OP1 A:A28 4.9 28.1 1.0 H5' A:A28 4.9 29.5 1.0 OP2 A:G29 4.9 24.7 1.0 H3' A:A28 5.0 23.8 1.0

Sodium binding site 3 out of 4 in the Crystal Structure of Theophylline Aptamer in Complex with TAL3


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of Theophylline Aptamer in Complex with TAL3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na102 b:32.2 occ:1.00 O B:HOH241 2.3 20.7 1.0 O2' B:U23 2.4 18.2 1.0 O B:HOH226 2.6 26.3 1.0 O B:HOH229 2.7 23.3 1.0 O2 B:U23 3.0 18.8 1.0 H1' B:U23 3.3 32.6 1.0 C2' B:U23 3.5 23.9 1.0 C2 B:U23 3.6 21.6 1.0 C1' B:U23 3.7 27.3 1.0 H5'' B:A28 3.7 41.2 1.0 N1 B:U23 4.0 22.4 1.0 O3' B:U23 4.2 25.7 1.0 H2' B:U23 4.2 28.6 1.0 H8 B:A28 4.2 36.9 1.0 N7 B:G29 4.4 30.2 1.0 O B:HOH231 4.5 28.7 1.0 C3' B:U23 4.5 23.2 1.0 N3 B:U23 4.5 23.5 1.0 C5' B:A28 4.7 34.5 1.0 H3 B:U23 4.7 28.0 1.0 O B:HOH227 4.7 23.9 1.0 OP2 B:G29 4.7 32.1 1.0 H3' B:A28 4.7 35.9 1.0 O4' B:U24 4.8 26.2 1.0 C8 B:A28 4.9 30.9 1.0 OP1 B:A28 4.9 36.1 1.0 H5' B:A28 4.9 41.2 1.0

Sodium binding site 4 out of 4 in the Crystal Structure of Theophylline Aptamer in Complex with TAL3


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of Theophylline Aptamer in Complex with TAL3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na104 b:19.1 occ:1.00 O4 B:U6 2.3 21.4 1.0 O2' B:C22 2.4 27.6 1.0 O B:HOH252 2.5 31.3 1.0 O B:HOH258 2.6 23.2 1.0 N7 B:A5 2.6 22.2 1.0 O B:HOH247 2.6 22.6 1.0 H62 B:A5 3.1 26.7 1.0 C4 B:U6 3.1 22.1 1.0 H5 B:U6 3.2 29.5 1.0 C8 B:A5 3.3 22.0 1.0 H8 B:A5 3.4 26.2 1.0 C5 B:U6 3.6 24.8 1.0 H5 B:U23 3.6 30.2 1.0 C5 B:A5 3.6 22.1 1.0 C2' B:C22 3.7 30.7 1.0 H6 B:C22 3.8 37.2 1.0 N6 B:A5 3.8 22.4 1.0 H1' B:C22 4.0 36.8 1.0 C6 B:C22 4.0 31.1 1.0 H2' B:C22 4.1 36.7 1.0 N1 B:C22 4.1 26.0 1.0 C1' B:C22 4.1 30.8 1.0 OP2 B:U23 4.1 21.3 1.0 OP2 B:A5 4.2 25.9 1.0 O B:HOH238 4.2 27.4 1.0 C6 B:A5 4.2 23.3 1.0 N3 B:U6 4.3 23.0 1.0 O B:HOH242 4.4 31.1 1.0 C5 B:U23 4.5 25.3 1.0 H3 B:U6 4.5 27.4 1.0 H61 B:A5 4.5 26.7 1.0 N9 B:A5 4.6 24.6 1.0 C5 B:C22 4.6 27.0 1.0 H3' B:G4 4.7 24.6 1.0 H6 B:U23 4.7 26.9 1.0 O3' B:C22 4.7 29.1 1.0 C4 B:A5 4.7 24.5 1.0 N7 B:G4 4.8 22.9 1.0 C6 B:U6 4.8 22.4 1.0 C3' B:C22 4.8 26.4 1.0 C2 B:C22 4.9 26.0 1.0 H5 B:C22 4.9 32.2 1.0 H2' B:G4 5.0 26.0 1.0 O5' B:A5 5.0 24.1 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