Sodium in PDB 7tzs: Crystal Structure of the E. Coli Thim Riboswitch in Complex with Quinoxalin-6-Ylmethanamine (Compound 17)

The structure of Crystal Structure of the E. Coli Thim Riboswitch in Complex with Quinoxalin-6-Ylmethanamine (Compound 17), PDB code: 7tzs was solved by A.Nuthanakanti, A.Serganov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.78 / 2.21
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	148.734, 30.4, 95.57, 90, 93.51, 90
R / Rfree (%)	20.4 / 24.5

The structure of Crystal Structure of the E. Coli Thim Riboswitch in Complex with Quinoxalin-6-Ylmethanamine (Compound 17) also contains other interesting chemical elements:

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

The binding sites of Sodium atom in the Crystal Structure of the E. Coli Thim Riboswitch in Complex with Quinoxalin-6-Ylmethanamine (Compound 17) (pdb code 7tzs). 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 the E. Coli Thim Riboswitch in Complex with Quinoxalin-6-Ylmethanamine (Compound 17), PDB code: 7tzs:

Sodium binding site 1 out of 1 in the Crystal Structure of the E. Coli Thim Riboswitch in Complex with Quinoxalin-6-Ylmethanamine (Compound 17)


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 the E. Coli Thim Riboswitch in Complex with Quinoxalin-6-Ylmethanamine (Compound 17) within 5.0Å range: probe atom residue distance (Å) B Occ X:Na109 b:35.9 occ:1.00 O X:HOH270 2.7 35.8 1.0 O6 X:G40 2.7 32.7 1.0 O X:HOH280 2.8 30.0 1.0 O X:HOH266 3.2 28.8 1.0 C6 X:G40 3.7 30.6 1.0 O X:HOH288 3.9 41.0 1.0 O X:HOH309 4.0 41.5 0.4 N7 X:G40 4.1 29.4 1.0 C5 X:G40 4.3 31.4 1.0 C5 X:U39 4.3 28.9 1.0 O X:HOH294 4.4 35.4 1.0 OP2 X:U39 4.5 29.9 1.0 O X:HOH259 4.7 35.9 1.0 OP2 X:C38 4.8 33.1 1.0 O4 X:U39 4.8 29.5 1.0 N1 X:G40 4.9 32.4 1.0 C4 X:U39 5.0 31.8 1.0

M.J.Zeller, O.Favorov, K.Li, A.Nuthanakanti, D.Hussein, A.Michaud, D.A.Lafontaine, S.Busan, A.Serganov, J.Aube, K.M.Weeks. Shape-Enabled Fragment-Based Ligand Discovery For Rna. Proc.Natl.Acad.Sci.Usa V. 119 60119 2022.
ISSN: ESSN 1091-6490
PubMed: 35561226
DOI: 10.1073/PNAS.2122660119