Sodium in PDB 9c6k: Cryo-Em Structure of the Tpp Riboswitch Embedded in An Rna Scaffold Bound to Thiamine Pyrophosphate

The structure of Cryo-Em Structure of the Tpp Riboswitch Embedded in An Rna Scaffold Bound to Thiamine Pyrophosphate also contains other interesting chemical elements:

Magnesium

(Mg)

6 atoms

The binding sites of Sodium atom in the Cryo-Em Structure of the Tpp Riboswitch Embedded in An Rna Scaffold Bound to Thiamine Pyrophosphate (pdb code 9c6k). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Cryo-Em Structure of the Tpp Riboswitch Embedded in An Rna Scaffold Bound to Thiamine Pyrophosphate, PDB code: 9c6k:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Cryo-Em Structure of the Tpp Riboswitch Embedded in An Rna Scaffold Bound to Thiamine Pyrophosphate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Cryo-Em Structure of the Tpp Riboswitch Embedded in An Rna Scaffold Bound to Thiamine Pyrophosphate within 5.0Å range: probe atom residue distance (Å) B Occ X:Na208 b:66.1 occ:1.00 N7 X:G40 3.3 86.2 1.0 C8 X:G40 3.8 86.2 1.0 OP2 X:U39 4.3 87.1 1.0 OP2 X:G40 4.5 86.2 1.0 C5 X:G40 4.6 86.2 1.0 OP2 X:G42 4.9 86.2 1.0

Sodium binding site 2 out of 2 in the Cryo-Em Structure of the Tpp Riboswitch Embedded in An Rna Scaffold Bound to Thiamine Pyrophosphate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Cryo-Em Structure of the Tpp Riboswitch Embedded in An Rna Scaffold Bound to Thiamine Pyrophosphate within 5.0Å range: probe atom residue distance (Å) B Occ X:Na209 b:112.2 occ:1.00 O4 X:U25 2.3 128.2 1.0 C4 X:U25 3.4 128.2 1.0 O4 X:U26 3.6 140.4 1.0 N6 X:A35 3.6 131.8 1.0 C4 X:C23 3.9 101.4 1.0 N3 X:C23 4.0 101.4 1.0 N4 X:C23 4.1 101.4 1.0 C5 X:U25 4.3 128.2 1.0 C5 X:C23 4.3 101.4 1.0 C2 X:C23 4.4 101.4 1.0 N3 X:U25 4.4 128.2 1.0 N6 X:A34 4.6 149.2 1.0 O6 X:G36 4.6 112.7 1.0 C6 X:C23 4.6 101.4 1.0 C4 X:U26 4.7 140.4 1.0 N1 X:C23 4.7 101.4 1.0 C6 X:A35 4.8 131.8 1.0 N1 X:G36 4.9 112.7 1.0 O2' X:C23 4.9 101.4 1.0 O2 X:C23 4.9 101.4 1.0 C6 X:G36 5.0 112.7 1.0

D.B.Haack, B.Rudolfs, S.Jin, K.M.Weeks, N.Toor. Scaffold-Enabled High-Resolution Cryo-Em Structure Determination of Rna. Biorxiv 2024.
ISSN: ISSN 2692-8205
PubMed: 38915706
DOI: 10.1101/2024.06.10.598011