Sodium in PDB 6hbx: The Structure of the G. Violaceus Guanidine II Riboswitch P2 Stem-Loop with Ethylguanidine

The structure of The Structure of the G. Violaceus Guanidine II Riboswitch P2 Stem-Loop with Ethylguanidine, PDB code: 6hbx was solved by L.Huang, D.M.J.Lilley, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.04 / 1.54
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	56.070, 56.070, 134.800, 90.00, 90.00, 120.00
R / Rfree (%)	19 / 23

The structure of The Structure of the G. Violaceus Guanidine II Riboswitch P2 Stem-Loop with Ethylguanidine also contains other interesting chemical elements:

Bromine

(Br)

1 atom

The binding sites of Sodium atom in the The Structure of the G. Violaceus Guanidine II Riboswitch P2 Stem-Loop with Ethylguanidine (pdb code 6hbx). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the The Structure of the G. Violaceus Guanidine II Riboswitch P2 Stem-Loop with Ethylguanidine, PDB code: 6hbx:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the The Structure of the G. Violaceus Guanidine II Riboswitch P2 Stem-Loop with Ethylguanidine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of The Structure of the G. Violaceus Guanidine II Riboswitch P2 Stem-Loop with Ethylguanidine within 5.0Å range: probe atom residue distance (Å) B Occ A:Na103 b:57.5 occ:1.00 O A:HOH224 3.1 43.6 1.0 N2 A:G1 3.3 28.6 1.0 O A:HOH232 3.8 44.5 1.0 C1' A:G2 4.2 29.0 1.0 C2 A:G1 4.2 24.3 1.0 N3 A:G1 4.3 27.1 1.0 O4' A:G2 4.4 29.4 1.0 O2' A:G2 4.4 31.0 1.0 O2 A:C18 4.9 27.9 1.0

Sodium binding site 2 out of 2 in the The Structure of the G. Violaceus Guanidine II Riboswitch P2 Stem-Loop with Ethylguanidine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of The Structure of the G. Violaceus Guanidine II Riboswitch P2 Stem-Loop with Ethylguanidine within 5.0Å range: probe atom residue distance (Å) B Occ A:Na104 b:66.2 occ:1.00 O2' A:G4 3.4 31.5 1.0 N3 A:G4 3.5 32.2 1.0 O A:HOH215 3.5 30.7 1.0 C1' A:G4 3.9 30.2 1.0 C2' A:G4 4.0 26.5 1.0 N2 A:G4 4.1 30.4 1.0 C2 A:G4 4.3 36.1 1.0 C4 A:G4 4.5 33.6 1.0 O4' A:G5 4.5 29.7 1.0 N9 A:G4 4.6 29.0 1.0 O4' A:G4 5.0 30.2 1.0

L.Huang, J.Wang, T.J.Wilson, D.M.J.Lilley. Structure-Guided Design of A High-Affinity Ligand For A Riboswitch. Rna V. 25 423 2019.
ISSN: ESSN 1469-9001
PubMed: 30609994
DOI: 10.1261/RNA.069567.118