Sodium in PDB 6ymm: Crystal Structure of the Sam-Sah Riboswitch with Sam From Space Group P312

The structure of Crystal Structure of the Sam-Sah Riboswitch with Sam From Space Group P312, PDB code: 6ymm 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)	38.18 / 2.20
Space group	P 3 1 2
Cell size a, b, c (Å), α, β, γ (°)	88.170, 88.170, 76.080, 90.00, 90.00, 120.00
R / Rfree (%)	19.2 / 22.1

The structure of Crystal Structure of the Sam-Sah Riboswitch with Sam From Space Group P312 also contains other interesting chemical elements:

Bromine

(Br)

2 atoms

The binding sites of Sodium atom in the Crystal Structure of the Sam-Sah Riboswitch with Sam From Space Group P312 (pdb code 6ymm). 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 Sam-Sah Riboswitch with Sam From Space Group P312, PDB code: 6ymm:

Sodium binding site 1 out of 1 in the Crystal Structure of the Sam-Sah Riboswitch with Sam From Space Group P312


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 Sam-Sah Riboswitch with Sam From Space Group P312 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na102 b:87.3 occ:1.00 O2' A:U28 4.0 71.7 1.0 O2 A:U28 4.2 65.2 1.0 O4' A:G29 4.4 66.1 1.0 C1' A:G29 4.5 58.9 1.0 O2' A:G29 4.6 54.6 1.0 O2 A:C12 4.7 63.7 1.0 C2' A:U28 4.8 66.5 1.0

L.Huang, T.W.Liao, J.Wang, T.Ha, D.M.J.Lilley. Crystal Structure and Ligand-Induced Folding of the Sam/Sah Riboswitch. Nucleic Acids Res. V. 48 7545 2020.
ISSN: ESSN 1362-4962
PubMed: 32520325
DOI: 10.1093/NAR/GKAA493