Sodium in PDB 6ymk: Crystal Structure of the Sam-Sah Riboswitch with Amp

The structure of Crystal Structure of the Sam-Sah Riboswitch with Amp, PDB code: 6ymk 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)	37.48 / 2.03
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	87.100, 147.847, 75.009, 90.00, 91.84, 90.00
R / Rfree (%)	22.5 / 26.4

The structure of Crystal Structure of the Sam-Sah Riboswitch with Amp also contains other interesting chemical elements:

Bromine

(Br)

6 atoms

The binding sites of Sodium atom in the Crystal Structure of the Sam-Sah Riboswitch with Amp (pdb code 6ymk). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of the Sam-Sah Riboswitch with Amp, PDB code: 6ymk:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of the Sam-Sah Riboswitch with Amp


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 Amp within 5.0Å range: probe atom residue distance (Å) B Occ D:Na102 b:92.6 occ:1.00 H41 D:C50 3.2 70.4 1.0 H62 D:A51 3.5 85.7 1.0 N4 D:C50 4.1 58.2 1.0 N6 D:A51 4.1 71.0 1.0 H5 D:C50 4.2 90.0 1.0 H61 D:A51 4.3 85.7 1.0 H42 D:C50 4.5 70.4 1.0 C5 D:C50 4.9 74.6 1.0 C4 D:C50 5.0 58.2 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of the Sam-Sah Riboswitch with Amp


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 the Sam-Sah Riboswitch with Amp within 5.0Å range: probe atom residue distance (Å) B Occ F:Na102 b:0.4 occ:1.00 H41 F:C32 2.5 74.2 1.0 N4 F:C32 3.3 61.4 1.0 H41 F:C31 3.3 54.3 1.0 H42 F:C32 3.6 74.2 1.0 H5 F:C31 3.7 69.4 1.0 N4 F:C31 4.0 47.4 1.0 H5 F:C32 4.2 87.6 1.0 C5 F:C31 4.3 57.4 1.0 C4 F:C32 4.4 63.2 1.0 H42 F:C31 4.5 54.3 1.0 C4 F:C31 4.5 56.3 1.0 C5 F:C32 4.7 72.6 1.0 O6 F:G7 5.0 71.3 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