Sodium in PDB 6ymj: Crystal Structure of the Sam-Sah Riboswitch with Adenosine

The structure of Crystal Structure of the Sam-Sah Riboswitch with Adenosine, PDB code: 6ymj 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)	37.34 / 2.04
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	86.599, 147.570, 75.013, 90.00, 91.36, 90.00
R / Rfree (%)	19.8 / 23.3

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

Bromine	(Br)	6 atoms
Magnesium	(Mg)	1 atom

The binding sites of Sodium atom in the Crystal Structure of the Sam-Sah Riboswitch with Adenosine (pdb code 6ymj). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Crystal Structure of the Sam-Sah Riboswitch with Adenosine, PDB code: 6ymj:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Crystal Structure of the Sam-Sah Riboswitch with Adenosine


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 Adenosine within 5.0Å range: probe atom residue distance (Å) B Occ A:Na104 b:81.8 occ:1.00 N4 A:CBV101 3.6 56.0 1.0 BR A:CBV101 4.3 73.7 1.0 O A:HOH204 4.7 59.7 1.0 C4 A:CBV101 4.7 58.2 1.0 N6 A:A11 4.8 51.5 1.0 O6 A:G29 4.9 67.1 1.0

Sodium binding site 2 out of 3 in the Crystal Structure of the Sam-Sah Riboswitch with Adenosine


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 Adenosine within 5.0Å range: probe atom residue distance (Å) B Occ M:Na103 b:76.5 occ:1.00 N4 M:C31 3.6 71.6 1.0 N4 M:C32 3.8 66.7 1.0 C5 M:C31 4.2 76.7 1.0 C4 M:C31 4.4 73.1 1.0 C4 M:C32 4.9 72.5 1.0

Sodium binding site 3 out of 3 in the Crystal Structure of the Sam-Sah Riboswitch with Adenosine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of the Sam-Sah Riboswitch with Adenosine within 5.0Å range: probe atom residue distance (Å) B Occ M:Na104 b:76.5 occ:1.00 N2 M:G8 3.8 76.2 1.0 C1' M:C32 4.2 85.8 1.0 O4' M:C32 4.3 86.3 1.0 O2' M:C32 4.4 89.2 1.0 O2 M:C31 4.9 72.7 1.0 C2 M:G8 4.9 70.5 1.0 C2' M:C32 5.0 86.5 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