Sodium in PDB 6tf1: Crystal Structure of the Adp-Binding Domain of the Nad+ Riboswitch with Adenosine Diphosphate (Adp)

The structure of Crystal Structure of the Adp-Binding Domain of the Nad+ Riboswitch with Adenosine Diphosphate (Adp), PDB code: 6tf1 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)	56.37 / 2.40
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	57.585, 59.014, 190.587, 90.00, 90.00, 90.00
R / Rfree (%)	21.6 / 24.5

The structure of Crystal Structure of the Adp-Binding Domain of the Nad+ Riboswitch with Adenosine Diphosphate (Adp) also contains other interesting chemical elements:

Magnesium

(Mg)

7 atoms

The binding sites of Sodium atom in the Crystal Structure of the Adp-Binding Domain of the Nad+ Riboswitch with Adenosine Diphosphate (Adp) (pdb code 6tf1). 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 Adp-Binding Domain of the Nad+ Riboswitch with Adenosine Diphosphate (Adp), PDB code: 6tf1:

Sodium binding site 1 out of 1 in the Crystal Structure of the Adp-Binding Domain of the Nad+ Riboswitch with Adenosine Diphosphate (Adp)


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 Adp-Binding Domain of the Nad+ Riboswitch with Adenosine Diphosphate (Adp) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na108 b:81.3 occ:1.00 N3 A:C15 2.8 59.9 1.0 O2 A:C15 3.1 55.7 1.0 O6 A:G36 3.1 73.0 1.0 C2 A:C15 3.4 60.6 1.0 C6 A:G36 3.6 64.2 1.0 C4 A:C15 4.0 62.3 1.0 C5 A:G36 4.0 56.2 1.0 N7 A:G36 4.2 63.6 1.0 N4 A:C15 4.2 63.1 1.0 N4 A:C14 4.3 75.0 1.0 N1 A:G36 4.4 62.6 1.0 N1 A:C15 4.8 54.8 1.0 N3 A:A10 4.9 57.3 1.0

L.Huang, J.Wang, D.M.J.Lilley. Structure and Ligand Binding of the Adp-Binding Domain of the Nad+ Riboswitch. Rna V. 26 878 2020.
ISSN: ESSN 1469-9001
PubMed: 32295864
DOI: 10.1261/RNA.074898.120