Sodium in PDB 8keb: Crystal Structure of 2'-Dg-III Riboswitch with 2'-Dg

The structure of Crystal Structure of 2'-Dg-III Riboswitch with 2'-Dg, PDB code: 8keb was solved by W.Liao, L.Huang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.43 / 2.20
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	139.516, 26.834, 65.227, 90, 112.71, 90
R / Rfree (%)	20.2 / 24.2

The structure of Crystal Structure of 2'-Dg-III Riboswitch with 2'-Dg also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Sodium atom in the Crystal Structure of 2'-Dg-III Riboswitch with 2'-Dg (pdb code 8keb). 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 2'-Dg-III Riboswitch with 2'-Dg, PDB code: 8keb:

Sodium binding site 1 out of 1 in the Crystal Structure of 2'-Dg-III Riboswitch with 2'-Dg


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 2'-Dg-III Riboswitch with 2'-Dg within 5.0Å range: probe atom residue distance (Å) B Occ A:Na105 b:68.5 occ:1.00 O6 A:G2 3.0 71.0 1.0 O4 A:U70 3.0 71.6 1.0 O6 A:GTP101 3.3 70.6 1.0 O4 A:U69 3.4 69.3 1.0 N6 A:A3 4.0 67.4 1.0 C4 A:U70 4.0 71.6 1.0 C6 A:G2 4.1 71.0 1.0 C6 A:GTP101 4.1 70.5 1.0 N3 A:U70 4.3 71.5 1.0 C4 A:U69 4.4 70.3 1.0 N4 A:C71 4.5 72.3 1.0 N7 A:GTP101 4.5 70.4 1.0 C5 A:GTP101 4.6 69.6 1.0 N7 A:G2 4.7 68.6 1.0 C5 A:G2 4.8 89.2 1.0 C6 A:A3 5.0 68.8 1.0

W.Liao, L.Huang. Crystal Structure of 2'-Dg-III Riboswitch with 2'-Dg To Be Published.