Sodium in PDB 5fjc: Sam-I Riboswitch Bearing the H. Marismortui Kt-7 Variant C-2BU

The structure of Sam-I Riboswitch Bearing the H. Marismortui Kt-7 Variant C-2BU, PDB code: 5fjc 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)	41.134 / 1.71
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	60.398, 60.398, 152.950, 90.00, 90.00, 90.00
R / Rfree (%)	20.09 / 24.05

The structure of Sam-I Riboswitch Bearing the H. Marismortui Kt-7 Variant C-2BU also contains other interesting chemical elements:

Magnesium	(Mg)	2 atoms
Potassium	(K)	4 atoms
Barium	(Ba)	21 atoms

The binding sites of Sodium atom in the Sam-I Riboswitch Bearing the H. Marismortui Kt-7 Variant C-2BU (pdb code 5fjc). 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 Sam-I Riboswitch Bearing the H. Marismortui Kt-7 Variant C-2BU, PDB code: 5fjc:

Sodium binding site 1 out of 1 in the Sam-I Riboswitch Bearing the H. Marismortui Kt-7 Variant C-2BU


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Sam-I Riboswitch Bearing the H. Marismortui Kt-7 Variant C-2BU within 5.0Å range: probe atom residue distance (Å) B Occ A:Na129 b:56.8 occ:1.00 N3 A:A83 2.4 45.0 1.0 O2' A:A83 2.9 42.0 1.0 C2' A:A83 3.1 39.4 1.0 C2 A:A83 3.2 45.7 1.0 O4' A:A84 3.3 41.2 1.0 O2 A:C69 3.4 32.0 1.0 C4 A:A83 3.4 39.0 1.0 C1' A:A83 3.4 42.6 1.0 N2 A:G82 3.8 30.5 1.0 N9 A:A83 3.8 45.3 1.0 C1' A:A84 4.1 46.4 1.0 C4' A:A84 4.3 47.0 1.0 C2 A:C69 4.4 29.5 1.0 O A:HOH2160 4.4 39.8 1.0 N1 A:A83 4.5 41.3 1.0 C3' A:A83 4.6 38.4 1.0 C5' A:A84 4.7 43.3 1.0 C5 A:A83 4.7 42.0 1.0 C2 A:G82 4.7 35.0 1.0 N9 A:A84 4.8 36.6 1.0 O4' A:A83 4.8 43.8 1.0 C1' A:C69 4.8 31.5 1.0

L.Huang, J.Wang, D.M.J.Lilley. A Critical Base Pair in K-Turns Determines the Conformational Class Adopted, and Correlates with Biological Function. Nucleic Acids Res. V. 44 5390 2016.
ISSN: ISSN 0305-1048
PubMed: 27016741
DOI: 10.1093/NAR/GKW201