Sodium in PDB 6tfh: Crystal Structure of the Adp-Binding Domain of the Nad+ Riboswitch with Nicotinamide Adenine Dinucleotide, Reduced (Nadh); Soaking with Manganese(II) (MN2+)

The structure of Crystal Structure of the Adp-Binding Domain of the Nad+ Riboswitch with Nicotinamide Adenine Dinucleotide, Reduced (Nadh); Soaking with Manganese(II) (MN2+), PDB code: 6tfh 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)	48.49 / 2.95
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	56.935, 58.360, 193.968, 90.00, 90.00, 90.00
R / Rfree (%)	22.1 / 26.6

The structure of Crystal Structure of the Adp-Binding Domain of the Nad+ Riboswitch with Nicotinamide Adenine Dinucleotide, Reduced (Nadh); Soaking with Manganese(II) (MN2+) also contains other interesting chemical elements:

Manganese	(Mn)	9 atoms
Bromine	(Br)	1 atom

The binding sites of Sodium atom in the Crystal Structure of the Adp-Binding Domain of the Nad+ Riboswitch with Nicotinamide Adenine Dinucleotide, Reduced (Nadh); Soaking with Manganese(II) (MN2+) (pdb code 6tfh). 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 Nicotinamide Adenine Dinucleotide, Reduced (Nadh); Soaking with Manganese(II) (MN2+), PDB code: 6tfh:

Sodium binding site 1 out of 1 in the Crystal Structure of the Adp-Binding Domain of the Nad+ Riboswitch with Nicotinamide Adenine Dinucleotide, Reduced (Nadh); Soaking with Manganese(II) (MN2+)


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 Nicotinamide Adenine Dinucleotide, Reduced (Nadh); Soaking with Manganese(II) (MN2+) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na111 b:1.0 occ:1.00 OP1 A:A30 2.9 91.8 1.0 OP2 A:A30 3.6 72.2 1.0 O6 A:G28 3.6 0.8 1.0 N7 A:G28 3.6 0.7 1.0 P A:A30 3.7 75.5 1.0 C5 A:G28 3.9 0.2 1.0 C6 A:G28 4.0 0.9 1.0 O3' A:A29 4.3 81.9 1.0 C8 A:G28 4.5 0.4 1.0 C5' A:A29 4.9 85.5 1.0 C4 A:G28 5.0 0.4 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