Sodium in PDB 6n2v: Manganese Riboswitch From Xanthmonas Oryzae Bound to Mn(II)

The structure of Manganese Riboswitch From Xanthmonas Oryzae Bound to Mn(II), PDB code: 6n2v was solved by I.R.Price, A.Ke, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	62.64 / 2.85
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	81.296, 85.167, 92.463, 90.00, 90.00, 90.00
R / Rfree (%)	20.9 / 22.1

The structure of Manganese Riboswitch From Xanthmonas Oryzae Bound to Mn(II) also contains other interesting chemical elements:

Strontium	(Sr)	9 atoms
Magnesium	(Mg)	39 atoms
Manganese	(Mn)	7 atoms

The binding sites of Sodium atom in the Manganese Riboswitch From Xanthmonas Oryzae Bound to Mn(II) (pdb code 6n2v). 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 Manganese Riboswitch From Xanthmonas Oryzae Bound to Mn(II), PDB code: 6n2v:

Sodium binding site 1 out of 1 in the Manganese Riboswitch From Xanthmonas Oryzae Bound to Mn(II)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Manganese Riboswitch From Xanthmonas Oryzae Bound to Mn(II) within 5.0Å range: probe atom residue distance (Å) B Occ B:Na128 b:84.2 occ:1.00 N7 B:G14 2.1 72.4 1.0 OP2 B:A13 2.5 62.1 1.0 C8 B:G14 3.1 69.3 1.0 C5 B:G14 3.1 67.5 1.0 O6 B:G14 3.4 67.4 1.0 C6 B:G14 3.6 65.2 1.0 P B:A13 3.7 63.0 1.0 O5' B:A13 4.0 58.9 1.0 N9 B:G14 4.3 68.4 1.0 C4 B:G14 4.3 68.0 1.0 N2 B:G89 4.4 60.7 1.0 OP1 B:A13 4.4 62.9 1.0 N7 B:A13 4.7 58.9 1.0 OP2 B:G14 4.7 72.5 1.0 C8 B:A13 4.7 59.0 1.0 N1 B:G14 5.0 65.7 1.0 O3' B:U12 5.0 55.5 1.0

K.C.Suddala, I.R.Price, S.S.Dandpat, M.Janecek, P.Kuhrova, J.Sponer, P.Banas, A.Ke, N.G.Walter. Local-to-Global Signal Transduction at the Core of A MN2+Sensing Riboswitch. Nat Commun V. 10 4304 2019.
ISSN: ESSN 2041-1723
PubMed: 31541094
DOI: 10.1038/S41467-019-12230-5