Sodium in PDB 6fz0: Crystal Structure of the Mety Sam V Riboswitch

The structure of Crystal Structure of the Mety Sam V Riboswitch, PDB code: 6fz0 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)	44.11 / 2.50
Space group	P 41 2 2
Cell size a, b, c (Å), α, β, γ (°)	87.828, 87.828, 62.670, 90.00, 90.00, 90.00
R / Rfree (%)	23.1 / 27

The structure of Crystal Structure of the Mety Sam V Riboswitch also contains other interesting chemical elements:

Magnesium	(Mg)	1 atom
Bromine	(Br)	1 atom

The binding sites of Sodium atom in the Crystal Structure of the Mety Sam V Riboswitch (pdb code 6fz0). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of the Mety Sam V Riboswitch, PDB code: 6fz0:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of the Mety Sam V Riboswitch


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 Mety Sam V Riboswitch within 5.0Å range: probe atom residue distance (Å) B Occ A:Na102 b:75.8 occ:1.00 OP1 A:U17 2.4 60.1 1.0 O A:HOH201 2.6 54.6 1.0 P A:U17 3.6 59.8 1.0 O3' A:G16 3.7 58.7 1.0 HA A:SAM104 3.9 76.1 1.0 HG1 A:SAM104 4.0 79.5 1.0 C5' A:U17 4.4 56.1 1.0 OP2 A:U8 4.4 81.5 1.0 O5' A:U17 4.5 55.3 1.0 OP2 A:A18 4.6 46.4 1.0 OP2 A:U17 4.8 68.8 1.0 CA A:SAM104 4.9 63.6 1.0 OP1 A:A18 5.0 56.5 1.0 CG A:SAM104 5.0 66.4 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of the Mety Sam V Riboswitch


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of the Mety Sam V Riboswitch within 5.0Å range: probe atom residue distance (Å) B Occ A:Na103 b:87.8 occ:1.00 OP2 A:A51 2.4 0.0 1.0 O A:HOH211 2.6 65.0 1.0 P A:A51 3.8 84.1 1.0 O3' A:G11 4.1 74.0 1.0 N3 A:G11 4.3 58.6 1.0 OP1 A:A12 4.3 0.7 1.0 C1' A:G11 4.4 68.9 1.0 O5' A:A51 4.5 66.3 1.0 C3' A:A50 4.6 68.8 1.0 OP1 A:A51 4.7 81.7 1.0 C5' A:A50 4.7 58.0 1.0 O3' A:A50 4.7 81.7 1.0 O4' A:G11 4.8 69.2 1.0 P A:A12 4.9 86.0 1.0 N2 A:G11 4.9 74.1 1.0 O4 A:U15 4.9 59.5 1.0

L.Huang, D.M.J.Lilley. Structure and Ligand Binding of the Sam-V Riboswitch. Nucleic Acids Res. V. 46 6869 2018.
ISSN: ESSN 1362-4962
PubMed: 29931337
DOI: 10.1093/NAR/GKY520