Sodium in PDB 5fk1: Sam-I Riboswitch Bearing the H. Marismortui Kt-7 Variant 3BN Is Ug

The structure of Sam-I Riboswitch Bearing the H. Marismortui Kt-7 Variant 3BN Is Ug, PDB code: 5fk1 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)	58.015 / 2.50
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	62.580, 62.580, 154.730, 90.00, 90.00, 90.00
R / Rfree (%)	23.85 / 28.9

The structure of Sam-I Riboswitch Bearing the H. Marismortui Kt-7 Variant 3BN Is Ug also contains other interesting chemical elements:

Barium

(Ba)

12 atoms

The binding sites of Sodium atom in the Sam-I Riboswitch Bearing the H. Marismortui Kt-7 Variant 3BN Is Ug (pdb code 5fk1). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Sam-I Riboswitch Bearing the H. Marismortui Kt-7 Variant 3BN Is Ug, PDB code: 5fk1:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Sam-I Riboswitch Bearing the H. Marismortui Kt-7 Variant 3BN Is Ug


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 3BN Is Ug within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1108 b:94.7 occ:1.00 O6 A:G16 3.1 0.1 1.0 N7 A:G16 3.2 0.6 1.0 C6 A:G16 3.8 0.5 1.0 C5 A:G16 3.8 0.3 1.0 O6 A:G15 4.3 0.5 1.0 N7 A:G15 4.3 0.9 1.0 C8 A:G16 4.4 0.4 1.0 C6 A:G15 4.5 0.9 1.0 O6 A:G17 4.5 0.6 1.0 C5 A:G15 4.5 0.2 1.0 BA A:BA1096 4.7 0.2 1.0 N7 A:G17 4.9 0.3 1.0 OP2 A:G16 4.9 0.8 1.0

Sodium binding site 2 out of 3 in the Sam-I Riboswitch Bearing the H. Marismortui Kt-7 Variant 3BN Is Ug


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Sam-I Riboswitch Bearing the H. Marismortui Kt-7 Variant 3BN Is Ug within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1109 b:86.2 occ:1.00 O4 A:U80 2.9 0.6 1.0 O6 A:G79 3.1 0.4 1.0 O6 A:G71 3.6 0.8 1.0 N6 A:A70 3.8 0.6 1.0 N4 A:C72 3.9 0.4 1.0 C4 A:U80 4.0 0.9 1.0 C6 A:G79 4.1 0.7 1.0 N3 A:U80 4.4 0.1 1.0 C6 A:A70 4.5 0.4 1.0 C6 A:G71 4.7 0.7 1.0 C5 A:G79 4.8 0.8 1.0 N7 A:G79 4.8 0.1 1.0 N7 A:A70 4.9 98.4 1.0 C5 A:A70 4.9 0.3 1.0 O4 A:U81 5.0 0.2 1.0

Sodium binding site 3 out of 3 in the Sam-I Riboswitch Bearing the H. Marismortui Kt-7 Variant 3BN Is Ug


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Sam-I Riboswitch Bearing the H. Marismortui Kt-7 Variant 3BN Is Ug within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1110 b:78.3 occ:1.00 O A:HOH2015 2.7 69.9 1.0 O6 A:G89 2.8 1.0 1.0 O4 A:U88 3.1 80.7 1.0 O4 A:U5 3.1 1.0 1.0 O4 A:U4 3.4 0.9 1.0 N6 A:A90 3.7 88.0 1.0 C6 A:G89 3.9 90.9 1.0 N6 A:A6 3.9 0.3 1.0 C4 A:U88 4.0 85.1 1.0 C4 A:U5 4.1 0.9 1.0 C4 A:U4 4.3 0.8 1.0 N3 A:U5 4.4 0.1 1.0 N7 A:G89 4.6 98.0 1.0 C5 A:G89 4.6 82.5 1.0 C5 A:U88 4.7 91.7 1.0 C6 A:A90 4.8 89.9 1.0 N3 A:U88 4.8 89.7 1.0 C6 A:A6 4.9 96.9 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