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

The structure of Sam-I Riboswitch Bearing the H. Marismortui Kt-7 Variant 3BN Is Gu, PDB code: 5fke 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)	58.071 / 2.80
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	62.670, 62.670, 154.430, 90.00, 90.00, 90.00
R / Rfree (%)	24.66 / 30.58

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

Barium	(Ba)	16 atoms
Potassium	(K)	1 atom

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

Sodium binding site 1 out of 2 in the Sam-I Riboswitch Bearing the H. Marismortui Kt-7 Variant 3BN Is Gu


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 Gu within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1110 b:0.7 occ:1.00 O4 A:U81 3.1 0.7 1.0 O6 A:G82 3.3 0.7 1.0 C4 A:U81 3.8 0.5 1.0 OP1 A:U67 4.1 0.7 1.0 C5 A:U81 4.3 0.7 1.0 C6 A:G82 4.3 0.7 1.0 N7 A:G82 4.5 0.1 1.0 N6 A:A70 4.5 0.9 1.0 N4 A:C69 4.5 0.2 1.0 C5 A:G82 4.8 0.6 1.0 N3 A:U81 4.9 0.8 1.0 OP2 A:G68 4.9 0.1 1.0

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


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 Gu within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1122 b:0.6 occ:1.00 K A:K1111 3.1 0.6 1.0 O4 A:U88 4.9 0.7 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