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

The structure of Sam-I Riboswitch Bearing the H. Marismortui Kt-7 Variant 3BN Is Uc, PDB code: 5fkf 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)	57.410 / 2.80
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	61.810, 61.810, 154.940, 90.00, 90.00, 90.00
R / Rfree (%)	20.45 / 25.75

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

Potassium	(K)	2 atoms
Barium	(Ba)	12 atoms

The binding sites of Sodium atom in the Sam-I Riboswitch Bearing the H. Marismortui Kt-7 Variant 3BN Is Uc (pdb code 5fkf). 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 Uc, PDB code: 5fkf:
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 Uc


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 Uc within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1105 b:34.8 occ:1.00 OP2 A:A62 2.7 0.7 1.0 OP2 A:C65 3.0 66.9 1.0 OP2 A:U64 3.3 62.0 1.0 O5' A:U64 3.4 73.8 1.0 P A:U64 4.0 74.4 1.0 P A:A62 4.2 91.8 1.0 P A:C65 4.5 62.1 1.0 C5' A:U64 4.5 58.1 1.0 C5' A:A61 4.6 78.6 1.0 OP1 A:C60 4.7 69.8 1.0 C4' A:U64 4.7 56.5 1.0 C5' A:C65 4.8 49.3 1.0 O5' A:A62 4.9 62.7 1.0 OP1 A:U64 4.9 79.7 1.0

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


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 Uc within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1108 b:36.1 occ:1.00 O6 A:G82 2.9 74.7 1.0 O4 A:U81 3.3 83.6 1.0 C6 A:G82 4.0 74.1 1.0 N4 A:C69 4.1 78.8 1.0 C4 A:U81 4.2 69.1 1.0 OP1 A:U67 4.2 59.3 1.0 N7 A:G82 4.4 86.2 1.0 N6 A:A83 4.4 67.0 1.0 C5 A:G82 4.6 79.3 1.0 C5 A:U81 4.7 68.8 1.0 OP2 A:G68 4.7 79.9 1.0 N6 A:A70 4.8 87.7 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