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

The structure of Sam-I Riboswitch Bearing the H. Marismortui Kt-7 Variant 3BN Is Cg, PDB code: 5fkg 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)	57.01 / 2.95
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	61.252, 61.252, 155.969, 90.00, 90.00, 90.00
R / Rfree (%)	23.4 / 29.9

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

Potassium	(K)	2 atoms
Barium	(Ba)	13 atoms

The binding sites of Sodium atom in the Sam-I Riboswitch Bearing the H. Marismortui Kt-7 Variant 3BN Is Cg (pdb code 5fkg). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Sam-I Riboswitch Bearing the H. Marismortui Kt-7 Variant 3BN Is Cg, PDB code: 5fkg:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Sam-I Riboswitch Bearing the H. Marismortui Kt-7 Variant 3BN Is Cg


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 Cg within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1108 b:76.8 occ:1.00 OP1 A:A62 2.4 0.8 1.0 OP2 A:G11 2.9 0.0 1.0 OP1 A:A10 3.4 0.9 1.0 P A:A62 3.9 0.5 1.0 C5' A:A62 4.3 86.7 1.0 P A:G11 4.3 0.7 1.0 P A:A10 4.4 1.0 1.0 O5' A:A62 4.5 85.8 1.0 O3' A:A61 4.5 0.4 1.0 OP2 A:A10 4.5 0.4 1.0 N7 A:G11 4.6 0.3 1.0 C8 A:G11 4.9 0.8 1.0 O5' A:G11 4.9 0.0 1.0 O5' A:A10 4.9 0.2 1.0 OP1 A:G11 4.9 0.7 1.0 OP2 A:A62 5.0 0.5 1.0

Sodium binding site 2 out of 4 in the Sam-I Riboswitch Bearing the H. Marismortui Kt-7 Variant 3BN Is Cg


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 Cg within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1109 b:74.8 occ:1.00 N7 A:G27 3.3 0.8 1.0 O6 A:G27 3.5 0.6 1.0 C5 A:U26 3.7 0.6 1.0 O6 A:G28 3.7 0.5 1.0 OP2 A:U26 3.8 0.9 1.0 C5 A:G27 4.0 0.2 1.0 C4 A:U26 4.0 0.2 1.0 C6 A:G27 4.1 0.0 1.0 C6 A:U26 4.1 0.3 1.0 N7 A:G28 4.2 0.3 1.0 O4 A:U26 4.3 0.7 1.0 C8 A:G27 4.3 0.4 1.0 C6 A:G28 4.5 0.2 1.0 O5' A:U26 4.7 0.5 1.0 N3 A:U26 4.7 0.9 1.0 C5 A:G28 4.7 0.4 1.0 N1 A:U26 4.8 0.9 1.0 OP2 A:G27 4.8 0.9 1.0 O6 A:G23 4.8 0.9 1.0 P A:U26 4.9 0.3 1.0

Sodium binding site 3 out of 4 in the Sam-I Riboswitch Bearing the H. Marismortui Kt-7 Variant 3BN Is Cg


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 Cg within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1110 b:69.1 occ:1.00 O4 A:U81 3.3 0.0 1.0 O6 A:G82 3.3 0.2 1.0 OP1 A:U67 4.1 88.5 1.0 C4 A:U81 4.2 1.0 1.0 N4 A:C69 4.2 0.2 1.0 N6 A:A70 4.4 0.7 1.0 C6 A:G82 4.5 0.9 1.0 OP2 A:G68 4.5 0.7 1.0 N6 A:A83 4.5 0.8 1.0 C5 A:U81 4.8 0.9 1.0 P A:U67 4.9 91.2 1.0 N7 A:G82 5.0 0.8 1.0

Sodium binding site 4 out of 4 in the Sam-I Riboswitch Bearing the H. Marismortui Kt-7 Variant 3BN Is Cg


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Sam-I Riboswitch Bearing the H. Marismortui Kt-7 Variant 3BN Is Cg within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1111 b:68.7 occ:1.00 O6 A:G79 2.7 95.9 1.0 O4 A:U80 2.8 0.8 1.0 O6 A:G71 3.3 1.0 1.0 N4 A:C72 3.5 0.4 1.0 C4 A:U80 3.7 0.5 1.0 C6 A:G79 3.8 97.6 1.0 N3 A:U80 3.9 89.4 1.0 N6 A:A70 4.1 0.7 1.0 C6 A:G71 4.4 0.7 1.0 C5 A:G79 4.6 96.7 1.0 N7 A:G79 4.6 86.8 1.0 C4 A:C72 4.7 0.4 1.0 N1 A:G79 4.7 0.5 1.0 C6 A:A70 4.8 0.7 1.0 O6 A:G73 4.8 0.6 1.0 O4 A:U81 5.0 0.0 1.0 C5 A:U80 5.0 0.3 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