Sodium in PDB 5nom: The Structure of the G. Violaceus Guanidine II Riboswitch P1 Stem-Loop with Guanidine

The structure of The Structure of the G. Violaceus Guanidine II Riboswitch P1 Stem-Loop with Guanidine, PDB code: 5nom was solved by L.Huang, J.Wang, D.M.J.Lilley, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.19 / 1.93
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	55.700, 55.700, 132.580, 90.00, 90.00, 120.00
R / Rfree (%)	19.7 / 22.4

The structure of The Structure of the G. Violaceus Guanidine II Riboswitch P1 Stem-Loop with Guanidine also contains other interesting chemical elements:

Bromine

(Br)

1 atom

The binding sites of Sodium atom in the The Structure of the G. Violaceus Guanidine II Riboswitch P1 Stem-Loop with Guanidine (pdb code 5nom). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the The Structure of the G. Violaceus Guanidine II Riboswitch P1 Stem-Loop with Guanidine, PDB code: 5nom:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the The Structure of the G. Violaceus Guanidine II Riboswitch P1 Stem-Loop with Guanidine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of The Structure of the G. Violaceus Guanidine II Riboswitch P1 Stem-Loop with Guanidine within 5.0Å range: probe atom residue distance (Å) B Occ A:Na103 b:58.3 occ:1.00 H22 A:G1 2.6 45.1 1.0 H1' A:G2 3.1 45.8 1.0 N2 A:G1 3.5 37.6 1.0 C1' A:G2 4.0 38.2 1.0 H21 A:G1 4.0 45.1 1.0 O4' A:G2 4.1 43.6 1.0 N3 A:G1 4.2 35.8 1.0 C2 A:G1 4.3 35.5 1.0 O2' A:G2 4.3 36.7 1.0 H4' A:G2 4.7 53.0 1.0 C2' A:G2 4.8 30.7 1.0 HO2' A:G2 4.9 44.0 1.0 N9 A:G2 4.9 32.5 1.0

Sodium binding site 2 out of 2 in the The Structure of the G. Violaceus Guanidine II Riboswitch P1 Stem-Loop with Guanidine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of The Structure of the G. Violaceus Guanidine II Riboswitch P1 Stem-Loop with Guanidine within 5.0Å range: probe atom residue distance (Å) B Occ A:Na104 b:86.0 occ:1.00 O A:HOH204 3.6 58.0 1.0 OP2 A:A11 3.7 51.4 1.0 H41 A:C12 4.4 68.4 1.0 H41 A:C13 4.6 47.3 1.0 H42 A:C12 4.6 68.4 1.0 H42 A:C13 4.6 47.3 1.0 O6 A:G6 4.7 37.8 1.0 P A:A11 4.7 61.7 1.0 O5' A:G10 4.8 50.4 1.0 OP2 A:G10 4.8 41.2 1.0 N4 A:C12 4.8 57.0 1.0 OP1 A:A11 4.9 70.4 1.0 OP1 A:G10 4.9 61.9 1.0 H3' A:G10 4.9 63.0 1.0 O6 A:G7 4.9 38.6 1.0 N4 A:C13 5.0 39.4 1.0

L.Huang, J.Wang, D.M.J.Lilley. The Structure of the Guanidine-II Riboswitch. Cell Chem Biol V. 24 695 2017.
ISSN: ESSN 2451-9456
PubMed: 28529131
DOI: 10.1016/J.CHEMBIOL.2017.05.014