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

The structure of The Structure of the G. Violaceus Guanidine II Riboswitch P1 Stem-Loop, PDB code: 5neo 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)	27.65 / 1.69
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	55.302, 55.302, 130.164, 90.00, 90.00, 120.00
R / Rfree (%)	21.6 / 23

The structure of The Structure of the G. Violaceus Guanidine II Riboswitch P1 Stem-Loop 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 (pdb code 5neo). 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, PDB code: 5neo:
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


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na102 b:64.0 occ:1.00 HN42 A:CBV17 2.6 50.7 1.0 N4 A:CBV17 3.3 42.2 1.0 HN41 A:CBV17 3.4 50.7 1.0 H62 A:A16 4.2 39.0 1.0 BR A:CBV17 4.3 38.2 1.0 H41 A:C18 4.4 40.9 1.0 C4 A:CBV17 4.6 30.2 1.0 N6 A:A16 4.8 32.5 1.0 O6 A:G2 4.8 38.8 1.0 H42 A:C18 4.9 40.9 1.0 N4 A:C18 5.0 34.1 1.0

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


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na103 b:69.0 occ:1.00 H22 A:G1 2.8 45.1 1.0 H1' A:G2 3.2 37.9 1.0 N2 A:G1 3.6 37.6 1.0 HO2' A:G2 3.9 43.8 1.0 H21 A:G1 4.0 45.1 1.0 C1' A:G2 4.1 31.6 1.0 O2' A:G2 4.2 36.5 1.0 O4' A:G2 4.2 35.9 1.0 C2 A:G1 4.6 34.3 1.0 H4' A:G2 4.6 46.3 1.0 N3 A:G1 4.6 33.7 1.0 C2' A:G2 4.8 45.4 1.0 HO2' A:G1 4.8 45.6 1.0 C4' A:G2 5.0 38.6 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