Sodium in PDB 5ndh: The Structure of the G. Violaceus Guanidine II Riboswitch P2 Stem-Loop

The structure of The Structure of the G. Violaceus Guanidine II Riboswitch P2 Stem-Loop, PDB code: 5ndh 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)	50.17 / 1.81
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	48.727, 57.825, 100.862, 90.00, 90.00, 90.00
R / Rfree (%)	20.7 / 22.2

The structure of The Structure of the G. Violaceus Guanidine II Riboswitch P2 Stem-Loop also contains other interesting chemical elements:

Magnesium	(Mg)	1 atom
Bromine	(Br)	4 atoms

The binding sites of Sodium atom in the The Structure of the G. Violaceus Guanidine II Riboswitch P2 Stem-Loop (pdb code 5ndh). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the The Structure of the G. Violaceus Guanidine II Riboswitch P2 Stem-Loop, PDB code: 5ndh:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the The Structure of the G. Violaceus Guanidine II Riboswitch P2 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 P2 Stem-Loop within 5.0Å range: probe atom residue distance (Å) B Occ A:Na102 b:73.7 occ:1.00 O C:HOH220 2.6 44.3 1.0 HO2' A:C8 3.4 44.1 1.0 O2' A:C8 3.5 36.8 1.0 O4' A:G9 3.9 37.2 1.0 H1' A:G9 4.3 42.4 1.0 H5' C:C11 4.3 41.3 1.0 H4' C:C11 4.3 48.6 1.0 H2' A:C8 4.4 48.0 1.0 O2 A:C8 4.4 36.7 1.0 H22 C:G9 4.4 43.0 1.0 C2' A:C8 4.5 40.0 1.0 H5' A:G9 4.5 44.1 1.0 O4' C:C11 4.5 36.7 1.0 H4' A:G9 4.6 42.4 1.0 H21 C:G9 4.6 43.0 1.0 C1' A:G9 4.7 35.3 1.0 O A:HOH210 4.7 47.7 1.0 H1' A:C8 4.7 40.1 1.0 H62 A:A10 4.7 49.4 1.0 C4' A:G9 4.8 35.3 1.0 O2' C:A10 4.8 61.5 1.0 C4' C:C11 4.8 40.5 1.0 HO2' C:A10 4.9 73.7 1.0 N2 C:G9 4.9 35.9 1.0

Sodium binding site 2 out of 4 in the The Structure of the G. Violaceus Guanidine II Riboswitch P2 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 P2 Stem-Loop within 5.0Å range: probe atom residue distance (Å) B Occ B:Na102 b:58.5 occ:1.00 O6 B:G3 2.9 32.2 1.0 O B:HOH208 3.3 39.3 1.0 N7 B:G3 3.4 36.4 1.0 HN42 B:CBV2 3.5 48.3 1.0 N4 B:CBV2 3.5 40.3 1.0 O6 B:G4 3.6 33.4 1.0 HN41 B:CBV2 3.6 48.3 1.0 C6 B:G3 3.7 32.0 1.0 C4 B:CBV2 3.8 35.2 1.0 C5 B:G3 3.9 33.6 1.0 H42 B:C14 4.1 41.1 1.0 C5 B:CBV2 4.3 46.3 1.0 H42 B:C13 4.4 47.4 1.0 N7 B:G4 4.4 34.8 1.0 C6 B:G4 4.4 36.2 1.0 N3 B:CBV2 4.5 34.7 1.0 BR B:CBV2 4.6 66.3 1.0 O6 B:G15 4.6 36.1 1.0 C8 B:G3 4.6 40.7 1.0 C5 B:G4 4.7 35.2 1.0 N4 B:C14 4.7 34.3 1.0 H41 B:C14 4.8 41.1 1.0 H41 B:C13 4.8 47.4 1.0 H1 B:G15 4.9 41.6 1.0 N4 B:C13 4.9 39.5 1.0 N1 B:G3 5.0 36.7 1.0 H8 B:G3 5.0 48.8 1.0

Sodium binding site 3 out of 4 in the The Structure of the G. Violaceus Guanidine II Riboswitch P2 Stem-Loop


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of The Structure of the G. Violaceus Guanidine II Riboswitch P2 Stem-Loop within 5.0Å range: probe atom residue distance (Å) B Occ B:Na103 b:63.1 occ:1.00 H22 B:G1 2.7 47.8 1.0 H1' B:CBV2 3.2 67.3 1.0 N2 B:G1 3.5 39.9 1.0 O C:HOH221 3.9 58.1 1.0 O4' B:CBV2 3.9 50.4 1.0 H21 B:G1 3.9 47.8 1.0 C1' B:CBV2 4.0 56.1 1.0 O C:HOH207 4.0 50.7 1.0 HO2' B:CBV2 4.2 49.3 1.0 N3 B:G1 4.5 40.7 1.0 C2 B:G1 4.5 40.6 1.0 O B:HOH213 4.5 57.1 1.0 O2' B:CBV2 4.6 41.1 1.0 HO2' B:G1 4.6 54.1 1.0 H4' B:CBV2 4.6 58.8 1.0 H22 C:G1 4.7 47.4 1.0 N1 B:CBV2 4.9 36.1 1.0 C4' B:CBV2 4.9 49.0 1.0 C2' B:CBV2 5.0 64.0 1.0 O2 B:CBV2 5.0 34.9 1.0

Sodium binding site 4 out of 4 in the The Structure of the G. Violaceus Guanidine II Riboswitch P2 Stem-Loop


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of The Structure of the G. Violaceus Guanidine II Riboswitch P2 Stem-Loop within 5.0Å range: probe atom residue distance (Å) B Occ C:Na102 b:59.4 occ:1.00 O2' C:C8 3.1 40.7 1.0 O2 C:C8 3.1 45.1 1.0 HO2' C:C8 3.3 48.8 1.0 H4' A:C11 3.3 49.4 1.0 H1' C:C8 3.5 57.8 1.0 O4' A:C11 3.5 41.7 1.0 H21 A:G9 3.7 48.0 1.0 H5' A:C11 3.7 54.6 1.0 H2' C:C8 3.7 64.1 1.0 C2' C:C8 3.8 53.4 1.0 C4' A:C11 3.8 41.2 1.0 H22 A:G9 3.9 48.0 1.0 O4' C:G9 4.0 45.6 1.0 C1' C:C8 4.1 48.2 1.0 N2 A:G9 4.2 40.0 1.0 H1' A:C11 4.3 44.0 1.0 C5' A:C11 4.3 45.5 1.0 H1' C:G9 4.3 51.5 1.0 C2 C:C8 4.3 45.0 1.0 C1' A:C11 4.5 36.7 1.0 HO2' A:A10 4.5 63.4 1.0 O2' A:A10 4.5 52.9 1.0 H5'' A:C11 4.6 54.6 1.0 C1' C:G9 4.7 42.9 1.0 N1 C:C8 4.7 45.8 1.0 H5' C:G9 4.8 53.4 1.0 H4' C:G9 4.9 47.1 1.0 O2' A:C11 4.9 43.5 1.0 C4' C:G9 5.0 39.2 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