Magnesium 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:

Bromine	(Br)	4 atoms
Sodium	(Na)	4 atoms

The binding sites of Magnesium 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 Magnesium atom.
In total only one binding site of Magnesium was determined in the The Structure of the G. Violaceus Guanidine II Riboswitch P2 Stem-Loop, PDB code: 5ndh:

Magnesium binding site 1 out of 1 in the The Structure of the G. Violaceus Guanidine II Riboswitch P2 Stem-Loop


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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:Mg103 b:47.0 occ:1.00 HO2' A:G15 1.9 44.0 1.0 O A:HOH216 2.1 41.5 1.0 O A:HOH218 2.5 42.4 1.0 O2' A:G15 2.7 36.6 1.0 H1' A:G15 2.8 43.9 1.0 N3 A:G15 2.9 33.0 1.0 H22 A:G15 3.2 48.5 1.0 H2' A:G15 3.2 42.9 1.0 C2' A:G15 3.2 35.8 1.0 C1' A:G15 3.4 36.6 1.0 O4' A:C16 3.5 35.0 1.0 O A:HOH205 3.6 38.5 1.0 C2 A:G15 3.8 39.7 1.0 N2 A:G15 3.8 40.4 1.0 H1' A:C16 3.9 44.5 1.0 C4 A:G15 3.9 42.8 1.0 N9 A:G15 4.1 37.9 1.0 H5' A:C16 4.2 43.1 1.0 H4' A:C16 4.2 44.3 1.0 C1' A:C16 4.2 37.1 1.0 C4' A:C16 4.3 36.9 1.0 O4' A:G15 4.6 35.7 1.0 H22 A:G3 4.6 44.2 1.0 H21 A:G15 4.6 48.5 1.0 C3' A:G15 4.7 35.2 1.0 C5' A:C16 4.8 35.9 1.0 N1 A:C16 5.0 40.9 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