Magnesium in PDB 6qn3: Structure of the Glutamine II Riboswitch

The structure of Structure of the Glutamine II Riboswitch, PDB code: 6qn3 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)	47.00 / 2.30
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	76.502, 115.725, 80.582, 90.00, 90.00, 90.00
R / Rfree (%)	24.2 / 29.4

The structure of Structure of the Glutamine II Riboswitch also contains other interesting chemical elements:

Bromine

(Br)

4 atoms

The binding sites of Magnesium atom in the Structure of the Glutamine II Riboswitch (pdb code 6qn3). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Structure of the Glutamine II Riboswitch, PDB code: 6qn3:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Structure of the Glutamine II Riboswitch


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of the Glutamine II Riboswitch within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg101 b:76.2 occ:1.00 O6 B:G35 4.1 74.9 1.0 O4 A:U3 4.2 56.8 1.0 O4 A:U4 4.2 54.6 1.0 N4 A:C5 4.4 59.0 1.0 OP2 A:G18 4.4 93.8 1.0 N7 B:G35 4.6 69.4 1.0 C5 A:U3 4.7 56.1 1.0 C4 A:U3 4.8 58.8 1.0

Magnesium binding site 2 out of 4 in the Structure of the Glutamine II Riboswitch


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of the Glutamine II Riboswitch within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg104 b:77.9 occ:1.00 O B:GLN205 2.3 0.6 1.0 OXT B:GLN205 3.1 0.5 1.0 C B:GLN205 3.1 1.0 1.0 O6 B:G18 3.8 69.8 1.0 OP2 A:A38 3.8 84.1 1.0 OP2 A:A37 3.8 66.6 1.0 N2 A:G35 3.9 68.3 1.0 N7 A:A38 4.0 78.1 1.0 N7 B:G18 4.2 55.6 1.0 C8 A:A38 4.4 66.8 1.0 C2 A:G35 4.5 69.3 1.0 N1 A:G35 4.6 58.2 1.0 CA B:GLN205 4.6 81.4 1.0 OP1 A:G35 4.7 61.1 1.0 C6 B:G18 4.7 61.0 1.0 C8 A:A37 4.8 62.5 1.0 C5 B:G18 4.9 46.8 1.0 N7 A:A37 4.9 61.0 1.0

Magnesium binding site 3 out of 4 in the Structure of the Glutamine II Riboswitch


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of the Glutamine II Riboswitch within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg201 b:61.5 occ:1.00 O A:HOH306 1.9 30.0 1.0 O B:HOH401 2.0 30.0 1.0 O B:HOH407 2.1 30.0 1.0 O B:HOH406 2.1 30.0 1.0 O A:HOH307 2.2 30.0 1.0 OXT A:GLN105 2.4 71.3 1.0 C A:GLN105 3.3 77.0 1.0 O A:GLN105 3.4 69.8 1.0 OP2 B:A38 3.8 50.0 1.0 OP2 B:A37 3.9 66.6 1.0 N2 B:G35 3.9 47.8 1.0 N7 A:G18 4.0 47.4 1.0 O6 A:G18 4.2 62.2 1.0 OP1 B:G35 4.2 62.6 1.0 N7 B:A38 4.2 57.6 1.0 C2 B:G35 4.5 47.3 1.0 C8 B:A38 4.7 56.9 1.0 CA A:GLN105 4.8 68.3 1.0 C5 A:G18 4.8 50.9 1.0 N1 B:G35 4.8 53.6 1.0 C6 A:G18 4.9 65.3 1.0 CG A:GLN105 5.0 69.7 1.0 C8 A:G18 5.0 50.7 1.0

Magnesium binding site 4 out of 4 in the Structure of the Glutamine II Riboswitch


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of the Glutamine II Riboswitch within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg202 b:80.6 occ:1.00 O6 A:G35 4.0 66.6 1.0 O4 B:U3 4.1 57.7 1.0 N7 A:G35 4.2 53.9 1.0 O4 B:U4 4.4 68.5 1.0 N4 B:C5 4.7 69.5 1.0 C6 A:G35 4.8 56.8 1.0 O6 A:G36 4.9 68.3 1.0 C4 B:U3 4.9 66.6 1.0 C5 A:G35 4.9 55.4 1.0 N2 B:G18 4.9 47.4 1.0 OP2 B:G18 5.0 60.4 1.0 C5 B:U3 5.0 73.1 1.0

L.Huang, J.Wang, A.M.Watkins, R.Das, D.M.J.Lilley. Structure and Ligand Binding of the Glutamine-II Riboswitch. Nucleic Acids Res. V. 47 7666 2019.
ISSN: ESSN 1362-4962
PubMed: 31216023
DOI: 10.1093/NAR/GKZ539