Magnesium in PDB 5ddq: L-Glutamine Riboswitch Bound with L-Glutamine Soaked with MN2+

The structure of L-Glutamine Riboswitch Bound with L-Glutamine Soaked with MN2+, PDB code: 5ddq was solved by A.Ren, D.J.Patel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.77 / 2.40
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	60.605, 85.701, 60.889, 90.00, 99.72, 90.00
R / Rfree (%)	19.7 / 25.7

The structure of L-Glutamine Riboswitch Bound with L-Glutamine Soaked with MN2+ also contains other interesting chemical elements:

Manganese	(Mn)	5 atoms
Sodium	(Na)	12 atoms

The binding sites of Magnesium atom in the L-Glutamine Riboswitch Bound with L-Glutamine Soaked with MN2+ (pdb code 5ddq). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the L-Glutamine Riboswitch Bound with L-Glutamine Soaked with MN2+, PDB code: 5ddq:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the L-Glutamine Riboswitch Bound with L-Glutamine Soaked with MN2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of L-Glutamine Riboswitch Bound with L-Glutamine Soaked with MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg105 b:36.5 occ:1.00 OP1 A:C34 2.3 34.9 1.0 P A:C34 3.4 31.0 1.0 OP2 A:C34 3.9 30.5 1.0 O5' A:C34 4.0 34.0 1.0 OP2 A:A35 4.3 38.5 1.0 C5' A:C34 4.6 29.8 1.0 O3' A:C33 4.8 31.5 1.0

Magnesium binding site 2 out of 3 in the L-Glutamine Riboswitch Bound with L-Glutamine Soaked with MN2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of L-Glutamine Riboswitch Bound with L-Glutamine Soaked with MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg104 b:60.1 occ:1.00 O B:HOH224 2.1 54.8 1.0 O B:HOH251 2.1 51.0 1.0 O6 B:G54 3.9 45.2 1.0 O B:HOH252 3.9 42.2 1.0 O4 B:U3 4.2 49.1 1.0 N7 B:G54 4.3 43.2 1.0 O4 B:U4 4.4 52.0 1.0 N2 B:G22 4.7 40.9 1.0 C6 B:G54 4.8 42.0 1.0 O B:HOH213 4.8 44.5 1.0 C2 B:G22 4.9 45.6 1.0 C4 B:U3 4.9 54.3 1.0 C5 B:G54 4.9 42.7 1.0

Magnesium binding site 3 out of 3 in the L-Glutamine Riboswitch Bound with L-Glutamine Soaked with MN2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of L-Glutamine Riboswitch Bound with L-Glutamine Soaked with MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg105 b:43.6 occ:1.00 N7 B:G12 2.0 29.6 1.0 O B:HOH249 2.1 32.4 1.0 O B:HOH257 2.1 42.1 1.0 O B:HOH263 2.1 25.8 1.0 O B:HOH234 2.1 34.8 1.0 O B:HOH221 2.1 39.6 1.0 C8 B:G12 2.9 31.3 1.0 C5 B:G12 3.0 30.9 1.0 NA B:NA106 3.1 36.2 1.0 O B:HOH253 3.3 37.7 1.0 O6 B:G12 3.4 39.2 1.0 C6 B:G12 3.5 34.2 1.0 OP2 B:A14 3.9 34.5 1.0 N9 B:G12 4.1 36.4 1.0 C4 B:G12 4.1 32.6 1.0 N7 B:G11 4.1 27.8 1.0 O B:HOH261 4.2 37.5 1.0 OP1 B:A14 4.3 33.8 1.0 O B:HOH216 4.4 34.2 1.0 C8 B:G11 4.6 28.9 1.0 P B:A14 4.7 34.9 1.0 C5 B:G11 4.8 30.1 1.0 N1 B:G12 4.8 29.6 1.0 O B:HOH245 4.9 32.6 1.0

A.Ren, Y.Xue, A.Peselis, A.Serganov, H.M.Al-Hashimi, D.J.Patel. Structural and Dynamic Basis For Low-Affinity, High-Selectivity Binding of L-Glutamine By the Glutamine Riboswitch. Cell Rep V. 13 1800 2015.
ISSN: ESSN 2211-1247
PubMed: 26655897
DOI: 10.1016/J.CELREP.2015.10.062