Manganese 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:

Magnesium	(Mg)	3 atoms
Sodium	(Na)	12 atoms

The binding sites of Manganese 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 Manganese atom.
In total 5 binding sites of Manganese where determined in the L-Glutamine Riboswitch Bound with L-Glutamine Soaked with MN2+, PDB code: 5ddq:
Jump to Manganese binding site number: 1; 2; 3; 4; 5;

Manganese binding site 1 out of 5 in the L-Glutamine Riboswitch Bound with L-Glutamine Soaked with MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn 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:Mn102 b:32.0 occ:1.00 OXT A:GLN101 2.2 31.5 1.0 O A:HOH222 2.2 33.1 1.0 O A:HOH227 2.2 36.2 1.0 O A:HOH215 2.2 26.9 1.0 O A:HOH247 2.2 26.8 1.0 O A:HOH239 2.3 34.6 1.0 O A:GLN101 2.4 36.3 1.0 C A:GLN101 2.7 31.7 1.0 N2 A:G54 3.7 33.8 1.0 OP2 A:A57 4.0 34.2 1.0 O6 A:G22 4.1 34.5 1.0 OP1 A:G54 4.1 27.8 1.0 N7 A:G22 4.2 33.1 1.0 CA A:GLN101 4.2 34.0 1.0 N7 A:A57 4.4 40.1 1.0 OP2 A:A56 4.5 30.7 1.0 C2 A:G54 4.5 35.4 1.0 CG A:GLN101 4.7 33.8 1.0 CB A:GLN101 4.8 31.5 1.0 C6 A:G22 4.8 32.8 1.0 C8 A:A57 4.9 37.6 1.0 N1 A:G54 4.9 35.9 1.0 C5 A:G22 4.9 33.7 1.0

Manganese binding site 2 out of 5 in the L-Glutamine Riboswitch Bound with L-Glutamine Soaked with MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn 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 A:Mn103 b:66.7 occ:1.00 O A:HOH286 2.2 39.5 1.0 O A:HOH250 2.3 43.8 1.0 O A:HOH240 2.3 36.1 1.0 O A:HOH258 2.3 47.9 1.0 O A:HOH280 2.3 38.6 1.0 N7 A:G12 2.3 36.7 1.0 NA A:NA107 3.2 38.6 1.0 C5 A:G12 3.2 37.4 1.0 O6 A:G12 3.3 39.7 1.0 C8 A:G12 3.4 37.5 1.0 C6 A:G12 3.6 39.7 1.0 O A:HOH287 4.0 39.6 1.0 OP1 A:A14 4.3 42.9 1.0 N7 A:G11 4.4 40.2 1.0 OP2 A:A14 4.4 35.8 1.0 C4 A:G12 4.4 35.9 1.0 N9 A:G12 4.5 32.0 1.0 O A:HOH285 4.5 37.4 1.0 O A:HOH208 4.6 35.7 1.0 C8 A:G11 4.9 38.6 1.0 P A:A14 4.9 39.0 1.0 N1 A:G12 4.9 35.8 1.0

Manganese binding site 3 out of 5 in the L-Glutamine Riboswitch Bound with L-Glutamine Soaked with MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn 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 A:Mn104 b:59.0 occ:1.00 OP1 A:A24 4.0 29.4 1.0 O2' A:G23 4.6 33.0 1.0 O2' A:G61 4.8 48.6 1.0 C2' A:G23 4.8 31.2 1.0 C3' A:G23 4.8 29.8 1.0

Manganese binding site 4 out of 5 in the L-Glutamine Riboswitch Bound with L-Glutamine Soaked with MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of L-Glutamine Riboswitch Bound with L-Glutamine Soaked with MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn102 b:59.1 occ:1.00 OP2 B:G26 2.8 54.1 1.0 P B:G26 3.7 51.8 1.0 O3' B:A25 4.0 45.6 1.0 OP1 B:G26 4.1 53.4 1.0 O2' B:A25 4.2 31.7 1.0 C3' B:A25 4.6 42.2 1.0 OP1 B:A24 4.9 37.0 1.0 C2' B:A25 4.9 38.9 1.0

Manganese binding site 5 out of 5 in the L-Glutamine Riboswitch Bound with L-Glutamine Soaked with MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of L-Glutamine Riboswitch Bound with L-Glutamine Soaked with MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn103 b:43.2 occ:1.00 O B:GLN101 2.2 39.7 1.0 O B:HOH227 2.2 41.5 1.0 O B:HOH238 2.2 43.7 1.0 O B:HOH230 2.2 33.5 1.0 O B:HOH255 2.2 37.2 1.0 O B:HOH228 2.2 37.2 1.0 C B:GLN101 3.2 40.0 1.0 OXT B:GLN101 3.3 42.2 1.0 N2 B:G54 4.0 42.4 1.0 OP2 B:A57 4.0 49.5 1.0 OP1 B:G54 4.2 39.4 1.0 N7 B:A57 4.3 48.9 1.0 O6 B:G22 4.3 49.3 1.0 N7 B:G22 4.3 37.9 1.0 OP2 B:A56 4.4 44.2 1.0 CA B:GLN101 4.6 36.9 1.0 C2 B:G54 4.6 41.4 1.0 O B:HOH242 4.7 37.9 1.0 C8 B:A57 4.8 50.3 1.0 CG B:GLN101 4.8 39.2 1.0 N1 B:G54 4.9 41.1 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