Magnesium in PDB 5ddr: L-Glutamine Riboswitch Bound with L-Glutamine Soaked with Cs+

The structure of L-Glutamine Riboswitch Bound with L-Glutamine Soaked with Cs+, PDB code: 5ddr 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)	29.37 / 2.61
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	60.967, 86.882, 62.218, 90.00, 102.61, 90.00
R / Rfree (%)	21.2 / 27.1

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

Potassium	(K)	7 atoms
Caesium	(Cs)	7 atoms
Sodium	(Na)	4 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 11;

Binding sites:

The binding sites of Magnesium atom in the L-Glutamine Riboswitch Bound with L-Glutamine Soaked with Cs+ (pdb code 5ddr). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 11 binding sites of Magnesium where determined in the L-Glutamine Riboswitch Bound with L-Glutamine Soaked with Cs+, PDB code: 5ddr:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 11 in the L-Glutamine Riboswitch Bound with L-Glutamine Soaked with Cs+


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 Cs+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg106 b:40.2 occ:1.00 O A:HOH217 2.1 32.7 1.0 O A:HOH265 2.1 37.2 1.0 O A:HOH219 2.1 32.6 1.0 O A:HOH310 2.1 31.4 1.0 O A:HOH305 2.1 35.2 1.0 O A:HOH264 2.2 30.7 1.0 O A:HOH223 3.8 38.8 1.0 O6 A:G19 3.9 34.8 1.0 N7 A:G18 3.9 29.5 1.0 O A:HOH228 3.9 32.3 1.0 N7 A:G19 4.0 30.8 1.0 O6 A:G18 4.2 31.0 1.0 CS A:CS113 4.3 65.1 1.0 C5 A:G18 4.6 29.3 1.0 C6 A:G19 4.6 34.7 1.0 C5 A:G19 4.7 33.1 1.0 C6 A:G18 4.7 31.2 1.0 C8 A:G18 4.8 31.3 1.0

Magnesium binding site 2 out of 11 in the L-Glutamine Riboswitch Bound with L-Glutamine Soaked with Cs+


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 Cs+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg107 b:42.2 occ:1.00 O A:HOH225 2.0 35.6 1.0 O A:HOH210 2.0 35.4 1.0 O A:HOH254 2.0 36.6 1.0 O A:GLN101 2.1 35.8 1.0 O A:HOH201 2.1 41.7 1.0 O A:HOH245 2.1 39.8 1.0 C A:GLN101 3.1 37.5 1.0 OXT A:GLN101 3.4 39.5 1.0 N2 A:G54 3.6 39.0 1.0 O6 A:G22 3.8 37.5 1.0 N7 A:G22 4.0 36.4 1.0 OP1 A:G54 4.1 33.1 1.0 C2 A:G54 4.2 36.5 1.0 CA A:GLN101 4.4 38.3 1.0 OP2 A:A56 4.5 39.3 1.0 CG A:GLN101 4.5 36.6 1.0 OP2 A:A57 4.5 51.1 1.0 N7 A:A57 4.6 43.2 1.0 C6 A:G22 4.6 36.0 1.0 C5 A:G22 4.7 35.8 1.0 N1 A:G54 4.7 36.7 1.0 CB A:GLN101 4.8 38.3 1.0 N3 A:G54 4.9 36.4 1.0

Magnesium binding site 3 out of 11 in the L-Glutamine Riboswitch Bound with L-Glutamine Soaked with Cs+


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 Cs+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg108 b:41.5 occ:1.00 O A:HOH289 2.1 32.1 1.0 O A:HOH276 2.1 28.0 1.0 O A:HOH258 2.1 34.3 1.0 O A:HOH307 2.1 31.3 1.0 O A:HOH247 2.2 27.0 1.0 O A:HOH226 3.7 30.4 1.0 N7 A:G12 3.7 30.8 1.0 O A:HOH298 4.2 39.9 1.0 C8 A:G12 4.4 28.4 1.0 CS A:CS112 4.5 64.6 1.0 C5 A:G12 4.6 31.4 1.0 OP1 A:A14 4.6 29.9 1.0 O A:HOH268 4.8 35.9 1.0 OP2 A:A14 4.8 29.7 1.0 O6 A:G12 4.9 30.3 1.0

Magnesium binding site 4 out of 11 in the L-Glutamine Riboswitch Bound with L-Glutamine Soaked with Cs+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of L-Glutamine Riboswitch Bound with L-Glutamine Soaked with Cs+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg109 b:41.0 occ:1.00 O A:HOH251 2.1 42.1 1.0 O A:HOH282 2.1 44.1 1.0 O A:HOH277 2.1 46.0 1.0 O A:HOH297 2.1 39.0 1.0 O A:HOH304 2.1 43.8 1.0 O A:HOH248 2.1 38.2 1.0 O A:HOH246 2.1 35.7 1.0 K A:K102 3.6 50.2 1.0 K A:K103 4.1 42.0 1.0 O4 A:U3 4.1 40.3 1.0 O4 A:U4 4.2 45.2 1.0 O6 A:G54 4.4 37.2 1.0 C5 A:U3 4.7 41.1 1.0 C4 A:U3 4.7 40.2 1.0 O6 A:G5 4.9 42.9 1.0

Magnesium binding site 5 out of 11 in the L-Glutamine Riboswitch Bound with L-Glutamine Soaked with Cs+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of L-Glutamine Riboswitch Bound with L-Glutamine Soaked with Cs+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg110 b:41.9 occ:1.00 O A:HOH218 2.1 37.0 1.0 O A:HOH253 2.1 36.2 1.0 O A:HOH286 2.1 38.5 1.0 O A:HOH309 2.1 44.9 1.0 O A:HOH242 2.1 39.2 1.0 OP2 A:A29 3.2 36.9 1.0 OP2 A:A28 3.9 39.9 1.0 OP1 A:A28 4.0 39.2 1.0 O A:HOH234 4.0 34.3 1.0 P A:A28 4.2 44.6 1.0 O A:HOH293 4.2 40.1 1.0 O5' A:A28 4.2 35.2 1.0 N7 A:A29 4.3 33.0 1.0 O A:HOH303 4.3 45.8 1.0 O A:HOH230 4.4 39.1 1.0 P A:A29 4.6 36.6 1.0 C8 A:A29 4.7 32.9 1.0 O5' A:A29 5.0 37.8 1.0

Magnesium binding site 6 out of 11 in the L-Glutamine Riboswitch Bound with L-Glutamine Soaked with Cs+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of L-Glutamine Riboswitch Bound with L-Glutamine Soaked with Cs+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg111 b:44.3 occ:1.00 O A:HOH302 2.1 39.2 1.0 O A:HOH303 2.1 45.8 1.0 O A:HOH288 2.2 37.9 1.0 O A:HOH243 2.2 39.2 1.0 O A:HOH295 2.2 38.5 1.0 O A:HOH257 3.2 33.1 1.0 O A:HOH255 3.8 42.8 1.0 OP2 A:G47 4.0 43.2 1.0 O A:HOH242 4.3 39.2 1.0 O A:HOH207 4.3 34.2 1.0 N4 A:C48 4.5 33.0 1.0

Magnesium binding site 7 out of 11 in the L-Glutamine Riboswitch Bound with L-Glutamine Soaked with Cs+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of L-Glutamine Riboswitch Bound with L-Glutamine Soaked with Cs+ within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg105 b:30.9 occ:1.00 O B:HOH292 2.1 37.3 1.0 O B:HOH293 2.1 38.1 1.0 OP1 B:C16 3.2 39.2 1.0 O2' B:A15 3.7 34.9 1.0 O3' B:A15 3.8 34.8 1.0 P B:C16 4.0 38.1 1.0 C5' B:C16 4.1 34.6 1.0 C2' B:A15 4.5 34.2 1.0 O5' B:C16 4.6 40.4 1.0 C3' B:A15 4.7 33.7 1.0

Magnesium binding site 8 out of 11 in the L-Glutamine Riboswitch Bound with L-Glutamine Soaked with Cs+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of L-Glutamine Riboswitch Bound with L-Glutamine Soaked with Cs+ within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg106 b:34.7 occ:1.00 O B:HOH221 2.1 33.6 1.0 O B:HOH231 2.1 30.6 1.0 O B:HOH223 2.1 33.5 1.0 O B:HOH212 2.1 30.2 1.0 O B:HOH205 2.1 29.2 1.0 OXT B:GLN101 2.2 31.7 1.0 C B:GLN101 3.2 29.4 1.0 O B:GLN101 3.4 29.7 1.0 N2 B:G54 3.5 31.2 1.0 OP2 B:A57 3.8 40.7 1.0 O6 B:G22 4.0 28.7 1.0 OP1 B:G54 4.1 32.3 1.0 N7 B:G22 4.2 27.6 1.0 OP2 B:A56 4.2 31.9 1.0 C2 B:G54 4.2 29.8 1.0 N7 B:A57 4.4 35.0 1.0 CA B:GLN101 4.6 28.3 1.0 N1 B:G54 4.6 30.1 1.0 CG B:GLN101 4.6 29.8 1.0 C6 B:G22 4.8 25.9 1.0 C8 B:A57 4.8 34.9 1.0 C5 B:G22 4.9 27.6 1.0 O B:HOH258 4.9 33.5 1.0 CB B:GLN101 5.0 27.1 1.0 N3 B:G54 5.0 28.2 1.0

Magnesium binding site 9 out of 11 in the L-Glutamine Riboswitch Bound with L-Glutamine Soaked with Cs+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of L-Glutamine Riboswitch Bound with L-Glutamine Soaked with Cs+ within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg107 b:45.0 occ:1.00 O B:HOH309 2.0 34.6 1.0 O B:HOH254 2.0 33.9 1.0 O B:HOH228 2.1 37.4 1.0 O B:HOH249 2.1 36.0 1.0 N7 B:G12 3.4 33.9 1.0 OP1 B:A14 3.5 37.1 1.0 OP2 B:A14 3.5 36.3 1.0 P B:A14 3.9 35.2 1.0 C5 B:G12 4.0 33.1 1.0 O6 B:G12 4.1 34.0 1.0 C8 B:G12 4.2 32.0 1.0 C6 B:G12 4.3 34.3 1.0 O3' B:A13 4.5 34.2 1.0 CS B:CS115 4.8 59.6 1.0 C4 B:G12 4.9 32.5 1.0

Magnesium binding site 10 out of 11 in the L-Glutamine Riboswitch Bound with L-Glutamine Soaked with Cs+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of L-Glutamine Riboswitch Bound with L-Glutamine Soaked with Cs+ within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg108 b:39.4 occ:1.00 O B:HOH202 2.1 32.2 1.0 O B:HOH288 2.1 36.8 1.0 O B:HOH283 2.1 37.8 1.0 O B:HOH311 2.1 35.5 1.0 O B:HOH269 2.2 32.9 1.0 O B:HOH263 3.1 29.8 1.0 N7 B:G18 3.7 34.1 1.0 O6 B:G18 3.7 32.1 1.0 O B:HOH252 3.8 30.3 1.0 O4 B:U17 3.8 30.7 1.0 C4 B:U17 4.2 31.1 1.0 C5 B:U17 4.2 32.6 1.0 C5 B:G18 4.3 32.8 1.0 C6 B:G18 4.3 31.0 1.0 O6 B:G19 4.4 34.1 1.0 N7 B:G19 4.6 32.9 1.0 C8 B:G18 4.7 34.0 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