Sodium 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
Manganese	(Mn)	5 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Sodium 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 Sodium atom.
In total 12 binding sites of Sodium where determined in the L-Glutamine Riboswitch Bound with L-Glutamine Soaked with MN2+, PDB code: 5ddq:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 12 in the L-Glutamine Riboswitch Bound with L-Glutamine Soaked with MN2+


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na 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:Na106 b:41.5 occ:1.00 O A:HOH225 2.4 37.3 1.0 O A:HOH231 2.6 34.6 1.0 O2' B:C33 3.2 40.0 1.0 N7 A:A13 3.3 40.2 1.0 O2' A:G12 3.3 35.6 1.0 O3' A:G12 3.6 42.2 1.0 O3' B:C33 3.7 39.7 1.0 N6 A:A14 3.9 41.4 1.0 C8 A:A13 4.0 40.0 1.0 C5' B:C34 4.0 42.0 1.0 C5 A:A13 4.4 46.0 1.0 C3' A:G12 4.4 36.8 1.0 C2' A:G12 4.4 36.5 1.0 C2' B:C33 4.4 37.6 1.0 OP1 A:A13 4.4 31.2 1.0 OP1 B:C34 4.4 47.4 1.0 N6 A:A13 4.5 41.1 1.0 C3' B:C33 4.5 40.1 1.0 C6 A:A14 4.6 45.3 1.0 C4' A:G12 4.6 37.3 1.0 P B:C34 4.6 35.8 1.0 P A:A13 4.7 43.9 1.0 N7 A:A14 4.7 39.3 1.0 O5' B:C34 4.8 35.0 1.0 C4' B:C33 4.8 39.4 1.0 C6 A:A13 4.9 44.9 1.0 C5 A:A14 4.9 45.1 1.0 C4' B:C34 4.9 44.0 1.0

Sodium binding site 2 out of 12 in the L-Glutamine Riboswitch Bound with L-Glutamine Soaked with MN2+


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na 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:Na107 b:38.6 occ:1.00 N7 A:G11 2.2 40.2 1.0 O A:HOH280 2.3 38.6 1.0 O A:HOH208 2.7 35.7 1.0 MN A:MN103 3.2 66.7 1.0 C5 A:G11 3.2 34.2 1.0 C8 A:G11 3.3 38.6 1.0 O6 A:G11 3.3 35.2 1.0 O A:HOH255 3.4 37.1 1.0 O6 A:G12 3.4 39.7 1.0 N7 A:G12 3.4 36.7 1.0 O A:HOH287 3.4 39.6 1.0 C6 A:G11 3.6 34.1 1.0 O A:HOH258 3.7 47.9 1.0 C6 A:G12 3.8 39.7 1.0 C5 A:G12 3.9 37.4 1.0 N7 A:A10 4.1 35.4 1.0 O A:HOH279 4.3 30.0 1.0 C4 A:G11 4.4 34.3 1.0 N6 A:A10 4.4 33.7 1.0 C5 A:A10 4.4 38.1 1.0 N9 A:G11 4.4 35.1 1.0 C8 A:G12 4.4 37.5 1.0 O A:HOH250 4.5 43.8 1.0 C6 A:A10 4.6 37.0 1.0 O A:HOH286 4.7 39.5 1.0 C8 A:A10 4.8 35.9 1.0 O A:HOH285 4.8 37.4 1.0 N1 A:G11 5.0 37.8 1.0

Sodium binding site 3 out of 12 in the L-Glutamine Riboswitch Bound with L-Glutamine Soaked with MN2+


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na 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:Na108 b:49.1 occ:1.00 O A:HOH259 2.5 38.5 1.0 O A:HOH241 2.5 40.2 1.0 O A:HOH275 2.6 40.9 1.0 N7 A:G20 3.4 40.6 1.0 O2' A:C21 3.5 36.0 1.0 O A:HOH228 3.5 33.1 1.0 O2 A:C21 3.6 32.4 1.0 O A:HOH237 3.6 44.2 1.0 O6 A:G20 3.8 42.3 1.0 O A:HOH281 4.1 32.8 1.0 C5 A:G20 4.2 40.8 1.0 C2 A:C21 4.3 37.1 1.0 C6 A:G20 4.4 42.3 1.0 N7 A:G19 4.4 40.3 1.0 C8 A:G20 4.4 43.4 1.0 C2' A:C21 4.7 37.4 1.0 C5 A:G19 4.9 38.5 1.0 C1' A:C21 4.9 37.0 1.0 N1 A:C21 4.9 36.4 1.0 O6 A:G19 5.0 37.9 1.0 N3 A:C21 5.0 35.3 1.0 C8 A:G19 5.0 39.5 1.0

Sodium binding site 4 out of 12 in the L-Glutamine Riboswitch Bound with L-Glutamine Soaked with MN2+


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na 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 A:Na109 b:34.1 occ:1.00 O A:HOH204 2.0 27.8 1.0 O6 A:G46 2.5 33.6 1.0 O A:HOH235 2.5 32.4 1.0 O A:HOH284 2.6 48.0 1.0 O A:HOH257 2.6 32.1 1.0 O A:HOH276 3.3 38.2 1.0 C6 A:G46 3.4 33.0 1.0 O A:HOH201 3.6 38.5 1.0 O6 A:G47 3.7 27.6 1.0 O4 A:U32 3.7 32.2 1.0 N7 A:G46 4.0 34.7 1.0 C5 A:G46 4.0 35.1 1.0 N4 A:C33 4.0 25.5 1.0 N7 A:G47 4.4 36.2 1.0 N1 A:G46 4.5 30.6 1.0 C6 A:G47 4.6 29.3 1.0 O6 A:G31 4.7 28.9 1.0 N4 A:C48 4.7 31.3 1.0 NA A:NA110 4.7 55.5 1.0 C4 A:U32 4.8 30.6 1.0 O6 A:G45 4.9 32.7 1.0 C5 A:G47 4.9 34.6 1.0

Sodium binding site 5 out of 12 in the L-Glutamine Riboswitch Bound with L-Glutamine Soaked with MN2+


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na 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 A:Na110 b:55.5 occ:1.00 O A:HOH201 2.4 38.5 1.0 O D:HOH228 2.4 34.6 1.0 O4 A:U32 3.4 32.2 1.0 O A:HOH272 3.4 30.3 1.0 O A:HOH284 3.6 48.0 1.0 N7 A:G31 3.7 31.6 1.0 NA A:NA111 4.0 42.4 1.0 C4 A:U32 4.3 30.6 1.0 N7 A:G30 4.3 34.1 1.0 OP2 A:G31 4.5 31.8 1.0 C8 A:G31 4.5 29.4 1.0 O A:HOH204 4.5 27.8 1.0 O6 A:G31 4.6 28.9 1.0 C5 A:U32 4.6 27.3 1.0 NA A:NA109 4.7 34.1 1.0 C5 A:G31 4.7 26.1 1.0 C8 A:G30 4.7 33.9 1.0 C5 A:G30 4.8 29.0 1.0 O A:HOH257 4.9 32.1 1.0

Sodium binding site 6 out of 12 in the L-Glutamine Riboswitch Bound with L-Glutamine Soaked with MN2+


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of L-Glutamine Riboswitch Bound with L-Glutamine Soaked with MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Na111 b:42.4 occ:1.00 N7 A:G30 2.2 34.1 1.0 O A:HOH274 2.4 39.5 1.0 O A:HOH282 2.5 37.1 1.0 C8 A:G30 3.1 33.9 1.0 C5 A:G30 3.3 29.0 1.0 N7 A:A29 3.6 38.0 1.0 O A:HOH284 3.6 48.0 1.0 O6 A:G30 3.6 29.5 1.0 C5 A:A29 3.7 33.9 1.0 C6 A:G30 3.8 29.1 1.0 N6 A:A29 3.9 30.7 1.0 C6 A:A29 3.9 34.6 1.0 O A:HOH213 3.9 43.6 1.0 NA A:NA110 4.0 55.5 1.0 C8 A:A29 4.3 36.1 1.0 N9 A:G30 4.4 30.9 1.0 C4 A:G30 4.4 30.4 1.0 C4 A:A29 4.5 33.4 1.0 OP2 A:G30 4.6 39.2 1.0 N1 A:A29 4.7 31.5 1.0 N9 A:A29 4.8 32.2 1.0

Sodium binding site 7 out of 12 in the L-Glutamine Riboswitch Bound with L-Glutamine Soaked with MN2+


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of L-Glutamine Riboswitch Bound with L-Glutamine Soaked with MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ B:Na106 b:36.2 occ:1.00 N7 B:G11 2.2 27.8 1.0 O B:HOH261 2.4 37.5 1.0 O B:HOH216 2.4 34.2 1.0 O B:HOH257 2.5 42.1 1.0 O B:HOH249 2.5 32.4 1.0 O B:HOH245 2.6 32.6 1.0 C8 B:G11 3.0 28.9 1.0 MG B:MG105 3.1 43.6 1.0 C5 B:G11 3.3 30.1 1.0 N7 B:G12 3.4 29.6 1.0 O6 B:G12 3.6 39.2 1.0 O6 B:G11 3.7 30.4 1.0 N7 B:A10 3.8 31.6 1.0 C6 B:G11 3.9 29.4 1.0 C5 B:G12 4.1 30.9 1.0 O B:HOH221 4.1 39.6 1.0 C6 B:G12 4.1 34.2 1.0 C5 B:A10 4.3 32.1 1.0 N9 B:G11 4.3 31.5 1.0 C8 B:A10 4.3 35.4 1.0 C4 B:G11 4.4 28.3 1.0 C8 B:G12 4.4 31.3 1.0 O B:HOH263 4.5 25.8 1.0 C6 B:A10 4.7 29.6 1.0 N6 B:A10 4.7 31.7 1.0 C4 B:A10 5.0 31.5 1.0 N9 B:A10 5.0 35.0 1.0

Sodium binding site 8 out of 12 in the L-Glutamine Riboswitch Bound with L-Glutamine Soaked with MN2+


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of L-Glutamine Riboswitch Bound with L-Glutamine Soaked with MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ B:Na107 b:30.2 occ:1.00 O B:HOH201 2.3 42.2 1.0 O B:HOH248 2.5 40.9 1.0 O6 B:G47 2.6 32.2 1.0 O6 B:G46 2.7 36.2 1.0 O4 B:U32 2.8 36.4 1.0 N4 B:C33 3.4 38.9 1.0 O B:HOH235 3.5 43.3 1.0 C6 B:G46 3.5 39.6 1.0 O6 B:G31 3.6 35.2 1.0 C6 B:G47 3.7 33.0 1.0 O B:HOH206 3.7 43.3 1.0 C4 B:U32 3.8 35.1 1.0 O B:HOH229 3.9 42.2 1.0 N3 B:U32 4.0 34.1 1.0 O B:HOH262 4.0 39.1 1.0 N4 B:C48 4.0 34.6 1.0 N7 B:G47 4.2 39.0 1.0 C5 B:G47 4.3 38.7 1.0 N1 B:G46 4.3 39.3 1.0 C5 B:G46 4.4 42.9 1.0 C4 B:C33 4.4 39.4 1.0 O B:HOH241 4.5 32.1 1.0 C6 B:G31 4.6 32.4 1.0 N7 B:G46 4.6 42.5 1.0 N3 B:C33 4.8 38.0 1.0 N1 B:G47 4.8 35.2 1.0 C4 B:C48 4.9 34.5 1.0

Sodium binding site 9 out of 12 in the L-Glutamine Riboswitch Bound with L-Glutamine Soaked with MN2+


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of L-Glutamine Riboswitch Bound with L-Glutamine Soaked with MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ B:Na108 b:44.4 occ:1.00 N7 B:G31 2.2 33.8 1.0 O B:HOH241 2.5 32.1 1.0 O B:HOH243 2.5 38.2 1.0 C8 B:G31 2.9 32.5 1.0 O B:HOH248 3.2 40.9 1.0 C5 B:G31 3.4 29.7 1.0 O B:HOH250 3.4 34.5 1.0 O4 B:U32 3.5 36.4 1.0 C5 B:G30 3.6 33.1 1.0 N7 B:G30 3.7 34.0 1.0 C6 B:G30 4.0 33.6 1.0 OP2 B:G31 4.0 33.6 1.0 O6 B:G31 4.0 35.2 1.0 C4 B:U32 4.0 35.1 1.0 C5 B:U32 4.0 36.7 1.0 C6 B:G31 4.1 32.4 1.0 C8 B:G30 4.1 36.2 1.0 C4 B:G30 4.1 30.7 1.0 NA B:NA109 4.1 48.8 1.0 N9 B:G31 4.2 32.2 1.0 O6 B:G30 4.3 37.3 1.0 N9 B:G30 4.3 31.1 1.0 C4 B:G31 4.4 31.4 1.0 N1 B:G30 4.6 31.1 1.0 O B:HOH229 4.7 42.2 1.0 O5' B:G31 4.7 29.9 1.0 N3 B:G30 4.8 31.0 1.0 C3' B:G30 4.9 32.1 1.0 C2 B:G30 4.9 31.1 1.0 P B:G31 5.0 35.0 1.0

Sodium binding site 10 out of 12 in the L-Glutamine Riboswitch Bound with L-Glutamine Soaked with MN2+


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 10 of L-Glutamine Riboswitch Bound with L-Glutamine Soaked with MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ B:Na109 b:48.8 occ:1.00 N7 B:G30 2.2 34.0 1.0 O B:HOH259 2.5 45.1 1.0 O B:HOH205 2.6 49.8 1.0 C8 B:G30 3.1 36.2 1.0 C5 B:G30 3.4 33.1 1.0 O B:HOH229 3.4 42.2 1.0 N7 B:A29 3.5 33.5 1.0 O B:HOH243 3.6 38.2 1.0 O6 B:G30 3.7 37.3 1.0 C5 B:A29 3.8 33.7 1.0 C6 B:G30 3.9 33.6 1.0 O B:HOH248 4.0 40.9 1.0 C8 B:A29 4.0 34.7 1.0 NA B:NA108 4.1 44.4 1.0 C6 B:A29 4.2 35.9 1.0 N6 B:A29 4.3 34.2 1.0 N9 B:G30 4.4 31.1 1.0 OP2 B:G30 4.5 36.7 1.0 C4 B:G30 4.5 30.7 1.0 C4 B:A29 4.5 33.3 1.0 N9 B:A29 4.6 32.5 1.0 OP2 B:A29 5.0 39.9 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