Sodium 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:

Magnesium	(Mg)	11 atoms
Potassium	(K)	7 atoms
Caesium	(Cs)	7 atoms

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

Sodium binding site 1 out of 4 in the L-Glutamine Riboswitch Bound with L-Glutamine Soaked with Cs+


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 Cs+ within 5.0Å range: probe atom residue distance (Å) B Occ B:Na109 b:34.5 occ:1.00 O B:HOH284 2.5 22.6 1.0 O B:HOH298 2.5 30.6 1.0 O6 B:G51 3.4 25.6 1.0 O B:HOH272 3.4 28.3 1.0 O B:HOH301 4.0 29.5 1.0 O B:HOH255 4.1 29.1 1.0 C8 B:G26 4.1 26.3 1.0 O2' B:G26 4.1 28.0 1.0 N7 B:G26 4.4 27.3 1.0 C6 B:G51 4.5 24.8 1.0 C5 B:U50 4.7 24.5 1.0 N9 B:G26 4.8 24.9 1.0 C2' B:G26 4.9 28.6 1.0 N7 B:G51 5.0 25.0 1.0

Sodium binding site 2 out of 4 in the L-Glutamine Riboswitch Bound with L-Glutamine Soaked with Cs+


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 Cs+ within 5.0Å range: probe atom residue distance (Å) B Occ B:Na110 b:28.9 occ:1.00 O B:HOH235 2.5 32.8 1.0 O B:HOH273 2.6 24.9 1.0 O B:HOH282 2.7 30.9 1.0 O4' B:G26 3.3 28.9 1.0 O2' B:A25 3.4 25.9 1.0 N3 B:A25 3.5 22.8 1.0 C4 B:G26 3.7 24.4 1.0 N3 B:G26 3.8 25.4 1.0 N9 B:G26 3.9 24.9 1.0 C2 B:A25 4.1 22.9 1.0 C5 B:G26 4.1 25.0 1.0 C1' B:G26 4.2 26.5 1.0 NA B:NA111 4.2 33.7 1.0 O3' B:A25 4.3 27.0 1.0 C2 B:G26 4.3 26.6 1.0 C8 B:G26 4.4 26.3 1.0 C4' B:G26 4.4 30.4 1.0 C2' B:A25 4.4 26.2 1.0 C1' B:A25 4.5 25.6 1.0 N7 B:G26 4.5 27.3 1.0 C5' B:G26 4.6 29.6 1.0 C4 B:A25 4.6 23.0 1.0 C6 B:G26 4.6 28.0 1.0 N1 B:G26 4.6 25.2 1.0

Sodium binding site 3 out of 4 in the L-Glutamine Riboswitch Bound with L-Glutamine Soaked with Cs+


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 Cs+ within 5.0Å range: probe atom residue distance (Å) B Occ B:Na111 b:33.7 occ:1.00 O B:HOH282 2.3 30.9 1.0 O B:HOH270 2.4 27.9 1.0 O B:HOH235 2.4 32.8 1.0 OP2 B:G26 2.5 35.2 1.0 O2' B:A25 3.3 25.9 1.0 O3' B:A25 3.6 27.0 1.0 P B:G26 3.7 34.0 1.0 C3' B:A25 4.2 24.7 1.0 NA B:NA110 4.2 28.9 1.0 C2' B:A25 4.3 26.2 1.0 OP1 B:G26 4.7 31.6 1.0 OP2 B:A24 4.7 28.7 1.0 O5' B:G26 4.7 33.1 1.0 OP1 B:A24 4.9 25.7 1.0 C5' B:G26 4.9 29.6 1.0

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


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 Cs+ within 5.0Å range: probe atom residue distance (Å) B Occ B:Na112 b:31.7 occ:1.00 O B:HOH284 2.6 22.6 1.0 O6 B:G26 3.2 32.0 1.0 O B:HOH301 3.3 29.5 1.0 OP2 B:G51 3.4 22.6 1.0 C6 B:G26 3.8 28.0 1.0 N7 B:G51 4.0 25.0 1.0 N7 B:G26 4.2 27.3 1.0 C5 B:G26 4.2 25.0 1.0 OP2 B:U50 4.3 35.8 1.0 C8 B:G51 4.5 24.7 1.0 O5' B:U50 4.5 26.2 1.0 P B:G51 4.7 27.3 1.0 P B:U50 4.8 32.2 1.0 N1 B:G26 4.8 25.2 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