Sodium in PDB 2gdi: Crystal Structure of Thiamine Pyrophosphate-Specific Riboswitch in Complex with Thiamine Pyrophosphate

The structure of Crystal Structure of Thiamine Pyrophosphate-Specific Riboswitch in Complex with Thiamine Pyrophosphate, PDB code: 2gdi was solved by A.Serganov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 2.05
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	148.819, 29.558, 95.170, 90.00, 94.55, 90.00
R / Rfree (%)	20.8 / 24.1

The structure of Crystal Structure of Thiamine Pyrophosphate-Specific Riboswitch in Complex with Thiamine Pyrophosphate also contains other interesting chemical elements:

Magnesium	(Mg)	6 atoms
Potassium	(K)	3 atoms

The binding sites of Sodium atom in the Crystal Structure of Thiamine Pyrophosphate-Specific Riboswitch in Complex with Thiamine Pyrophosphate (pdb code 2gdi). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of Thiamine Pyrophosphate-Specific Riboswitch in Complex with Thiamine Pyrophosphate, PDB code: 2gdi:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Thiamine Pyrophosphate-Specific Riboswitch in Complex with Thiamine Pyrophosphate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Thiamine Pyrophosphate-Specific Riboswitch in Complex with Thiamine Pyrophosphate within 5.0Å range: probe atom residue distance (Å) B Occ X:Na121 b:41.0 occ:1.00 O X:HOH357 2.3 30.0 1.0 O X:HOH359 2.4 40.2 1.0 O X:HOH358 2.5 27.3 1.0 N3 X:A61 2.9 32.0 1.0 O2' X:A61 3.0 33.6 1.0 O X:HOH356 3.0 22.2 1.0 O X:HOH233 3.1 31.3 1.0 C2 X:A61 3.7 31.8 1.0 C1' X:A61 3.9 33.3 1.0 C4 X:A61 4.0 32.7 1.0 C2' X:A61 4.0 34.1 1.0 O X:HOH453 4.4 27.8 1.0 N9 X:A61 4.4 33.0 1.0 O3' X:A61 4.4 35.8 1.0 O X:HOH378 4.5 29.2 1.0 OP2 X:U59 4.5 36.0 1.0 O X:HOH490 4.5 31.1 1.0 O X:HOH201 4.6 39.2 1.0 O X:HOH406 4.6 24.7 1.0 N7 X:G60 4.7 30.1 1.0 C3' X:A61 4.9 35.0 1.0 O X:HOH370 4.9 27.4 1.0 OP2 X:G60 4.9 33.0 1.0 O X:HOH213 5.0 48.1 1.0 N1 X:A61 5.0 31.8 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Thiamine Pyrophosphate-Specific Riboswitch in Complex with Thiamine Pyrophosphate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Thiamine Pyrophosphate-Specific Riboswitch in Complex with Thiamine Pyrophosphate within 5.0Å range: probe atom residue distance (Å) B Occ X:Na122 b:36.3 occ:1.00 O X:HOH396 2.3 37.2 1.0 O X:HOH380 2.5 21.6 1.0 O X:HOH403 2.6 25.7 1.0 O6 X:G65 2.7 29.7 1.0 O4 X:U64 2.8 34.1 1.0 C4 X:U64 3.5 33.1 1.0 O6 X:G66 3.5 29.9 1.0 C6 X:G65 3.7 30.7 1.0 N7 X:G65 3.9 32.5 1.0 N4 X:C74 3.9 27.3 1.0 C5 X:U64 4.1 33.9 1.0 O X:HOH383 4.1 30.2 1.0 O X:HOH230 4.1 33.1 1.0 C5 X:G65 4.2 31.6 1.0 N3 X:U64 4.3 32.7 1.0 N4 X:C73 4.4 28.4 1.0 C6 X:G66 4.4 30.4 1.0 N6 X:A75 4.5 28.7 1.0 OP2 X:G72 4.6 32.2 1.0 O X:HOH389 4.7 29.4 1.0 N7 X:G66 4.7 30.9 1.0 C5 X:G66 4.9 30.2 1.0 N1 X:G65 5.0 30.1 1.0 O X:HOH395 5.0 25.2 1.0 N1 X:A75 5.0 28.7 1.0

A.Serganov, A.Polonskaia, A.T.Phan, R.R.Breaker, D.J.Patel. Structural Basis For Gene Regulation By A Thiamine Pyrophosphate-Sensing Riboswitch. Nature V. 441 1167 2006.
ISSN: ISSN 0028-0836
PubMed: 16728979
DOI: 10.1038/NATURE04740