Potassium 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
Sodium	(Na)	2 atoms

The binding sites of Potassium 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 Potassium atom.
In total 3 binding sites of Potassium where determined in the Crystal Structure of Thiamine Pyrophosphate-Specific Riboswitch in Complex with Thiamine Pyrophosphate, PDB code: 2gdi:
Jump to Potassium binding site number: 1; 2; 3;

Potassium binding site 1 out of 3 in the Crystal Structure of Thiamine Pyrophosphate-Specific Riboswitch in Complex with Thiamine Pyrophosphate


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K 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:K123 b:38.3 occ:1.00 O X:HOH361 2.6 51.1 1.0 N7 X:G72 2.7 35.6 1.0 O X:HOH360 2.8 22.5 1.0 O2' X:G21 2.8 34.1 1.0 O3' X:G21 2.9 34.5 1.0 O6 X:G72 2.9 35.3 1.0 C5 X:G72 3.4 34.6 1.0 C6 X:G72 3.5 34.7 1.0 C3' X:G21 3.7 32.8 1.0 C2' X:G21 3.8 33.1 1.0 C8 X:G72 3.8 34.9 1.0 OP1 X:C22 3.9 33.5 1.0 C4' X:G21 3.9 33.6 1.0 P X:C22 4.0 32.8 1.0 O X:HOH422 4.2 36.0 1.0 C5' X:C22 4.3 30.4 1.0 O5' X:C22 4.6 32.3 1.0 O4' X:G21 4.7 33.5 1.0 C4 X:G72 4.7 34.1 1.0 C1' X:G21 4.8 32.4 1.0 O2' X:U71 4.8 33.4 1.0 N1 X:G72 4.9 34.4 1.0 N9 X:G72 4.9 34.8 1.0

Potassium binding site 2 out of 3 in the Crystal Structure of Thiamine Pyrophosphate-Specific Riboswitch in Complex with Thiamine Pyrophosphate


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K 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:K124 b:39.7 occ:1.00 OP1 X:C73 2.5 35.2 1.0 O2' X:U71 2.7 33.4 1.0 N3 X:G21 2.9 32.6 1.0 O X:HOH365 3.1 24.1 1.0 O2' X:G21 3.1 34.1 1.0 O2 X:U71 3.2 34.0 1.0 C2' X:G21 3.4 33.1 1.0 C2' X:U71 3.5 31.8 1.0 O4' X:C22 3.6 27.8 1.0 N2 X:G21 3.6 29.4 1.0 P X:C73 3.7 33.1 1.0 C2 X:G21 3.7 30.6 1.0 C1' X:U71 3.7 31.6 1.0 C1' X:G21 3.7 32.4 1.0 C4 X:G21 3.9 31.0 1.0 OP2 X:C73 4.0 32.9 1.0 C2 X:U71 4.1 31.5 1.0 N6 X:A43 4.1 29.5 1.0 N9 X:G21 4.2 31.6 1.0 C1' X:C22 4.3 28.6 1.0 N1 X:A43 4.3 30.5 1.0 N1 X:U71 4.4 31.2 1.0 C3' X:G72 4.4 32.9 1.0 C6 X:A43 4.5 30.1 1.0 O3' X:G72 4.5 33.9 1.0 C4' X:C22 4.7 29.8 1.0 C8 X:G72 4.8 34.9 1.0 C2' X:G72 4.8 32.9 1.0 N1 X:C22 4.8 28.7 1.0 O5' X:C73 4.9 33.3 1.0 O4' X:U71 4.9 31.3 1.0 N7 X:G72 4.9 35.6 1.0 C3' X:U71 4.9 32.0 1.0 C3' X:G21 4.9 32.8 1.0 O X:HOH360 5.0 22.5 1.0

Potassium binding site 3 out of 3 in the Crystal Structure of Thiamine Pyrophosphate-Specific Riboswitch in Complex with Thiamine Pyrophosphate


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 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:K125 b:39.4 occ:1.00 O2' X:C38 2.7 34.5 1.0 O X:HOH376 2.7 21.2 1.0 O4 X:U71 2.9 33.6 1.0 O4' X:U39 3.0 36.1 1.0 O4' X:C73 3.2 32.4 1.0 C4' X:U39 3.6 34.8 1.0 N6 X:A70 3.6 27.1 1.0 C4 X:U71 3.7 31.1 1.0 N3 X:U71 3.8 30.8 1.0 C2' X:C38 3.8 33.4 1.0 C4' X:C73 3.8 31.3 1.0 C1' X:C73 3.9 30.0 1.0 O X:HOH418 3.9 29.9 1.0 C5' X:U39 4.0 35.6 1.0 C1' X:U39 4.0 34.1 1.0 O X:HOH460 4.0 29.5 1.0 N1 X:A70 4.1 26.6 1.0 C6 X:A70 4.2 26.5 1.0 O2' X:C73 4.3 30.2 1.0 C5' X:C73 4.6 31.4 1.0 C2' X:C73 4.7 30.5 1.0 C1' X:C38 4.7 33.6 1.0 O2 X:C38 4.8 33.9 1.0 O5' X:U39 4.8 34.2 1.0 N1 X:U39 4.9 33.3 1.0 O3' X:C38 5.0 33.9 1.0 C2' X:U39 5.0 34.7 1.0 C3' X:C38 5.0 33.6 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