Magnesium 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:

Potassium	(K)	3 atoms
Sodium	(Na)	2 atoms

The binding sites of Magnesium 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 Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Crystal Structure of Thiamine Pyrophosphate-Specific Riboswitch in Complex with Thiamine Pyrophosphate, PDB code: 2gdi:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in the Crystal Structure of Thiamine Pyrophosphate-Specific Riboswitch in Complex with Thiamine Pyrophosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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:Mg101 b:32.5 occ:1.00 O2B X:TPP100 2.2 34.3 1.0 O6 X:G60 2.2 29.4 1.0 O6 X:G78 2.2 30.7 1.0 O X:HOH488 2.2 29.7 1.0 O X:HOH489 2.2 30.0 1.0 O X:HOH490 2.2 31.1 1.0 C6 X:G60 3.1 29.8 1.0 C6 X:G78 3.2 29.8 1.0 PB X:TPP100 3.5 33.6 1.0 N1 X:G60 3.5 28.7 1.0 O4 X:U59 3.6 31.7 1.0 O3A X:TPP100 3.6 33.9 1.0 N1 X:G78 3.7 29.9 1.0 N3 X:C77 4.0 29.1 1.0 N1 X:A61 4.0 31.8 1.0 O X:HOH443 4.0 24.9 1.0 O X:HOH409 4.1 24.9 1.0 C2 X:A61 4.2 31.8 1.0 O X:HOH356 4.2 22.2 1.0 O3B X:TPP100 4.3 34.9 1.0 C4 X:U59 4.4 31.6 1.0 C5 X:G60 4.4 29.9 1.0 N4 X:C77 4.4 28.8 1.0 O1B X:TPP100 4.5 34.7 1.0 C5 X:G78 4.5 30.3 1.0 O X:HOH458 4.5 30.7 1.0 C4 X:C77 4.7 28.8 1.0 O2 X:C77 4.7 29.4 1.0 C2 X:C77 4.8 29.6 1.0 C5 X:U59 4.8 31.7 1.0 C2 X:G60 4.9 28.8 1.0 O X:HOH406 4.9 24.7 1.0

Magnesium binding site 2 out of 6 in the Crystal Structure of Thiamine Pyrophosphate-Specific Riboswitch in Complex with Thiamine Pyrophosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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:Mg102 b:34.9 occ:1.00 O1B X:TPP100 2.2 34.7 1.0 O2A X:TPP100 2.2 34.0 1.0 O X:HOH491 2.2 34.8 1.0 O X:HOH492 2.2 34.4 1.0 O X:HOH494 2.2 35.1 1.0 O X:HOH493 2.2 34.1 1.0 PB X:TPP100 3.3 33.6 1.0 PA X:TPP100 3.4 33.7 1.0 OP2 X:A75 3.6 29.7 1.0 O3A X:TPP100 3.7 33.9 1.0 O X:HOH441 3.7 26.4 1.0 O3B X:TPP100 3.9 34.9 1.0 O X:HOH410 4.0 27.7 1.0 O X:HOH373 4.2 21.7 1.0 O7 X:TPP100 4.2 33.6 1.0 O X:HOH443 4.2 24.9 1.0 O X:HOH429 4.3 30.9 1.0 O X:HOH425 4.4 22.1 1.0 N7 X:A75 4.4 28.1 1.0 OP2 X:C74 4.5 32.8 1.0 O2B X:TPP100 4.6 34.3 1.0 O1A X:TPP100 4.6 34.7 1.0 C8 X:A75 4.8 29.1 1.0 N4 X:C77 4.9 28.8 1.0 O X:HOH381 5.0 28.4 1.0 O X:HOH374 5.0 22.3 1.0

Magnesium binding site 3 out of 6 in the Crystal Structure of Thiamine Pyrophosphate-Specific Riboswitch in Complex with Thiamine Pyrophosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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:Mg103 b:42.6 occ:1.00 O X:HOH495 2.2 42.1 1.0 O X:HOH499 2.2 43.0 1.0 O X:HOH497 2.2 42.6 1.0 O X:HOH496 2.2 42.5 1.0 O X:HOH498 2.2 41.4 1.0 N7 X:A41 2.6 33.6 1.0 C8 X:A41 3.5 33.3 1.0 C5 X:A41 3.7 32.6 1.0 N6 X:A41 3.7 32.8 1.0 C6 X:A41 4.1 32.7 1.0 O X:HOH398 4.4 30.2 1.0 O X:HOH404 4.4 37.3 1.0 O2' X:G40 4.5 30.7 1.0 O6 X:G42 4.5 30.2 1.0 O X:HOH407 4.6 32.4 1.0 N9 X:A41 4.7 32.5 1.0 C4 X:A41 4.8 32.3 1.0 O X:HOH234 4.9 39.0 1.0 OP1 X:C57 4.9 30.7 1.0

Magnesium binding site 4 out of 6 in the Crystal Structure of Thiamine Pyrophosphate-Specific Riboswitch in Complex with Thiamine Pyrophosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Thiamine Pyrophosphate-Specific Riboswitch in Complex with Thiamine Pyrophosphate within 5.0Å range: probe atom residue distance (Å) B Occ Y:Mg111 b:32.0 occ:1.00 O6 Y:G60 2.2 33.6 1.0 O Y:HOH502 2.2 31.4 1.0 O6 Y:G78 2.2 30.3 1.0 O Y:HOH500 2.2 30.6 1.0 O Y:HOH501 2.2 30.6 1.0 O2B Y:TPP100 2.2 34.4 1.0 C6 Y:G78 3.2 30.2 1.0 C6 Y:G60 3.2 34.3 1.0 PB Y:TPP100 3.4 35.6 1.0 N1 Y:G78 3.6 29.6 1.0 O4 Y:U59 3.6 33.8 1.0 N1 Y:G60 3.6 34.3 1.0 O3A Y:TPP100 3.7 37.3 1.0 O3B Y:TPP100 3.8 36.5 1.0 O Y:HOH505 3.9 30.4 1.0 N1 Y:A61 4.1 40.6 1.0 N3 Y:C77 4.2 29.0 1.0 C2 Y:A61 4.3 40.6 1.0 O Y:HOH337 4.4 30.9 1.0 C4 Y:U59 4.4 33.6 1.0 C5 Y:G78 4.5 30.2 1.0 C5 Y:G60 4.5 34.6 1.0 N4 Y:C77 4.5 29.2 1.0 O Y:HOH257 4.5 39.3 1.0 O1B Y:TPP100 4.7 34.0 1.0 C4 Y:C77 4.9 29.0 1.0 C5 Y:U59 4.9 33.5 1.0 C2 Y:G78 4.9 29.8 1.0 O6 Y:G76 5.0 30.7 1.0 C2 Y:G60 5.0 34.5 1.0

Magnesium binding site 5 out of 6 in the Crystal Structure of Thiamine Pyrophosphate-Specific Riboswitch in Complex with Thiamine Pyrophosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of Thiamine Pyrophosphate-Specific Riboswitch in Complex with Thiamine Pyrophosphate within 5.0Å range: probe atom residue distance (Å) B Occ Y:Mg112 b:31.7 occ:1.00 O1B Y:TPP100 2.2 34.0 1.0 O Y:HOH504 2.2 31.4 1.0 O Y:HOH503 2.2 31.4 1.0 O Y:HOH505 2.2 30.4 1.0 O Y:HOH506 2.2 30.8 1.0 O1A Y:TPP100 2.3 38.5 1.0 PA Y:TPP100 3.1 38.5 1.0 PB Y:TPP100 3.1 35.6 1.0 O2B Y:TPP100 3.3 34.4 1.0 O2A Y:TPP100 3.4 40.1 1.0 O3A Y:TPP100 3.4 37.3 1.0 O Y:HOH282 4.0 39.0 1.0 N4 Y:C77 4.1 29.2 1.0 N7 Y:A75 4.2 33.2 1.0 O6 Y:G76 4.3 30.7 1.0 O Y:HOH241 4.5 40.9 1.0 O3B Y:TPP100 4.5 36.5 1.0 N7 Y:G76 4.5 30.7 1.0 O7 Y:TPP100 4.6 38.1 1.0 N6 Y:A75 4.7 33.0 1.0 C5 Y:A75 4.9 32.8 1.0 C8 Y:A75 4.9 32.8 1.0 O Y:HOH501 5.0 30.6 1.0 O Y:HOH251 5.0 52.9 1.0

Magnesium binding site 6 out of 6 in the Crystal Structure of Thiamine Pyrophosphate-Specific Riboswitch in Complex with Thiamine Pyrophosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of Thiamine Pyrophosphate-Specific Riboswitch in Complex with Thiamine Pyrophosphate within 5.0Å range: probe atom residue distance (Å) B Occ Y:Mg113 b:38.8 occ:1.00 O Y:HOH511 2.2 39.2 1.0 O Y:HOH509 2.2 38.4 1.0 O Y:HOH508 2.2 38.8 1.0 O Y:HOH507 2.2 38.7 1.0 O Y:HOH510 2.2 38.6 1.0 N7 Y:A41 2.5 30.0 1.0 C8 Y:A41 3.4 30.3 1.0 C5 Y:A41 3.5 30.0 1.0 N6 Y:A41 3.7 29.5 1.0 C6 Y:A41 4.1 29.8 1.0 O Y:HOH336 4.2 41.2 1.0 O2' Y:G40 4.4 33.4 1.0 O6 Y:G42 4.5 29.1 1.0 O Y:HOH304 4.5 38.4 1.0 O Y:HOH303 4.5 47.5 1.0 N9 Y:A41 4.6 30.5 1.0 C4 Y:A41 4.7 29.8 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