Magnesium in PDB 3d2x: Structure of the Thiamine Pyrophosphate-Specific Riboswitch Bound to Oxythiamine Pyrophosphate

The structure of Structure of the Thiamine Pyrophosphate-Specific Riboswitch Bound to Oxythiamine Pyrophosphate, PDB code: 3d2x was solved by S.Thore, C.Frick, N.Ban, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	15.00 / 2.50
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	75.497, 111.172, 55.375, 90.00, 90.00, 90.00
R / Rfree (%)	23.3 / 26.7

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 13;

Binding sites:

The binding sites of Magnesium atom in the Structure of the Thiamine Pyrophosphate-Specific Riboswitch Bound to Oxythiamine Pyrophosphate (pdb code 3d2x). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 13 binding sites of Magnesium where determined in the Structure of the Thiamine Pyrophosphate-Specific Riboswitch Bound to Oxythiamine Pyrophosphate, PDB code: 3d2x:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 13 in the Structure of the Thiamine Pyrophosphate-Specific Riboswitch Bound to Oxythiamine Pyrophosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of the Thiamine Pyrophosphate-Specific Riboswitch Bound to Oxythiamine Pyrophosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg78 b:13.2 occ:1.00 N7 A:A29 2.5 27.9 1.0 O A:HOH92 2.6 14.8 1.0 N6 A:A29 3.4 30.4 1.0 C5 A:A29 3.4 29.0 1.0 C8 A:A29 3.5 28.9 1.0 C6 A:A29 3.8 29.1 1.0 OP2 A:A44 4.3 21.5 1.0 O2' A:G28 4.4 35.8 1.0 O6 A:G30 4.6 30.1 1.0 C4 A:A29 4.7 28.9 1.0 N9 A:A29 4.7 29.0 1.0 O3' A:G28 4.8 32.5 1.0

Magnesium binding site 2 out of 13 in the Structure of the Thiamine Pyrophosphate-Specific Riboswitch Bound to Oxythiamine Pyrophosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of the Thiamine Pyrophosphate-Specific Riboswitch Bound to Oxythiamine Pyrophosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg79 b:21.7 occ:1.00 O A:HOH93 2.5 23.0 1.0 O A:HOH139 2.5 41.3 1.0 N7 A:G28 2.9 39.4 1.0 C8 A:G28 3.5 37.5 1.0 O A:HOH96 3.7 66.7 1.0 C5 A:G28 4.1 39.4 1.0 OP2 A:G28 4.3 34.2 1.0 C5 A:U27 4.3 30.6 1.0 O6 A:G28 4.5 41.2 1.0 OP2 A:U27 4.5 35.3 1.0 C6 A:U27 4.7 30.7 1.0 C6 A:G28 4.7 39.7 1.0 N9 A:G28 4.9 37.5 1.0

Magnesium binding site 3 out of 13 in the Structure of the Thiamine Pyrophosphate-Specific Riboswitch Bound to Oxythiamine Pyrophosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of the Thiamine Pyrophosphate-Specific Riboswitch Bound to Oxythiamine Pyrophosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg80 b:24.5 occ:1.00 O A:HOH136 2.2 22.4 1.0 OAZ A:D2X85 2.3 25.7 1.0 O6 A:G48 2.3 16.9 1.0 O A:HOH135 2.4 12.3 1.0 O6 A:G66 2.6 18.4 1.0 C6 A:G48 3.4 16.5 1.0 PAW A:D2X85 3.5 25.4 1.0 OAV A:D2X85 3.7 27.6 1.0 C6 A:G66 3.7 19.4 1.0 N1 A:G48 4.0 17.1 1.0 N1 A:A49 4.0 14.7 1.0 N1 A:G66 4.0 18.0 1.0 OAX A:D2X85 4.1 28.1 1.0 C2 A:A49 4.1 13.3 1.0 N3 A:C65 4.4 11.2 1.0 O4 A:U47 4.4 17.7 1.0 OAI A:D2X85 4.4 28.9 1.0 PAU A:D2X85 4.4 27.6 1.0 O A:HOH117 4.5 23.9 1.0 OAY A:D2X85 4.5 26.2 1.0 C5 A:G48 4.5 16.3 1.0 O A:HOH112 4.6 19.3 1.0 N4 A:C65 4.7 10.9 1.0 OAJ A:D2X85 4.7 27.6 1.0 O A:HOH94 4.8 19.6 1.0 C5 A:G66 5.0 20.2 1.0

Magnesium binding site 4 out of 13 in the Structure of the Thiamine Pyrophosphate-Specific Riboswitch Bound to Oxythiamine Pyrophosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of the Thiamine Pyrophosphate-Specific Riboswitch Bound to Oxythiamine Pyrophosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg81 b:33.3 occ:1.00 O A:HOH141 2.5 43.4 1.0 O A:HOH140 2.5 40.8 1.0 OP2 A:A52 2.5 27.1 1.0 OP1 A:C51 2.7 24.1 1.0 O A:HOH106 3.6 13.4 1.0 P A:C51 4.0 23.0 1.0 P A:A52 4.0 30.2 1.0 N1 B:A50 4.2 23.6 1.0 OP2 A:C51 4.4 21.9 1.0 O5' A:A52 4.6 29.5 1.0 C2 B:A50 4.7 21.7 1.0 N7 A:A52 4.8 26.6 1.0 C3' A:C51 4.8 26.9 1.0 O3' A:C51 4.9 28.5 1.0 C8 A:A52 4.9 27.9 1.0 OP1 A:A52 5.0 29.6 1.0 O5' A:C51 5.0 24.6 1.0

Magnesium binding site 5 out of 13 in the Structure of the Thiamine Pyrophosphate-Specific Riboswitch Bound to Oxythiamine Pyrophosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Structure of the Thiamine Pyrophosphate-Specific Riboswitch Bound to Oxythiamine Pyrophosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg82 b:19.2 occ:1.00 OAX A:D2X85 2.2 28.1 1.0 O A:HOH117 2.4 23.9 1.0 O A:HOH137 2.5 51.1 1.0 OAY A:D2X85 2.5 26.2 1.0 PAW A:D2X85 3.7 25.4 1.0 PAU A:D2X85 3.8 27.6 1.0 O4 A:U63 4.2 25.5 1.0 O A:HOH101 4.2 19.0 1.0 C5 A:U63 4.2 23.0 1.0 OAV A:D2X85 4.3 27.6 1.0 N4 A:C65 4.4 10.9 1.0 C4 A:U63 4.5 24.2 1.0 OAT A:D2X85 4.5 27.4 1.0 OAJ A:D2X85 4.7 27.6 1.0 OAZ A:D2X85 4.7 25.7 1.0 O A:HOH94 4.7 19.6 1.0 N7 A:G64 4.7 17.5 1.0 O6 A:G64 4.7 14.7 1.0 O A:HOH136 4.9 22.4 1.0 O A:HOH138 4.9 22.1 1.0 O2' A:G60 4.9 35.1 1.0

Magnesium binding site 6 out of 13 in the Structure of the Thiamine Pyrophosphate-Specific Riboswitch Bound to Oxythiamine Pyrophosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Structure of the Thiamine Pyrophosphate-Specific Riboswitch Bound to Oxythiamine Pyrophosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg83 b:40.0 occ:1.00 N7 A:G1 2.4 51.1 1.0 C8 A:G1 3.1 51.6 1.0 OP3 A:G1 3.1 60.0 1.0 C5 A:G1 3.6 51.6 1.0 O6 A:G1 4.1 52.5 1.0 C6 A:G1 4.2 51.5 1.0 N9 A:G1 4.4 52.5 1.0 P A:G1 4.5 60.2 1.0 C4 A:G1 4.6 51.2 1.0 OP2 A:G1 4.8 60.4 1.0

Magnesium binding site 7 out of 13 in the Structure of the Thiamine Pyrophosphate-Specific Riboswitch Bound to Oxythiamine Pyrophosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Structure of the Thiamine Pyrophosphate-Specific Riboswitch Bound to Oxythiamine Pyrophosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg84 b:38.5 occ:1.00 OP2 A:G42 2.3 27.1 1.0 O A:HOH143 2.6 49.1 1.0 O A:HOH145 2.6 26.4 1.0 P A:G42 3.7 28.8 1.0 N7 A:G42 4.0 20.6 1.0 C8 A:G42 4.3 20.2 1.0 O5' A:G42 4.4 27.5 1.0 C5' A:U41 4.5 32.4 1.0 OP1 A:G42 4.5 28.8 1.0 C4' A:U41 4.6 31.8 1.0 O3' A:U41 4.7 29.8 1.0 C3' A:U41 4.9 31.9 1.0

Magnesium binding site 8 out of 13 in the Structure of the Thiamine Pyrophosphate-Specific Riboswitch Bound to Oxythiamine Pyrophosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Structure of the Thiamine Pyrophosphate-Specific Riboswitch Bound to Oxythiamine Pyrophosphate within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg78 b:21.7 occ:1.00 N7 B:A29 2.5 35.9 1.0 O B:HOH139 2.7 27.4 1.0 C8 B:A29 3.4 35.9 1.0 C5 B:A29 3.5 35.9 1.0 N6 B:A29 3.6 37.3 1.0 C6 B:A29 4.0 35.9 1.0 O2' B:G28 4.1 35.7 1.0 O6 B:G30 4.5 29.6 1.0 O3' B:G28 4.6 36.2 1.0 N9 B:A29 4.6 35.8 1.0 C4 B:A29 4.7 35.6 1.0 OP1 B:A29 4.9 35.2 1.0 OP2 B:A44 4.9 26.1 1.0

Magnesium binding site 9 out of 13 in the Structure of the Thiamine Pyrophosphate-Specific Riboswitch Bound to Oxythiamine Pyrophosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Structure of the Thiamine Pyrophosphate-Specific Riboswitch Bound to Oxythiamine Pyrophosphate within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg79 b:19.4 occ:1.00 O B:HOH133 2.2 22.5 1.0 OAZ B:D2X84 2.2 26.3 1.0 O B:HOH100 2.3 19.3 1.0 O6 B:G48 2.3 28.1 1.0 O B:HOH125 2.4 45.6 1.0 O6 B:G66 2.6 28.8 1.0 OAV B:D2X84 3.3 24.3 1.0 PAW B:D2X84 3.4 25.3 1.0 C6 B:G48 3.5 25.6 1.0 O B:HOH123 3.5 32.4 1.0 C6 B:G66 3.5 30.3 1.0 N1 B:G66 3.7 30.2 1.0 O B:HOH134 3.9 41.3 1.0 N1 B:G48 4.0 25.2 1.0 N1 B:A49 4.1 22.5 1.0 OAX B:D2X84 4.2 24.4 1.0 O4 B:U47 4.4 15.8 1.0 C2 B:A49 4.4 22.2 1.0 N3 B:C65 4.4 26.6 1.0 PAU B:D2X84 4.4 23.6 1.0 OAJ B:D2X84 4.6 22.9 1.0 OAI B:D2X84 4.6 24.9 1.0 N4 B:C65 4.6 29.0 1.0 C5 B:G48 4.7 24.2 1.0 OAY B:D2X84 4.7 22.9 1.0 C5 B:G66 4.9 30.1 1.0

Magnesium binding site 10 out of 13 in the Structure of the Thiamine Pyrophosphate-Specific Riboswitch Bound to Oxythiamine Pyrophosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Structure of the Thiamine Pyrophosphate-Specific Riboswitch Bound to Oxythiamine Pyrophosphate within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg80 b:20.5 occ:1.00 O B:HOH126 2.3 31.0 1.0 O B:HOH99 2.3 35.4 1.0 O B:HOH136 2.4 37.5 1.0 O A:HOH142 2.5 40.0 1.0 OP1 B:C51 2.5 21.1 1.0 OP2 B:A52 2.5 23.2 1.0 P B:C51 3.8 19.9 1.0 P B:A52 3.9 24.4 1.0 OP2 B:C51 4.2 20.3 1.0 N1 A:A50 4.3 20.2 1.0 C2 A:A50 4.5 21.0 1.0 O5' B:A52 4.6 24.3 1.0 O5' B:C51 4.7 20.8 1.0 C3' B:C51 4.7 21.9 1.0 O3' B:C51 4.7 23.4 1.0 N7 B:A52 4.7 27.0 1.0 O B:HOH112 4.8 38.8 1.0 O3' B:A50 4.8 19.2 1.0 C8 B:A52 4.9 26.8 1.0 OP1 B:A52 4.9 23.5 1.0

S.Thore, C.Frick, N.Ban. Structural Basis of Thiamine Pyrophosphate Analogues Binding to the Eukaryotic Riboswitch J.Am.Chem.Soc. V. 130 8116 2008.
ISSN: ISSN 0002-7863
PubMed: 18533652
DOI: 10.1021/JA801708E