Magnesium in PDB 8gxb: Crystal Structure of Nad+ -II Riboswitch in Complex with Nad+

The structure of Crystal Structure of Nad+ -II Riboswitch in Complex with Nad+, PDB code: 8gxb was solved by X.C.Xu, A.M.Ren, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.73 / 2.15
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	57.46, 122.611, 154.649, 90, 90, 90
R / Rfree (%)	21.9 / 26.9

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 19;

Binding sites:

The binding sites of Magnesium atom in the Crystal Structure of Nad+ -II Riboswitch in Complex with Nad+ (pdb code 8gxb). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 19 binding sites of Magnesium where determined in the Crystal Structure of Nad+ -II Riboswitch in Complex with Nad+, PDB code: 8gxb:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 19 in the Crystal Structure of Nad+ -II Riboswitch in Complex with Nad+


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 Nad+ -II Riboswitch in Complex with Nad+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg102 b:70.4 occ:1.00 O A:HOH265 1.9 70.9 1.0 O A:HOH220 2.1 58.2 1.0 O A:HOH241 2.1 58.8 1.0 O A:HOH216 2.1 55.6 1.0 O A:HOH269 2.6 63.8 1.0 O A:HOH232 2.8 65.1 1.0 N7 A:G6 4.0 48.8 1.0 OP1 A:A16 4.2 49.3 1.0 O A:HOH207 4.5 63.0 1.0 O2N A:NAD101 4.5 65.5 1.0 C8 A:G6 4.6 47.6 1.0 C5B A:NAD101 4.7 82.3 1.0 O1A A:NAD101 4.7 79.2 1.0 N7 A:A16 4.8 59.5 1.0 OP2 A:A16 4.9 51.7 1.0 OP2 A:C5 5.0 56.1 1.0

Magnesium binding site 2 out of 19 in the Crystal Structure of Nad+ -II Riboswitch in Complex with Nad+


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 Nad+ -II Riboswitch in Complex with Nad+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg103 b:66.7 occ:1.00 O A:HOH210 2.0 52.0 1.0 OP2 A:A17 2.2 55.7 1.0 O A:HOH255 2.3 53.5 1.0 O A:HOH260 2.3 48.4 1.0 O A:HOH256 2.6 60.4 1.0 O A:HOH262 2.6 63.3 1.0 P A:A17 3.7 56.2 1.0 O A:HOH272 4.2 57.9 1.0 O5' A:A17 4.4 52.2 1.0 C4' A:A16 4.4 55.2 1.0 OP1 A:A17 4.5 59.3 1.0 N7 A:A18 4.6 51.4 1.0 O3' A:A16 4.6 56.3 1.0 N7 A:A17 4.6 51.0 1.0 C5' A:A16 4.7 54.1 1.0 C8 A:A17 4.8 50.4 1.0 N6 A:A18 4.8 49.3 1.0 C3' A:A16 4.9 55.9 1.0

Magnesium binding site 3 out of 19 in the Crystal Structure of Nad+ -II Riboswitch in Complex with Nad+


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 Nad+ -II Riboswitch in Complex with Nad+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg104 b:59.5 occ:1.00 OP2 A:G11 1.8 49.3 1.0 O A:HOH205 1.8 60.3 1.0 OP2 A:C10 2.2 49.4 1.0 O A:HOH246 2.3 60.9 1.0 O A:HOH227 2.5 53.9 1.0 O A:HOH235 2.5 51.9 1.0 P A:G11 3.1 53.2 1.0 P A:C10 3.5 50.8 1.0 OP1 A:G11 3.6 51.1 1.0 O5' A:C10 3.9 49.7 1.0 C5' A:C10 3.9 47.4 1.0 O5' A:G11 4.0 47.8 1.0 O3' A:C10 4.1 51.9 1.0 OP1 A:C10 4.3 48.8 1.0 O A:HOH231 4.3 51.3 1.0 C3' A:C10 4.3 45.5 1.0 O3' A:A9 4.6 46.3 1.0 C4' A:C10 4.7 45.8 1.0 C3' A:A9 4.7 42.8 1.0

Magnesium binding site 4 out of 19 in the Crystal Structure of Nad+ -II Riboswitch in Complex with Nad+


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 Nad+ -II Riboswitch in Complex with Nad+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg105 b:45.4 occ:1.00 O2' A:A61 1.8 53.9 1.0 O A:HOH233 1.8 52.4 1.0 O A:HOH238 1.8 65.5 1.0 O A:HOH201 2.0 58.0 1.0 O3' A:A61 2.1 60.2 1.0 C3' A:A61 2.6 50.2 1.0 C2' A:A61 2.6 53.6 1.0 O A:HOH259 2.7 61.6 1.0 C4' A:A61 2.9 48.6 1.0 C1' A:A61 3.6 47.1 1.0 O4' A:A61 3.7 49.1 1.0 C5' B:C10 4.1 62.5 1.0 C5' A:A61 4.2 51.3 1.0 C4' B:C10 4.5 63.3 1.0 O4' B:C10 4.6 64.1 1.0 O2' A:A18 4.8 52.7 1.0 O5' B:C10 4.9 63.4 1.0 N9 A:A61 4.9 45.7 1.0 O A:HOH242 5.0 51.8 1.0

Magnesium binding site 5 out of 19 in the Crystal Structure of Nad+ -II Riboswitch in Complex with Nad+


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 Nad+ -II Riboswitch in Complex with Nad+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg106 b:77.5 occ:1.00 O A:HOH251 2.0 72.5 1.0 O A:HOH214 2.2 61.5 1.0 O3 A:NAD101 2.6 79.5 1.0 O A:HOH243 2.7 60.0 1.0 O1N A:NAD101 2.9 59.0 1.0 O A:HOH252 3.0 62.2 1.0 PN A:NAD101 3.3 70.1 1.0 O A:HOH217 3.5 53.4 1.0 PA A:NAD101 3.8 83.4 1.0 O5B A:NAD101 3.9 81.0 1.0 O2A A:NAD101 4.1 84.5 1.0 OP2 A:A3 4.2 53.9 1.0 O2N A:NAD101 4.3 65.5 1.0 O5D A:NAD101 4.5 61.8 1.0 C5D A:NAD101 4.7 53.7 1.0 O A:HOH270 4.8 60.1 1.0 N7 A:A3 4.9 51.2 1.0 MG A:MG107 5.0 53.1 1.0

Magnesium binding site 6 out of 19 in the Crystal Structure of Nad+ -II Riboswitch in Complex with Nad+


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 Nad+ -II Riboswitch in Complex with Nad+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg107 b:53.1 occ:1.00 O A:HOH229 2.2 50.7 1.0 O A:HOH270 2.6 60.1 1.0 O A:HOH263 2.7 55.6 1.0 O3D A:NAD101 2.7 48.4 1.0 O A:HOH214 2.8 61.5 1.0 O6 A:G42 2.9 44.6 1.0 O A:HOH217 3.2 53.4 1.0 C3D A:NAD101 3.5 51.6 1.0 C6 A:G42 3.9 47.2 1.0 N7 A:G42 4.0 45.8 1.0 O1N A:NAD101 4.1 59.0 1.0 C2D A:NAD101 4.3 48.3 1.0 C5 A:G42 4.3 44.7 1.0 N4 A:C43 4.4 47.6 1.0 O A:HOH243 4.4 60.0 1.0 O2D A:NAD101 4.6 46.3 1.0 OP2 A:G41 4.7 48.7 1.0 N4 A:C5 4.7 49.0 1.0 C4D A:NAD101 4.9 50.4 1.0 O6 A:G4 4.9 53.7 1.0 MG A:MG106 5.0 77.5 1.0

Magnesium binding site 7 out of 19 in the Crystal Structure of Nad+ -II Riboswitch in Complex with Nad+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structure of Nad+ -II Riboswitch in Complex with Nad+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg108 b:64.7 occ:1.00 O A:HOH225 2.0 52.5 1.0 O A:HOH209 2.1 51.4 1.0 O2' A:G41 4.2 49.6 1.0 N2 A:G41 4.3 47.8 1.0 O4' A:G42 4.4 51.5 1.0 N3 A:G41 4.4 43.8 1.0 C4' A:G42 4.5 50.8 1.0 C1' A:A55 4.7 49.7 1.0 C2 A:G41 4.8 44.6 1.0 C2' A:G41 4.8 50.8 1.0 O2' A:A55 4.9 52.8 1.0 O4' A:A55 4.9 47.9 1.0

Magnesium binding site 8 out of 19 in the Crystal Structure of Nad+ -II Riboswitch in Complex with Nad+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Crystal Structure of Nad+ -II Riboswitch in Complex with Nad+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg109 b:75.2 occ:1.00 O2B A:GTP1 2.1 83.6 1.0 O2A A:GTP1 2.3 73.7 1.0 PA A:GTP1 3.2 67.5 1.0 PB A:GTP1 3.3 100.3 1.0 O A:HOH270 3.3 60.1 1.0 O1A A:GTP1 3.5 71.1 1.0 O3A A:GTP1 3.6 64.1 1.0 O1B A:GTP1 4.1 80.1 1.0 OP2 A:G2 4.4 58.3 1.0 O3B A:GTP1 4.6 93.7 1.0 O1G A:GTP1 4.7 84.1 1.0 O5' A:GTP1 4.7 60.7 1.0

Magnesium binding site 9 out of 19 in the Crystal Structure of Nad+ -II Riboswitch in Complex with Nad+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Crystal Structure of Nad+ -II Riboswitch in Complex with Nad+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg110 b:61.0 occ:1.00 O A:HOH224 1.9 61.4 1.0 O A:HOH219 2.1 58.4 1.0 O A:HOH208 2.2 51.9 1.0 O A:HOH257 2.2 59.6 1.0 O A:HOH261 2.6 48.9 1.0 O2' A:G59 3.2 40.1 1.0 C8 A:A39 4.0 42.9 1.0 MG A:MG111 4.2 60.9 1.0 C2 A:C38 4.2 58.7 1.0 O2 A:C38 4.2 54.2 1.0 O4' A:A39 4.3 43.8 1.0 N3 A:C38 4.3 54.4 1.0 N2 A:G19 4.4 57.7 1.0 C2' A:G59 4.4 45.4 1.0 N7 A:A39 4.5 41.3 1.0 C1' A:G59 4.6 44.8 1.0 C2' A:C38 4.6 62.8 1.0 N9 A:A39 4.6 45.9 1.0 O4' A:G59 4.7 46.1 1.0 N1 A:A18 4.7 50.3 1.0 C4' A:G59 4.8 48.1 1.0 N1 A:C38 4.8 61.6 1.0 C4 A:C38 4.9 57.9 1.0 C1' A:A39 4.9 46.7 1.0 O5' A:A39 5.0 60.0 1.0

Magnesium binding site 10 out of 19 in the Crystal Structure of Nad+ -II Riboswitch in Complex with Nad+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Crystal Structure of Nad+ -II Riboswitch in Complex with Nad+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg111 b:60.9 occ:1.00 O A:HOH261 1.9 48.9 1.0 O A:HOH274 2.2 67.3 1.0 O A:HOH257 3.3 59.6 1.0 O A:HOH266 3.4 61.5 1.0 N4 A:C38 3.5 54.6 1.0 C4 A:C38 3.6 57.9 1.0 C5 A:C38 3.6 63.2 1.0 O A:HOH272 3.9 57.9 1.0 N6 A:A18 4.0 49.3 1.0 O A:HOH219 4.1 58.4 1.0 MG A:MG110 4.2 61.0 1.0 N3 A:C38 4.3 54.4 1.0 C6 A:C38 4.4 59.9 1.0 O A:HOH224 4.6 61.4 1.0 O A:HOH256 4.9 60.4 1.0 C2 A:C38 5.0 58.7 1.0 N1 A:C38 5.0 61.6 1.0

X.Xu, M.Egger, C.Li, H.Chen, R.Micura, A.Ren. Structure-Based Investigations of the Nad+-II Riboswitch. Nucleic Acids Res. 2023.
ISSN: ESSN 1362-4962
PubMed: 36610789
DOI: 10.1093/NAR/GKAC1227