Magnesium in PDB 8xzq: Crystal Structure of Fole Riboswitch with 8-N Guanine

The structure of Crystal Structure of Fole Riboswitch with 8-N Guanine, PDB code: 8xzq was solved by C.Y.Li, A.M.Ren, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.63 / 1.83
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	49.268, 56.843, 62.778, 90, 90, 90
R / Rfree (%)	20.9 / 23.5

The binding sites of Magnesium atom in the Crystal Structure of Fole Riboswitch with 8-N Guanine (pdb code 8xzq). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 7 binding sites of Magnesium where determined in the Crystal Structure of Fole Riboswitch with 8-N Guanine, PDB code: 8xzq:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in the Crystal Structure of Fole Riboswitch with 8-N Guanine


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 Fole Riboswitch with 8-N Guanine within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg103 b:60.1 occ:1.00 O2' A:U53 1.9 64.8 1.0 O A:HOH201 2.1 65.9 1.0 O3' A:U53 2.9 63.9 1.0 C2' A:U53 3.1 60.9 1.0 C3' A:U53 3.4 60.7 1.0 C4' A:U53 3.8 58.8 1.0 C1' A:U53 4.1 61.3 1.0 O4' A:U53 4.4 57.9 1.0

Magnesium binding site 2 out of 7 in the Crystal Structure of Fole Riboswitch with 8-N Guanine


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 Fole Riboswitch with 8-N Guanine within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg104 b:65.2 occ:1.00 O6 A:G2 3.0 56.8 1.0 O6 A:G3 3.2 48.5 1.0 C6 A:G2 3.9 58.3 1.0 N7 A:G2 4.1 65.4 1.0 C6 A:G3 4.3 49.6 1.0 N4 A:C51 4.3 42.9 1.0 O A:HOH223 4.3 48.0 1.0 C5 A:G2 4.3 60.5 1.0 N4 A:C52 4.6 47.8 1.0 N7 A:G3 4.6 55.8 1.0 C5 A:G3 4.8 53.3 1.0

Magnesium binding site 3 out of 7 in the Crystal Structure of Fole Riboswitch with 8-N Guanine


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 Fole Riboswitch with 8-N Guanine within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg105 b:48.0 occ:1.00 O A:HOH223 2.7 48.0 1.0 N7 A:G50 2.9 40.4 1.0 C5 A:C49 3.6 41.4 1.0 C4 A:C49 3.6 40.4 1.0 N4 A:C49 3.7 41.0 1.0 N4 A:C51 3.8 42.9 1.0 C8 A:G50 3.8 39.8 1.0 C5 A:G50 4.0 39.5 1.0 O6 A:G50 4.0 41.4 1.0 C6 A:C49 4.3 39.8 1.0 N3 A:C49 4.3 39.6 1.0 C6 A:G50 4.4 40.2 1.0 OP2 A:G50 4.5 38.5 1.0 C4 A:C51 4.7 40.5 1.0 N1 A:C49 4.8 40.0 1.0 C2 A:C49 4.9 39.0 1.0 C5 A:C51 4.9 38.8 1.0 O A:HOH234 5.0 51.0 1.0

Magnesium binding site 4 out of 7 in the Crystal Structure of Fole Riboswitch with 8-N Guanine


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 Fole Riboswitch with 8-N Guanine within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg106 b:57.8 occ:1.00 O A:HOH234 2.3 51.0 1.0 O A:HOH224 2.4 40.1 1.0 O A:HOH226 2.6 49.9 1.0 O6 A:G5 2.7 38.5 1.0 O4 A:U4 2.8 47.0 1.0 C4 A:U4 3.5 47.8 1.0 O A:HOH210 3.6 52.7 1.0 O4 A:U6 3.7 40.6 1.0 C6 A:G5 3.7 40.9 1.0 N4 A:C49 4.0 41.0 1.0 N3 A:U4 4.0 45.4 1.0 N7 A:G5 4.1 41.0 1.0 C5 A:G5 4.3 41.2 1.0 C5 A:U4 4.4 50.4 1.0 O6 A:G50 4.4 41.4 1.0 C4 A:U6 4.5 37.7 1.0 O A:HOH207 4.8 43.3 1.0 N1 A:G5 5.0 40.8 1.0

Magnesium binding site 5 out of 7 in the Crystal Structure of Fole Riboswitch with 8-N Guanine


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 Fole Riboswitch with 8-N Guanine within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg107 b:55.3 occ:1.00 O A:HOH211 2.0 46.0 1.0 O A:HOH238 2.1 52.0 1.0 O6 A:G46 3.1 37.6 1.0 N7 A:G45 3.5 36.8 1.0 O A:HOH227 3.7 43.0 1.0 OP2 A:G45 3.7 41.8 1.0 O A:HOH233 3.7 46.2 1.0 O A:HOH230 3.8 42.1 1.0 C6 A:G46 3.8 40.4 1.0 C8 A:G45 3.9 38.3 1.0 N7 A:G46 3.9 40.4 1.0 N7 A:G44 4.0 36.0 1.0 C8 A:G44 4.1 39.7 1.0 C5 A:G46 4.2 40.4 1.0 OP2 A:G44 4.4 37.1 1.0 C5 A:G44 4.5 36.1 1.0 N7 A:G7 4.6 41.4 1.0 O6 A:G7 4.7 39.7 1.0 N9 A:G44 4.7 37.2 1.0 O5' A:G44 4.7 38.3 1.0 C5 A:G45 4.8 39.9 1.0 C5 A:G7 4.9 41.4 1.0 C6 A:G7 4.9 39.5 1.0 C3' A:G44 4.9 39.9 1.0 P A:G45 4.9 44.2 1.0 C4 A:G44 4.9 36.0 1.0 N1 A:G46 5.0 36.0 1.0

Magnesium binding site 6 out of 7 in the Crystal Structure of Fole Riboswitch with 8-N Guanine


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 Fole Riboswitch with 8-N Guanine within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg108 b:47.4 occ:1.00 N2 A:G44 3.4 37.5 1.0 C1' A:G45 3.9 42.4 1.0 O4' A:G45 4.0 40.6 1.0 C2 A:G44 4.3 38.1 1.0 N3 A:G44 4.3 37.0 1.0 C1' A:G12 4.5 43.4 1.0 O2' A:G45 4.7 38.6 1.0 N9 A:G45 4.7 38.3 1.0 O2' A:G12 4.7 42.1 1.0 O4' A:G12 4.9 43.3 1.0 C4' A:G45 4.9 41.1 1.0 C2' A:G45 5.0 41.9 1.0

Magnesium binding site 7 out of 7 in the Crystal Structure of Fole Riboswitch with 8-N Guanine


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 Fole Riboswitch with 8-N Guanine within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg109 b:42.1 occ:1.00 O A:HOH218 2.5 45.7 1.0 O4 A:U22 2.5 36.4 1.0 O A:HOH222 2.7 39.0 1.0 O A:HOH217 2.7 32.9 1.0 C4 A:U22 3.5 34.1 1.0 O A:HOH215 3.8 39.7 1.0 C5 A:U22 4.0 32.9 1.0 N7 A:G21 4.2 34.1 1.0 N4 A:C23 4.2 35.6 1.0 O A:HOH228 4.2 37.6 1.0 N6 A:A39 4.4 37.4 1.0 O6 A:G21 4.4 34.0 1.0 O A:HOH204 4.4 39.9 1.0 O6 A:G38 4.6 41.8 1.0 C5 A:G21 4.7 34.2 1.0 O A:HOH237 4.8 43.4 1.0 N3 A:U22 4.8 33.6 1.0 C6 A:G21 4.8 33.3 1.0 OP1 A:G21 5.0 36.3 1.0

C.Li, X.Xu, Z.Geng, L.Zheng, Q.Song, X.Shen, J.Wu, J.Zhao, H.Li, M.He, X.Tai, L.Zhang, J.Ma, Y.Dong, A.Ren. Structure-Based Characterization and Compound Identification of the Wild-Type Thf Class-II Riboswitch. Nucleic Acids Res. 2024.
ISSN: ESSN 1362-4962
PubMed: 38769061
DOI: 10.1093/NAR/GKAE377