Magnesium in PDB 8xzr: Crystal Structure of Fole Riboswitch with 8-NH2 Guanine

The structure of Crystal Structure of Fole Riboswitch with 8-NH2 Guanine, PDB code: 8xzr 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)	25.15 / 1.83
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	50.299, 58.59, 61.119, 90, 90, 90
R / Rfree (%)	21.6 / 25

The binding sites of Magnesium atom in the Crystal Structure of Fole Riboswitch with 8-NH2 Guanine (pdb code 8xzr). 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-NH2 Guanine, PDB code: 8xzr:
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-NH2 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-NH2 Guanine within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg103 b:59.3 occ:1.00 O3' A:U53 2.0 58.4 1.0 C3' A:U53 2.3 59.5 1.0 O2' A:U53 2.5 64.0 1.0 C2' A:U53 2.8 57.6 1.0 O A:HOH245 3.3 56.8 1.0 C4' A:U53 3.8 53.0 1.0 C1' A:U53 4.0 53.3 1.0 O4' A:U53 4.5 50.7 1.0 C5' A:U53 4.6 53.2 1.0

Magnesium binding site 2 out of 7 in the Crystal Structure of Fole Riboswitch with 8-NH2 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-NH2 Guanine within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg104 b:55.6 occ:1.00 O A:HOH233 2.0 40.3 1.0 O A:HOH238 2.4 48.0 1.0 O6 A:G5 2.8 38.1 1.0 O4 A:U4 3.3 44.1 1.0 O4 A:U6 3.4 35.1 1.0 C6 A:G5 4.0 38.5 1.0 C4 A:U4 4.0 42.2 1.0 N4 A:C49 4.1 38.8 1.0 C4 A:U6 4.4 38.9 1.0 N7 A:G5 4.4 38.7 1.0 N3 A:U4 4.6 39.2 1.0 C5 A:G5 4.6 38.3 1.0 O6 A:G48 4.8 41.1 1.0 N3 A:U6 4.9 36.0 1.0 C5 A:U4 4.9 41.9 1.0 O6 A:G50 4.9 37.9 1.0

Magnesium binding site 3 out of 7 in the Crystal Structure of Fole Riboswitch with 8-NH2 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-NH2 Guanine within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg105 b:51.1 occ:1.00 O A:HOH226 2.0 46.0 1.0 O6 A:G46 3.3 35.7 1.0 N7 A:G45 3.9 36.1 1.0 OP2 A:G45 3.9 47.2 1.0 N7 A:G44 4.0 34.0 1.0 OP2 A:G44 4.1 40.5 1.0 O A:HOH244 4.1 46.0 1.0 C6 A:G46 4.1 38.6 1.0 C8 A:G44 4.2 38.0 1.0 N7 A:G46 4.3 38.9 1.0 C8 A:G45 4.3 39.6 1.0 C5 A:G46 4.5 39.1 1.0 O5' A:G44 4.6 42.2 1.0 C5 A:G44 4.6 35.1 1.0 N7 A:G7 4.6 36.5 1.0 O6 A:G7 4.6 44.7 1.0 C5 A:G7 4.9 40.9 1.0 C6 A:G7 4.9 40.3 1.0 N9 A:G44 4.9 37.8 1.0 P A:G44 5.0 37.5 1.0

Magnesium binding site 4 out of 7 in the Crystal Structure of Fole Riboswitch with 8-NH2 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-NH2 Guanine within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg106 b:48.0 occ:1.00 N3 A:G12 2.8 38.6 1.0 O A:HOH212 2.9 46.6 1.0 O2' A:G12 3.1 39.2 1.0 O4' A:U13 3.3 38.9 1.0 C2' A:G12 3.5 40.6 1.0 N2 A:G12 3.5 36.5 1.0 C2 A:G12 3.6 35.6 1.0 C1' A:G12 3.7 38.4 1.0 C4 A:G12 3.9 36.1 1.0 C1' A:U13 4.0 38.3 1.0 O A:HOH243 4.1 46.4 1.0 N3 A:G44 4.2 40.0 1.0 N9 A:G12 4.2 38.2 1.0 C4' A:U13 4.3 42.3 1.0 N2 A:G44 4.4 37.0 1.0 C2 A:G44 4.6 38.6 1.0 N1 A:U13 4.6 38.1 1.0 C5' A:U13 4.7 41.0 1.0 C6 A:U13 4.9 40.4 1.0 O4' A:G12 4.9 41.1 1.0 C3' A:G12 5.0 43.9 1.0 N1 A:G12 5.0 36.3 1.0

Magnesium binding site 5 out of 7 in the Crystal Structure of Fole Riboswitch with 8-NH2 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-NH2 Guanine within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg107 b:47.8 occ:1.00 O2' A:U14 2.2 40.0 1.0 OP2 A:C15 2.3 49.9 1.0 O A:HOH237 2.6 54.6 1.0 O3' A:U14 3.0 52.9 1.0 P A:C15 3.2 50.1 1.0 C2' A:U14 3.3 46.9 1.0 C3' A:U14 3.7 48.2 1.0 C1' A:U14 3.8 43.5 1.0 OP1 A:C15 4.2 48.8 1.0 OP1 A:G21 4.3 40.7 1.0 O5' A:C15 4.4 55.1 1.0 C5' A:C15 4.5 65.2 1.0 OP2 A:A17 4.5 46.2 1.0 OP2 A:G21 4.5 38.5 1.0 O A:HOH217 4.5 43.8 1.0 O2 A:U14 4.6 38.3 1.0 N1 A:U14 4.7 40.4 1.0 O4' A:U14 4.8 43.0 1.0 N4 A:C18 4.8 34.0 1.0 C4' A:U14 4.9 46.0 1.0 P A:G21 4.9 38.1 1.0 C2 A:U14 5.0 40.7 1.0

Magnesium binding site 6 out of 7 in the Crystal Structure of Fole Riboswitch with 8-NH2 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-NH2 Guanine within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg108 b:59.0 occ:1.00 O A:HOH235 2.8 49.6 1.0 O A:HOH249 3.3 51.5 1.0 OP1 A:U14 3.3 44.9 1.0 O A:HOH247 3.5 49.9 1.0 OP2 A:U14 3.5 41.9 1.0 OP1 A:G37 3.8 47.0 1.0 P A:U14 3.9 46.2 1.0 OP2 A:G37 4.2 45.6 1.0 O A:HOH241 4.5 50.8 1.0 P A:G37 4.5 45.2 1.0 O A:HOH216 4.8 48.5 1.0 O5' A:U14 5.0 41.7 1.0

Magnesium binding site 7 out of 7 in the Crystal Structure of Fole Riboswitch with 8-NH2 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-NH2 Guanine within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg109 b:40.8 occ:1.00 O A:HOH214 2.1 39.0 1.0 O A:HOH205 2.1 36.2 1.0 O A:HOH209 2.2 33.6 1.0 O A:HOH250 2.2 39.0 1.0 O A:HOH215 2.2 40.8 1.0 O A:HOH251 2.2 37.4 1.0 O6 A:G37 4.0 41.9 1.0 O6 A:G38 4.2 39.0 1.0 O4 A:U22 4.2 35.0 1.0 O A:HOH222 4.3 39.0 1.0 N7 A:G37 4.3 39.6 1.0 O A:HOH221 4.4 41.1 1.0 O A:HOH239 4.5 33.5 1.0 O A:HOH240 4.6 36.7 1.0 O A:HOH219 4.7 38.3 1.0 C6 A:G37 4.7 39.1 1.0 N4 A:C23 4.7 31.8 1.0 C5 A:G37 4.8 39.0 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