Magnesium in PDB 8xzm: Crystal Structure of Fole Riboswitch with Dhn

The structure of Crystal Structure of Fole Riboswitch with Dhn, PDB code: 8xzm 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)	28.54 / 1.98
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	48.808, 57.085, 63.422, 90, 90, 90
R / Rfree (%)	20.8 / 23.8

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

Magnesium binding site 1 out of 5 in the Crystal Structure of Fole Riboswitch with Dhn


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 Dhn within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg101 b:65.6 occ:1.00 O3' A:U53 1.9 66.7 1.0 O2' A:U53 2.1 62.9 1.0 O A:HOH202 2.1 60.2 1.0 C3' A:U53 2.4 61.7 1.0 C2' A:U53 2.6 57.5 1.0 C1' A:U53 3.9 60.7 1.0 C4' A:U53 3.9 57.8 1.0 O4' A:U53 4.5 56.5 1.0 O A:HOH233 4.8 58.2 1.0 C5' A:U53 5.0 55.1 1.0 N1 A:U53 5.0 57.0 1.0

Magnesium binding site 2 out of 5 in the Crystal Structure of Fole Riboswitch with Dhn


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 Dhn within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg102 b:58.1 occ:1.00 O A:HOH229 1.9 52.3 1.0 O A:HOH214 2.5 46.0 1.0 OP2 A:G45 3.5 39.0 1.0 OP2 A:G44 3.6 36.8 1.0 O A:HOH226 3.7 47.0 1.0 O6 A:G46 3.7 40.0 1.0 O A:HOH227 4.0 44.4 1.0 N7 A:G7 4.3 37.6 1.0 O5' A:G44 4.3 39.2 1.0 O6 A:G7 4.5 39.5 1.0 O A:HOH219 4.5 46.0 1.0 P A:G44 4.6 40.9 1.0 C6 A:G46 4.7 41.0 1.0 C8 A:G44 4.7 36.6 1.0 N7 A:G44 4.7 39.2 1.0 N7 A:G46 4.8 39.5 1.0 C5 A:G7 4.8 38.4 1.0 N7 A:G45 4.8 38.7 1.0 C6 A:G7 4.8 41.5 1.0 P A:G45 4.9 44.1 1.0

Magnesium binding site 3 out of 5 in the Crystal Structure of Fole Riboswitch with Dhn


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 Dhn within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg103 b:54.6 occ:1.00 O A:HOH221 2.6 49.8 1.0 O6 A:G7 2.7 39.5 1.0 O4 A:U6 2.8 41.9 1.0 C6 A:G7 3.5 41.5 1.0 O A:HOH206 3.6 49.9 1.0 C4 A:U6 3.8 38.9 1.0 N1 A:G7 3.9 40.8 1.0 O A:HOH230 4.0 40.7 1.0 O A:HOH205 4.1 47.6 1.0 C5 A:U6 4.2 37.4 1.0 C5 A:G7 4.6 38.4 1.0 N7 A:G5 4.7 41.7 1.0

Magnesium binding site 4 out of 5 in the Crystal Structure of Fole Riboswitch with Dhn


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 Dhn within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg104 b:60.7 occ:1.00 O A:HOH227 2.1 44.4 1.0 O A:HOH219 2.3 46.0 1.0 O A:HOH226 2.3 47.0 1.0 OP2 A:U8 4.0 40.8 1.0 O A:HOH229 4.1 52.3 1.0 O6 A:G46 4.4 40.0 1.0 O6 A:G44 4.4 40.2 1.0 N4 A:C43 4.7 36.1 1.0 N7 A:G44 4.8 39.2 1.0 N1 A:G46 4.8 42.0 1.0 C5 A:C43 4.8 37.7 1.0 OP1 A:U8 4.9 39.6 1.0 P A:U8 4.9 42.6 1.0 C6 A:G46 4.9 41.0 1.0 O6 A:G45 5.0 43.8 1.0

Magnesium binding site 5 out of 5 in the Crystal Structure of Fole Riboswitch with Dhn


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 Dhn within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg105 b:51.0 occ:1.00 O A:HOH224 2.6 47.1 1.0 O4 A:U22 2.6 39.7 1.0 O A:HOH218 2.7 41.3 1.0 O A:HOH231 2.8 54.8 1.0 C4 A:U22 3.6 38.6 1.0 N4 A:C23 4.0 35.8 1.0 C5 A:U22 4.0 35.1 1.0 O A:HOH210 4.2 43.7 1.0 N6 A:A39 4.3 36.0 1.0 N7 A:G21 4.3 37.8 1.0 O6 A:G21 4.3 36.3 1.0 O6 A:G38 4.4 40.8 1.0 O A:HOH211 4.6 45.9 1.0 C5 A:G21 4.7 35.0 1.0 C6 A:G21 4.8 35.8 1.0 N3 A:U22 4.8 35.6 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