Magnesium in PDB 8xzw: Crystal Structure of Thf-II Riboswitch with Thf and Soaked with Ir

The structure of Crystal Structure of Thf-II Riboswitch with Thf and Soaked with Ir, PDB code: 8xzw 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)	19.50 / 1.91
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	49.105, 57.5, 62.185, 90, 90, 90
R / Rfree (%)	21.5 / 25.1

The binding sites of Magnesium atom in the Crystal Structure of Thf-II Riboswitch with Thf and Soaked with Ir (pdb code 8xzw). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of Thf-II Riboswitch with Thf and Soaked with Ir, PDB code: 8xzw:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Crystal Structure of Thf-II Riboswitch with Thf and Soaked with Ir


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 Thf-II Riboswitch with Thf and Soaked with Ir within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg103 b:68.4 occ:1.00 O3' A:U53 1.8 71.8 1.0 O2' A:U53 2.0 74.7 1.0 O A:HOH202 2.4 66.4 1.0 C3' A:U53 2.6 68.5 1.0 C2' A:U53 2.7 70.6 1.0 C1' A:U53 3.6 67.2 1.0 C4' A:U53 4.0 68.1 1.0 O4' A:U53 4.4 68.1 1.0 O A:HOH218 4.7 63.0 1.0 N1 A:U53 4.8 66.7 1.0 O2 A:U53 4.9 68.6 1.0

Magnesium binding site 2 out of 3 in the Crystal Structure of Thf-II Riboswitch with Thf and Soaked with Ir


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 Thf-II Riboswitch with Thf and Soaked with Ir within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg104 b:62.8 occ:1.00 O A:HOH208 2.0 56.0 1.0 O6 A:G46 3.5 44.9 1.0 O A:HOH216 3.5 58.0 1.0 O A:HOH213 3.6 54.6 1.0 OP2 A:G45 3.7 51.6 1.0 N7 A:G45 3.9 46.9 1.0 OP2 A:G44 4.1 51.1 1.0 N7 A:G44 4.1 44.8 1.0 C8 A:G44 4.1 46.7 1.0 N7 A:G46 4.2 47.7 1.0 C8 A:G45 4.2 44.7 1.0 C6 A:G46 4.3 48.1 1.0 O5' A:G44 4.4 51.2 1.0 C5 A:G46 4.6 46.6 1.0 O6 A:G7 4.6 47.2 1.0 N7 A:G7 4.6 51.1 1.0 C5 A:G44 4.7 42.3 1.0 N9 A:G44 4.8 44.9 1.0 C3' A:G44 4.8 52.0 1.0 P A:G44 4.9 54.7 1.0 C5 A:G7 4.9 47.3 1.0 C6 A:G7 4.9 47.3 1.0 P A:G45 4.9 49.3 1.0 O A:HOH209 5.0 54.2 1.0

Magnesium binding site 3 out of 3 in the Crystal Structure of Thf-II Riboswitch with Thf and Soaked with Ir


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 Thf-II Riboswitch with Thf and Soaked with Ir within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg105 b:65.3 occ:1.00 O A:HOH207 2.1 60.8 1.0 O A:HOH203 2.3 53.8 1.0 O A:HOH204 2.4 51.2 1.0 O6 A:G37 4.1 51.3 1.0 O6 A:G38 4.3 52.2 1.0 O4 A:U22 4.6 45.9 1.0 N7 A:G37 4.6 58.7 1.0 N4 A:C23 4.7 46.6 1.0 C6 A:G37 4.9 54.3 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