Magnesium in PDB 8xze: 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: 8xze 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)	39.07 / 2.34
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	50.276, 58.127, 62.096, 90, 90, 90
R / Rfree (%)	19.7 / 24.5

The structure of Crystal Structure of Thf-II Riboswitch with Thf and Soaked with Ir also contains other interesting chemical elements:

Iridium

(Ir)

3 atoms

The binding sites of Magnesium atom in the Crystal Structure of Thf-II Riboswitch with Thf and Soaked with Ir (pdb code 8xze). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of Thf-II Riboswitch with Thf and Soaked with Ir, PDB code: 8xze:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 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:Mg102 b:60.1 occ:1.00 O A:HOH214 1.9 62.6 1.0 O A:HOH202 2.4 54.8 1.0 OP2 A:C20 3.5 45.3 1.0 OP1 A:A17 4.0 63.5 1.0 OP2 A:C18 4.2 41.4 1.0 P A:C20 4.5 46.5 1.0 OP2 A:A17 4.8 51.0 1.0 OP1 A:C20 4.8 53.5 1.0 P A:A17 4.9 58.5 1.0 O3' A:C20 5.0 49.7 1.0 O5' A:C20 5.0 53.2 1.0

Magnesium binding site 2 out of 4 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:Mg103 b:69.3 occ:1.00 O A:HOH203 1.9 62.8 1.0 O A:HOH205 2.2 76.8 1.0 O6 A:GTP1 3.2 66.4 1.0 N7 A:GTP1 3.6 82.8 1.0 C6 A:GTP1 3.9 65.6 1.0 C5 A:GTP1 4.0 66.6 1.0 O4 A:U53 4.3 56.0 1.0 O1B A:GTP1 4.6 118.6 1.0 C8 A:GTP1 4.7 87.6 1.0

Magnesium binding site 3 out of 4 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:Mg104 b:61.4 occ:1.00 O3' A:U53 1.8 65.1 1.0 O2' A:U53 2.3 66.5 1.0 C3' A:U53 2.6 67.3 1.0 C2' A:U53 2.9 60.5 1.0 C1' A:U53 3.9 61.2 1.0 C4' A:U53 4.0 65.3 1.0 O4' A:U53 4.6 58.1 1.0

Magnesium binding site 4 out of 4 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 4 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:55.1 occ:1.00 O A:HOH212 2.0 62.3 1.0 O A:HOH206 2.1 51.5 1.0 O A:HOH213 2.1 52.3 1.0 O A:HOH208 2.6 48.9 1.0 N7 A:G7 3.7 48.4 1.0 O A:HOH211 3.8 55.6 1.0 OP2 A:G44 3.9 40.8 1.0 O6 A:G7 4.1 37.8 1.0 O A:HOH209 4.2 53.9 1.0 OP2 A:G45 4.2 53.4 1.0 OP2 A:U6 4.4 39.0 1.0 C5 A:G7 4.6 45.2 1.0 C6 A:G7 4.7 39.9 1.0 C8 A:G7 4.7 44.7 1.0 P A:G44 4.9 45.7 1.0 C5 A:U6 5.0 41.1 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