Magnesium in PDB 8vqv: Structure of S. Odontolytica Ztp Riboswitch Bound to M-1-Pyridinyl- Aica

The structure of Structure of S. Odontolytica Ztp Riboswitch Bound to M-1-Pyridinyl- Aica, PDB code: 8vqv was solved by C.P.Jones, A.R.Ferre D'amare, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.44 / 2.43
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	41.035, 41.035, 237.398, 90, 90, 90
R / Rfree (%)	20.7 / 25.6

The binding sites of Magnesium atom in the Structure of S. Odontolytica Ztp Riboswitch Bound to M-1-Pyridinyl- Aica (pdb code 8vqv). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Structure of S. Odontolytica Ztp Riboswitch Bound to M-1-Pyridinyl- Aica, PDB code: 8vqv:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Structure of S. Odontolytica Ztp Riboswitch Bound to M-1-Pyridinyl- Aica


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of S. Odontolytica Ztp Riboswitch Bound to M-1-Pyridinyl- Aica within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg101 b:62.1 occ:1.00 O A:HOH213 2.0 55.6 1.0 O06 A:UG4103 2.1 57.4 1.0 O A:HOH207 2.2 60.9 1.0 C04 A:UG4103 3.0 58.8 1.0 N05 A:UG4103 3.3 61.5 1.0 N3 A:G59 4.0 65.2 1.0 N2 A:G59 4.1 57.4 1.0 C03 A:UG4103 4.3 54.4 1.0 C2 A:G59 4.5 59.6 1.0 O2' A:G59 4.6 69.1 1.0 N01 A:UG4103 4.7 51.8 1.0 C1' A:G59 5.0 68.7 1.0 C02 A:UG4103 5.0 51.1 1.0

Magnesium binding site 2 out of 2 in the Structure of S. Odontolytica Ztp Riboswitch Bound to M-1-Pyridinyl- Aica


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of S. Odontolytica Ztp Riboswitch Bound to M-1-Pyridinyl- Aica within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg102 b:82.7 occ:1.00 O A:HOH222 2.2 80.2 1.0 O A:HOH223 2.2 84.5 1.0 O A:HOH204 2.2 85.2 1.0 O A:HOH218 2.2 85.7 1.0 O A:HOH217 2.2 77.9 1.0 O A:HOH212 2.2 74.1 1.0 O6 A:G24 4.2 92.2 1.0 O6 A:G23 4.2 86.4 1.0 OP1 A:G13 4.3 62.5 1.0 O4 A:U22 4.6 82.0 1.0 N7 A:G23 4.7 91.1 1.0 N4 A:C29 4.8 75.6 1.0

C.Fullenkamp, S.Mehdi, C.Jones, L.Tenney, P.Pichling, P.R.Prestwood, A.R.Ferre-D'amare, P.Tiwary, J.Schneekloth. Machine Learning-Augmented Molecular Dynamics Simulations (Md) Reveal Insights Into the Disconnect Between Affinity and Activation of Ztp Riboswitch Ligands. Angew.Chem.Int.Ed.Engl. 05971 2025.
ISSN: ESSN 1521-3773
PubMed: 40310613
DOI: 10.1002/ANIE.202505971