Magnesium in PDB 7tzu: Crystal Structure of the E. Coli Thim Riboswitch Bound to 1-(4- (Piperazin-1-Yl)Pyridin-3-Yl)-N-(Quinoxalin-6-Ylmethyl)Methanamine (Linked Compound 38)

The structure of Crystal Structure of the E. Coli Thim Riboswitch Bound to 1-(4- (Piperazin-1-Yl)Pyridin-3-Yl)-N-(Quinoxalin-6-Ylmethyl)Methanamine (Linked Compound 38), PDB code: 7tzu was solved by A.Nuthanakanti, A.Serganov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.55 / 2.87
Space group	P 32 1 2
Cell size a, b, c (Å), α, β, γ (°)	61.702, 61.702, 102.789, 90, 90, 120
R / Rfree (%)	22.9 / 27

The structure of Crystal Structure of the E. Coli Thim Riboswitch Bound to 1-(4- (Piperazin-1-Yl)Pyridin-3-Yl)-N-(Quinoxalin-6-Ylmethyl)Methanamine (Linked Compound 38) also contains other interesting chemical elements:

Manganese

(Mn)

4 atoms

The binding sites of Magnesium atom in the Crystal Structure of the E. Coli Thim Riboswitch Bound to 1-(4- (Piperazin-1-Yl)Pyridin-3-Yl)-N-(Quinoxalin-6-Ylmethyl)Methanamine (Linked Compound 38) (pdb code 7tzu). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of the E. Coli Thim Riboswitch Bound to 1-(4- (Piperazin-1-Yl)Pyridin-3-Yl)-N-(Quinoxalin-6-Ylmethyl)Methanamine (Linked Compound 38), PDB code: 7tzu:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of the E. Coli Thim Riboswitch Bound to 1-(4- (Piperazin-1-Yl)Pyridin-3-Yl)-N-(Quinoxalin-6-Ylmethyl)Methanamine (Linked Compound 38)


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 the E. Coli Thim Riboswitch Bound to 1-(4- (Piperazin-1-Yl)Pyridin-3-Yl)-N-(Quinoxalin-6-Ylmethyl)Methanamine (Linked Compound 38) within 5.0Å range:

Magnesium binding site 2 out of 2 in the Crystal Structure of the E. Coli Thim Riboswitch Bound to 1-(4- (Piperazin-1-Yl)Pyridin-3-Yl)-N-(Quinoxalin-6-Ylmethyl)Methanamine (Linked Compound 38)


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 the E. Coli Thim Riboswitch Bound to 1-(4- (Piperazin-1-Yl)Pyridin-3-Yl)-N-(Quinoxalin-6-Ylmethyl)Methanamine (Linked Compound 38) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg103 b:98.5 occ:1.00 OP1 A:A80 2.2 123.4 1.0 OP2 A:G81 2.8 107.7 1.0 P A:A80 3.3 120.5 1.0 O5' A:A80 3.3 112.2 1.0 OP2 A:U54 4.1 159.3 1.0 N7 A:G81 4.1 83.4 1.0 OP2 A:A80 4.1 122.4 1.0 P A:G81 4.2 109.0 1.0 C8 A:G81 4.4 85.7 1.0 O3' A:U79 4.5 122.7 1.0 O5' A:G81 4.5 94.3 1.0 C3' A:A80 4.5 103.9 1.0 C5' A:A80 4.6 115.0 1.0 O6 A:G83 4.8 83.8 1.0 O3' A:A80 4.9 103.7 1.0

M.J.Zeller, O.Favorov, K.Li, A.Nuthanakanti, D.Hussein, A.Michaud, D.A.Lafontaine, S.Busan, A.Serganov, J.Aube, K.M.Weeks. Shape-Enabled Fragment-Based Ligand Discovery For Rna. Proc.Natl.Acad.Sci.Usa V. 119 60119 2022.
ISSN: ESSN 1091-6490
PubMed: 35561226
DOI: 10.1073/PNAS.2122660119