Magnesium in PDB 7tzs: Crystal Structure of the E. Coli Thim Riboswitch in Complex with Quinoxalin-6-Ylmethanamine (Compound 17)

The structure of Crystal Structure of the E. Coli Thim Riboswitch in Complex with Quinoxalin-6-Ylmethanamine (Compound 17), PDB code: 7tzs 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)	29.78 / 2.21
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	148.734, 30.4, 95.57, 90, 93.51, 90
R / Rfree (%)	20.4 / 24.5

The structure of Crystal Structure of the E. Coli Thim Riboswitch in Complex with Quinoxalin-6-Ylmethanamine (Compound 17) also contains other interesting chemical elements:

Potassium	(K)	5 atoms
Sodium	(Na)	1 atom

The binding sites of Magnesium atom in the Crystal Structure of the E. Coli Thim Riboswitch in Complex with Quinoxalin-6-Ylmethanamine (Compound 17) (pdb code 7tzs). 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 the E. Coli Thim Riboswitch in Complex with Quinoxalin-6-Ylmethanamine (Compound 17), PDB code: 7tzs:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Crystal Structure of the E. Coli Thim Riboswitch in Complex with Quinoxalin-6-Ylmethanamine (Compound 17)


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 in Complex with Quinoxalin-6-Ylmethanamine (Compound 17) within 5.0Å range: probe atom residue distance (Å) B Occ X:Mg102 b:30.4 occ:1.00 O6 X:G72 2.3 34.0 1.0 O4 X:U59 2.4 28.2 1.0 O X:HOH277 2.4 28.9 1.0 O6 X:G78 2.4 25.3 1.0 O6 X:G60 2.4 28.9 1.0 O X:HOH286 2.6 27.8 1.0 C4 X:U59 3.2 29.4 1.0 C6 X:G60 3.3 28.4 1.0 C6 X:G72 3.4 36.2 1.0 C6 X:G78 3.4 29.8 1.0 N1 X:G60 3.6 26.9 1.0 C5 X:U59 3.7 29.1 1.0 N1 X:G78 3.7 29.1 1.0 O X:HOH243 3.7 29.4 1.0 N1 X:G72 3.9 32.0 1.0 N6 X:A80 4.2 29.4 1.0 N4 X:C58 4.3 26.4 1.0 O X:HOH264 4.3 30.1 1.0 C5 X:C58 4.4 26.3 1.0 O X:HOH244 4.4 27.4 1.0 C4 X:C58 4.4 29.2 1.0 N3 X:U59 4.4 28.5 1.0 C5 X:G60 4.5 29.6 1.0 O X:HOH254 4.5 30.0 1.0 C5 X:G72 4.6 35.3 1.0 C5 X:G78 4.7 30.1 1.0 C2 X:G60 4.9 29.5 1.0 C6 X:U59 5.0 30.9 1.0 C2 X:G78 5.0 28.3 1.0

Magnesium binding site 2 out of 5 in the Crystal Structure of the E. Coli Thim Riboswitch in Complex with Quinoxalin-6-Ylmethanamine (Compound 17)


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 in Complex with Quinoxalin-6-Ylmethanamine (Compound 17) within 5.0Å range: probe atom residue distance (Å) B Occ X:Mg103 b:33.1 occ:1.00 O X:HOH269 2.3 24.7 1.0 O X:HOH265 2.3 33.5 1.0 O X:HOH296 2.5 37.0 1.0 N7 X:A41 2.5 27.1 1.0 O X:HOH240 2.5 30.2 1.0 C8 X:A41 3.5 28.3 1.0 C5 X:A41 3.6 27.7 1.0 N6 X:A41 3.6 29.4 1.0 MG X:MG104 3.7 48.3 1.0 C6 X:A41 4.0 28.2 1.0 O X:HOH235 4.1 39.6 1.0 O6 X:G42 4.2 24.7 1.0 O X:HOH298 4.4 42.5 1.0 O2' X:G40 4.5 28.5 1.0 O X:HOH219 4.6 28.6 1.0 OP1 X:C57 4.7 28.9 1.0 N9 X:A41 4.7 29.0 1.0 C4 X:A41 4.8 29.5 1.0 C6 X:G42 4.9 27.2 1.0 O X:HOH303 4.9 37.1 1.0

Magnesium binding site 3 out of 5 in the Crystal Structure of the E. Coli Thim Riboswitch in Complex with Quinoxalin-6-Ylmethanamine (Compound 17)


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 the E. Coli Thim Riboswitch in Complex with Quinoxalin-6-Ylmethanamine (Compound 17) within 5.0Å range: probe atom residue distance (Å) B Occ X:Mg104 b:48.3 occ:1.00 O X:HOH269 2.6 24.7 1.0 O X:HOH240 3.6 30.2 1.0 MG X:MG103 3.7 33.1 1.0 N12 X:KX3101 4.0 25.7 1.0 OP1 X:C74 4.3 30.9 1.0 O6 X:G42 4.4 24.7 1.0 OP1 X:C57 4.5 28.9 1.0 O X:HOH235 4.6 39.6 1.0 O X:HOH230 4.7 24.8 1.0

Magnesium binding site 4 out of 5 in the Crystal Structure of the E. Coli Thim Riboswitch in Complex with Quinoxalin-6-Ylmethanamine (Compound 17)


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 the E. Coli Thim Riboswitch in Complex with Quinoxalin-6-Ylmethanamine (Compound 17) within 5.0Å range: probe atom residue distance (Å) B Occ Y:Mg102 b:49.2 occ:1.00 O6 Y:G72 2.2 49.4 1.0 O4 Y:U59 2.4 45.8 1.0 O6 Y:G60 2.5 46.5 1.0 O6 Y:G78 2.6 47.4 1.0 O Y:HOH212 2.6 43.5 1.0 C4 Y:U59 3.3 47.5 1.0 C6 Y:G72 3.3 48.5 1.0 C6 Y:G60 3.4 51.1 1.0 C6 Y:G78 3.6 49.0 1.0 C5 Y:U59 3.7 52.3 1.0 N1 Y:G60 3.7 47.9 1.0 N1 Y:G78 3.9 47.8 1.0 N1 Y:G72 3.9 49.7 1.0 N4 Y:C58 4.1 47.7 1.0 C5 Y:C58 4.2 48.7 1.0 C4 Y:C58 4.2 51.4 1.0 N6 Y:A80 4.4 47.7 1.0 N3 Y:U59 4.5 49.3 1.0 C5 Y:G72 4.5 49.1 1.0 C5 Y:G60 4.6 52.4 1.0 C5 Y:G78 4.8 48.9 1.0 C6 Y:C58 4.9 48.1 1.0 OP2 Y:C58 4.9 49.7 1.0 N3 Y:C58 5.0 47.9 1.0

Magnesium binding site 5 out of 5 in the Crystal Structure of the E. Coli Thim Riboswitch in Complex with Quinoxalin-6-Ylmethanamine (Compound 17)


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 the E. Coli Thim Riboswitch in Complex with Quinoxalin-6-Ylmethanamine (Compound 17) within 5.0Å range: probe atom residue distance (Å) B Occ Y:Mg103 b:48.5 occ:1.00 N7 Y:A41 2.3 51.0 1.0 O Y:HOH207 2.5 40.3 1.0 C8 Y:A41 3.1 48.5 1.0 C5 Y:A41 3.4 49.6 1.0 N6 Y:A41 3.7 50.0 1.0 C6 Y:A41 4.0 47.5 1.0 O6 Y:G42 4.0 44.4 1.0 O2' Y:G40 4.3 47.0 1.0 N9 Y:A41 4.4 49.2 1.0 C4 Y:A41 4.5 52.3 1.0 C6 Y:G42 4.6 47.8 1.0 OP1 Y:C57 4.9 45.4 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