Potassium 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:

Sodium	(Na)	1 atom
Magnesium	(Mg)	5 atoms

The binding sites of Potassium 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 Potassium atom.
In total 5 binding sites of Potassium 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 Potassium binding site number: 1; 2; 3; 4; 5;

Potassium 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 Potassium with other atoms in the K 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:K105 b:31.6 occ:0.57 OP1 X:C73 2.6 30.3 1.0 O2' X:U71 2.7 30.8 1.0 O2' X:G21 2.8 27.2 1.0 N3 X:G21 2.8 27.9 1.0 C2' X:G21 3.1 32.7 1.0 O2 X:U71 3.2 29.4 1.0 C1' X:G21 3.3 30.2 1.0 O4' X:C22 3.5 28.9 1.0 C2' X:U71 3.6 28.7 1.0 C4 X:G21 3.7 28.3 1.0 C2 X:G21 3.8 27.9 1.0 O X:HOH262 3.8 28.9 1.0 N9 X:G21 3.8 29.4 1.0 N2 X:G21 3.8 28.5 1.0 C1' X:U71 3.9 26.9 1.0 N6 X:A43 4.0 26.1 1.0 P X:C73 4.0 29.8 1.0 C2 X:U71 4.3 31.1 1.0 C1' X:C22 4.3 28.5 1.0 N1 X:A43 4.4 27.4 1.0 O5' X:C73 4.4 32.6 1.0 C6 X:A43 4.4 29.5 1.0 C3' X:G21 4.6 33.6 1.0 C5' X:G72 4.6 31.6 1.0 C4' X:C22 4.6 29.9 1.0 N1 X:U71 4.7 27.8 1.0 O4' X:G21 4.7 34.0 1.0 C6 X:C22 4.7 29.0 1.0 N1 X:C22 4.7 26.8 1.0 C5' X:C22 4.9 30.2 1.0 O3' X:G72 4.9 35.5 1.0 C3' X:U71 5.0 27.3 1.0

Potassium 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 Potassium with other atoms in the K 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:K106 b:69.4 occ:1.00 O3' X:U20 3.2 38.5 1.0 OP2 X:G21 3.3 44.3 1.0 O X:HOH285 3.4 37.6 1.0 O2' X:U20 3.5 32.9 1.0 OP2 X:A44 3.8 37.7 1.0 P X:G21 3.9 36.8 1.0 C5' X:G21 3.9 33.7 1.0 C8 X:G21 4.0 30.4 1.0 O2' X:A43 4.2 41.0 1.0 N7 X:G21 4.2 31.5 1.0 C3' X:U20 4.3 33.0 1.0 C2' X:U20 4.3 36.5 1.0 O5' X:G21 4.4 39.4 1.0 O4' X:G21 4.9 34.0 1.0 C4' X:G21 4.9 32.0 1.0

Potassium 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 Potassium with other atoms in the K 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:K107 b:30.4 occ:0.36 O2' X:C57 2.9 27.7 1.0 O2 X:C57 2.9 28.4 1.0 C4' X:G18 3.4 27.4 1.0 C2' X:C57 3.5 28.1 1.0 O X:HOH278 3.5 30.6 1.0 O4' X:C58 3.5 25.3 1.0 C1' X:C57 3.6 27.9 1.0 C5' X:G18 3.7 26.7 1.0 O3' X:G18 3.7 25.2 1.0 C2 X:C57 4.0 29.0 1.0 N2 X:G82 4.1 22.0 1.0 C3' X:G18 4.2 26.2 1.0 N6 X:A56 4.2 29.6 1.0 C6 X:A56 4.3 27.3 1.0 N1 X:A56 4.4 27.3 1.0 N1 X:C57 4.4 27.2 1.0 C1' X:C58 4.4 29.4 1.0 C4' X:C58 4.5 28.6 1.0 O4' X:G18 4.5 29.2 1.0 O2' X:G18 4.6 27.0 1.0 O4' X:C57 4.8 25.4 1.0 OP1 X:G19 4.8 25.9 1.0 C5' X:C58 4.8 24.5 1.0 C6 X:C58 4.9 25.3 1.0 N1 X:C58 4.9 28.4 1.0 O2' X:G83 4.9 28.7 1.0 P X:G19 4.9 24.8 1.0 C3' X:C57 5.0 25.8 1.0 C2' X:G18 5.0 27.6 1.0

Potassium 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 Potassium with other atoms in the K 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 X:K108 b:52.4 occ:1.00 N7 X:A80 3.1 31.6 1.0 N3 X:G78 3.2 26.9 1.0 C4 X:G78 3.4 31.7 1.0 O X:HOH241 3.6 33.7 1.0 C2 X:G78 3.6 28.3 1.0 O X:HOH254 3.7 30.0 1.0 N9 X:G78 3.8 31.6 1.0 N6 X:A80 3.9 29.4 1.0 O X:HOH267 4.0 34.7 1.0 C1' X:G78 4.1 30.9 1.0 C5 X:A80 4.1 31.7 1.0 C8 X:A80 4.1 34.6 1.0 C5 X:G78 4.1 30.1 1.0 N2 X:G78 4.1 31.0 1.0 O6 X:G81 4.2 32.8 1.0 O4' X:G78 4.2 36.4 1.0 N1 X:G78 4.3 29.1 1.0 C6 X:A80 4.4 31.1 1.0 C6 X:G78 4.6 29.8 1.0 C8 X:G78 4.6 31.4 1.0 N7 X:G78 4.8 31.5 1.0 N4 X:C58 4.9 26.4 1.0

Potassium 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 Potassium with other atoms in the K 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:K104 b:71.7 occ:1.00 N3 Y:G78 3.1 47.3 1.0 N7 Y:A80 3.3 48.4 1.0 C4 Y:G78 3.4 49.6 1.0 C2 Y:G78 3.4 49.5 1.0 N6 Y:A80 3.5 47.7 1.0 N9 Y:G78 3.9 47.0 1.0 C5 Y:G78 3.9 48.9 1.0 N1 Y:G78 3.9 47.8 1.0 N2 Y:G78 3.9 49.9 1.0 C5 Y:A80 4.1 52.3 1.0 C6 Y:A80 4.2 49.5 1.0 O6 Y:G81 4.2 49.3 1.0 C6 Y:G78 4.3 49.0 1.0 C1' Y:G78 4.3 49.5 1.0 C8 Y:A80 4.4 48.8 1.0 O4' Y:G78 4.5 49.8 1.0 C8 Y:G78 4.6 50.4 1.0 N4 Y:C58 4.6 47.7 1.0 N7 Y:G78 4.7 52.7 1.0 O2' Y:C55 5.0 60.9 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