Manganese in PDB 8fza: Class I Type III PREQ1 Riboswitch From E. Coli

The structure of Class I Type III PREQ1 Riboswitch From E. Coli, PDB code: 8fza was solved by J.E.Wedekind, G.M.Schroeder, J.L.Jenkins, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	36.53 / 2.30
Space group	P 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	46.739, 32.272, 51.206, 90, 96.93, 90
R / Rfree (%)	20.5 / 25.2

The binding sites of Manganese atom in the Class I Type III PREQ1 Riboswitch From E. Coli (pdb code 8fza). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Class I Type III PREQ1 Riboswitch From E. Coli, PDB code: 8fza:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in the Class I Type III PREQ1 Riboswitch From E. Coli


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Class I Type III PREQ1 Riboswitch From E. Coli within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn102 b:47.7 occ:1.00 O A:HOH212 2.2 36.1 1.0 O A:HOH203 2.2 47.0 1.0 N7 A:G30 2.3 39.7 1.0 C8 A:G30 3.1 40.6 1.0 C5 A:G30 3.4 38.9 1.0 O6 A:G30 3.9 44.4 1.0 C6 A:G30 4.0 41.5 1.0 N9 A:G30 4.3 41.0 1.0 OP2 A:G30 4.4 45.9 1.0 C4 A:G30 4.5 37.2 1.0 N7 A:G29 4.7 40.6 1.0 OP2 A:G29 4.9 52.8 1.0

Manganese binding site 2 out of 4 in the Class I Type III PREQ1 Riboswitch From E. Coli


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Class I Type III PREQ1 Riboswitch From E. Coli within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn103 b:67.9 occ:1.00 O A:HOH211 2.1 51.6 1.0 O A:HOH210 2.2 60.6 1.0 O A:HOH216 2.2 50.1 1.0 O A:HOH217 2.2 59.9 1.0 O A:HOH206 2.2 55.5 1.0 N7 A:G4 2.5 46.4 1.0 C8 A:G4 3.4 45.7 1.0 C5 A:G4 3.6 48.6 1.0 O6 A:G4 3.9 50.6 1.0 C5 A:C12 3.9 65.7 1.0 C6 A:G4 4.1 47.7 1.0 C6 A:C12 4.3 72.1 1.0 N7 A:G3 4.5 45.4 1.0 N9 A:G4 4.6 45.1 1.0 C4 A:G4 4.7 46.8 1.0 OP2 A:C12 4.8 50.4 1.0 C5 A:G3 4.9 44.6 1.0 C8 A:G3 5.0 49.5 1.0

Manganese binding site 3 out of 4 in the Class I Type III PREQ1 Riboswitch From E. Coli


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Class I Type III PREQ1 Riboswitch From E. Coli within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn102 b:43.3 occ:1.00 O B:HOH202 2.2 55.3 1.0 O B:HOH209 2.2 51.8 1.0 O B:HOH206 2.2 55.1 1.0 N7 B:G30 2.5 50.9 1.0 C8 B:G30 3.1 50.6 1.0 C5 B:G30 3.6 51.1 1.0 OP2 B:G30 4.2 66.8 1.0 O6 B:G30 4.3 39.6 1.0 C6 B:G30 4.3 44.9 1.0 N9 B:G30 4.3 54.1 1.0 C4 B:G30 4.6 44.5 1.0 OP2 B:G29 4.8 63.5 1.0 O5' B:G30 5.0 59.3 1.0

Manganese binding site 4 out of 4 in the Class I Type III PREQ1 Riboswitch From E. Coli


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Class I Type III PREQ1 Riboswitch From E. Coli within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn103 b:52.2 occ:1.00 OP2 B:A18 2.1 50.4 1.0 O B:HOH203 2.2 61.6 1.0 P B:A18 3.5 54.7 1.0 C8 B:A18 4.1 43.7 1.0 O5' B:A18 4.1 46.0 1.0 N7 B:A18 4.3 40.2 1.0 OP1 B:A18 4.4 57.7 1.0 O3' B:C17 4.6 56.2 1.0 C3' B:C17 4.7 51.8 1.0

G.M.Schroeder, D.Kiliushik, J.L.Jenkins, J.E.Wedekind. Structure and Function Analysis of A Type III PREQ1-I Riboswitch From E. Coli Reveals Direct Metabolite-Sensing By the Shine-Dalgarno Sequence. J.Biol.Chem. 2023.
ISSN: ESSN 1083-351X