Manganese in PDB 6vui: Metabolite-Bound PREQ1 Riboswitch with MN2+

The structure of Metabolite-Bound PREQ1 Riboswitch with MN2+, PDB code: 6vui was solved by J.L.Jenkins, J.E.Wededkind, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.63 / 2.68
Space group	P 63 2 2
Cell size a, b, c (Å), α, β, γ (°)	112.309, 112.309, 59.385, 90.00, 90.00, 120.00
R / Rfree (%)	17.5 / 20.2

The binding sites of Manganese atom in the Metabolite-Bound PREQ1 Riboswitch with MN2+ (pdb code 6vui). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 6 binding sites of Manganese where determined in the Metabolite-Bound PREQ1 Riboswitch with MN2+, PDB code: 6vui:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6;

Manganese binding site 1 out of 6 in the Metabolite-Bound PREQ1 Riboswitch with MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Metabolite-Bound PREQ1 Riboswitch with MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn102 b:72.6 occ:1.00 O A:HOH208 2.0 54.5 1.0 O A:HOH220 2.1 54.5 1.0 O A:HOH209 2.1 67.9 1.0 O A:HOH211 2.1 69.4 1.0 N7 A:G8 2.1 96.3 1.0 O A:HOH202 2.2 60.4 1.0 C8 A:G8 3.0 89.7 1.0 C5 A:G8 3.1 84.8 1.0 H8 A:G8 3.2 0.5 1.0 O6 A:G8 3.5 89.9 1.0 C6 A:G8 3.7 84.7 1.0 OP2 A:A10 3.9 83.7 1.0 H5 A:C7 4.0 0.8 1.0 OP1 A:A10 4.1 84.3 1.0 N9 A:G8 4.2 85.5 1.0 C4 A:G8 4.3 81.8 1.0 OP2 A:C7 4.4 82.3 1.0 C5 A:C7 4.4 84.0 1.0 P A:A10 4.5 88.6 1.0 H41 A:C7 4.8 99.1 1.0 H5'' A:C7 4.8 1.0 1.0 OP2 A:G8 4.9 86.4 1.0 H6 A:C7 4.9 0.9 1.0 C6 A:C7 5.0 85.8 1.0 N1 A:G8 5.0 81.8 1.0

Manganese binding site 2 out of 6 in the Metabolite-Bound PREQ1 Riboswitch with MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Metabolite-Bound PREQ1 Riboswitch with MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn103 b:65.0 occ:1.00 OP2 A:A32 1.9 92.6 1.0 N7 A:G33 2.0 85.3 1.0 O A:HOH203 2.1 55.3 1.0 O A:HOH207 2.1 62.5 1.0 O A:HOH206 2.1 66.7 1.0 O A:HOH204 2.1 55.1 1.0 C8 A:G33 2.8 79.5 1.0 H8 A:G33 2.9 95.3 1.0 C5 A:G33 3.2 80.8 1.0 P A:A32 3.2 84.5 1.0 H3' A:A31 3.5 95.0 1.0 O6 A:G33 3.7 87.0 1.0 C6 A:G33 3.8 82.5 1.0 OP1 A:A32 3.8 82.9 1.0 N9 A:G33 4.1 79.2 1.0 H2' A:A31 4.1 93.3 1.0 O3' A:A31 4.2 79.2 1.0 C3' A:A31 4.2 79.2 1.0 C4 A:G33 4.2 80.1 1.0 O5' A:A32 4.3 84.1 1.0 N1 A:A10 4.5 84.4 1.0 C2' A:A31 4.7 77.8 1.0 H2 A:A10 4.8 99.9 1.0 H8 A:A32 4.8 99.3 1.0 H61 A:A10 4.9 99.2 1.0

Manganese binding site 3 out of 6 in the Metabolite-Bound PREQ1 Riboswitch with MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Metabolite-Bound PREQ1 Riboswitch with MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn104 b:97.1 occ:1.00 O A:HOH212 2.1 64.1 1.0 O A:HOH218 2.1 61.3 1.0 O A:HOH205 2.2 65.1 1.0 O A:HOH213 2.2 76.3 1.0 O A:HOH216 2.4 65.7 1.0 N7 A:G4 2.4 64.8 1.0 C8 A:G4 3.3 67.4 1.0 H8 A:G4 3.4 80.8 1.0 C5 A:G4 3.5 62.9 1.0 O6 A:G4 3.7 67.3 1.0 C6 A:G4 4.0 65.1 1.0 N7 A:G3 4.2 65.8 1.0 N9 A:G4 4.5 64.9 1.0 C5 A:G3 4.6 58.7 1.0 C4 A:G4 4.6 60.9 1.0 O6 A:G3 4.7 70.8 1.0 C6 A:G3 4.8 63.4 1.0 C8 A:G3 4.8 63.0 1.0

Manganese binding site 4 out of 6 in the Metabolite-Bound PREQ1 Riboswitch with MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Metabolite-Bound PREQ1 Riboswitch with MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn105 b:98.7 occ:1.00 OP2 A:A23 2.1 88.3 1.0 O A:HOH217 2.3 70.0 1.0 O A:HOH210 2.3 67.5 1.0 H4' A:U22 3.4 81.2 1.0 P A:A23 3.6 72.0 1.0 H5'' A:U22 3.8 83.7 1.0 C4' A:U22 4.1 67.7 1.0 H5' A:U22 4.2 83.7 1.0 H8 A:A23 4.2 78.8 1.0 C5' A:U22 4.2 69.8 1.0 OP1 A:A23 4.3 72.6 1.0 O5' A:A23 4.3 67.1 1.0 O3' A:U22 4.5 63.1 1.0 H3' A:U22 4.6 75.4 1.0 C3' A:U22 4.7 62.9 1.0 N7 A:A23 4.7 69.0 1.0 C8 A:A23 4.8 65.8 1.0

Manganese binding site 5 out of 6 in the Metabolite-Bound PREQ1 Riboswitch with MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Metabolite-Bound PREQ1 Riboswitch with MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn106 b:89.8 occ:0.50 O A:HOH219 1.9 67.1 1.0 O A:HOH201 2.0 71.3 1.0 O A:HOH221 2.0 68.5 1.0 H62 A:A19 4.1 73.7 1.0 O6 A:G20 4.2 63.4 1.0 N6 A:A19 4.7 61.5 1.0 H42 A:C1 4.8 67.9 1.0 H41 A:C1 4.9 67.9 1.0 H61 A:A19 5.0 73.7 1.0

Manganese binding site 6 out of 6 in the Metabolite-Bound PREQ1 Riboswitch with MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Metabolite-Bound PREQ1 Riboswitch with MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn107 b:0.9 occ:1.00 OP2 A:G33 2.1 93.9 1.0 OP1 A:A32 2.7 82.9 1.0 H5'' A:A32 2.9 97.0 1.0 P A:G33 3.4 86.0 1.0 O5' A:A32 3.6 84.1 1.0 C5' A:A32 3.6 80.9 1.0 H5'' A:G33 3.7 95.7 1.0 P A:A32 3.7 84.5 1.0 OP1 A:G33 4.1 81.4 1.0 O A:HOH207 4.2 62.5 1.0 H5' A:A32 4.2 97.0 1.0 H3' A:A32 4.3 95.9 1.0 O3' A:A32 4.3 82.1 1.0 C5' A:G33 4.5 79.8 1.0 O5' A:G33 4.5 81.0 1.0 OP2 A:A32 4.5 92.6 1.0 H8 A:G33 4.6 95.3 1.0 C3' A:A32 4.6 80.0 1.0 C4' A:A32 4.6 76.2 1.0 H5' A:G33 4.8 95.7 1.0 O3' A:A31 4.9 79.2 1.0 H4' A:A32 5.0 91.4 1.0

G.Schroeder, D.Dutta, C.Cavender, J.L.Jenkins, E.Pritchett, C.Baker, J.Ashton, D.Mathews, J.E.Wedekind. Analysis of A PREQ1-I Riboswitch in Effector-Free and Bound States Reveals A Metabolite-Programmed Nucleobase-Stacking Spine That Controls Gene Regulation Nucleic Acids Res..
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