Manganese in PDB 6vuh: Apo PREQ1 Riboswitch Aptamer Grown in MN2+

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

Resolution Low / High (Å)	37.78 / 2.00
Space group	P 63 2 2
Cell size a, b, c (Å), α, β, γ (°)	115.422, 115.422, 57.682, 90.00, 90.00, 120.00
R / Rfree (%)	19 / 22.5

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

Manganese binding site 1 out of 6 in the Apo PREQ1 Riboswitch Aptamer Grown in MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Apo PREQ1 Riboswitch Aptamer Grown in MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn101 b:58.4 occ:1.00 O A:HOH233 2.2 55.8 1.0 O A:HOH222 2.2 58.8 1.0 O A:HOH229 2.2 73.8 1.0 N7 A:G5 2.3 58.2 1.0 O A:HOH203 2.3 64.0 1.0 O A:HOH218 2.4 57.4 1.0 C8 A:G5 3.2 56.2 1.0 C5 A:G5 3.3 52.2 1.0 H8 A:G5 3.3 67.5 1.0 O6 A:G5 3.6 52.7 1.0 C6 A:G5 3.8 55.9 1.0 OP2 A:G5 4.2 68.7 1.0 N9 A:G5 4.3 54.6 1.0 O A:HOH214 4.3 52.9 1.0 OP1 A:A14 4.3 86.7 1.0 C4 A:G5 4.4 52.5 1.0 N7 A:A14 4.5 61.1 1.0 N7 A:G4 4.7 57.0 1.0 H8 A:A14 4.7 76.7 1.0 C5 A:G4 4.7 56.7 1.0 HO2' A:G11 4.8 76.7 1.0 C6 A:G4 4.9 53.8 1.0 O A:HOH209 5.0 46.4 1.0 O6 A:G4 5.0 55.0 1.0 C8 A:A14 5.0 63.9 1.0

Manganese binding site 2 out of 6 in the Apo PREQ1 Riboswitch Aptamer Grown in MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Apo PREQ1 Riboswitch Aptamer Grown in MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn102 b:57.2 occ:1.00 O A:HOH215 2.0 51.8 1.0 O A:HOH220 2.0 49.6 1.0 N7 A:G8 2.2 71.3 1.0 O A:HOH234 2.2 63.0 1.0 O A:HOH230 2.3 60.7 1.0 O A:HOH211 2.4 59.5 1.0 C8 A:G8 2.9 66.3 1.0 H8 A:G8 3.0 79.6 1.0 C5 A:G8 3.3 63.9 1.0 O6 A:G8 3.8 66.7 1.0 C6 A:G8 3.9 69.8 1.0 OP2 A:A10 4.0 62.2 1.0 H5 A:C7 4.2 67.9 1.0 N9 A:G8 4.2 65.4 1.0 OP2 A:C7 4.3 60.6 1.0 C4 A:G8 4.3 65.5 1.0 OP1 A:A10 4.4 67.2 1.0 O A:HOH223 4.5 56.3 1.0 C5 A:C7 4.6 56.8 1.0 OP2 A:G8 4.6 63.7 1.0 P A:A10 4.7 65.4 1.0 H3' A:G8 5.0 76.0 1.0 H41 A:C7 5.0 73.2 1.0

Manganese binding site 3 out of 6 in the Apo PREQ1 Riboswitch Aptamer Grown in MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Apo PREQ1 Riboswitch Aptamer Grown in MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn103 b:58.8 occ:1.00 N7 A:G33 2.1 75.2 1.0 OP2 A:A32 2.2 89.8 1.0 O A:HOH207 2.2 62.1 1.0 O A:HOH201 2.2 51.4 1.0 C8 A:G33 3.1 68.7 1.0 H8 A:G33 3.2 82.4 1.0 C5 A:G33 3.2 68.1 1.0 O6 A:G33 3.5 65.3 1.0 P A:A32 3.6 77.7 1.0 C6 A:G33 3.7 60.9 1.0 O5' A:A32 4.1 84.7 1.0 O2' A:A31 4.2 67.2 1.0 N9 A:G33 4.3 66.2 1.0 OP2 A:G33 4.3 81.5 1.0 C4 A:G33 4.4 64.8 1.0 HO2' A:A31 4.5 80.6 1.0 OP1 A:A32 4.6 90.0 1.0 O3' A:A31 4.6 68.9 1.0 H3' A:A32 4.8 84.9 1.0 H3' A:A31 4.9 73.4 1.0 H8 A:A32 4.9 73.5 1.0

Manganese binding site 4 out of 6 in the Apo PREQ1 Riboswitch Aptamer Grown in MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Apo PREQ1 Riboswitch Aptamer Grown in MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn104 b:0.2 occ:1.00 O A:HOH208 2.3 57.7 1.0 O A:HOH209 2.3 46.4 1.0 O A:HOH212 2.4 54.1 1.0 OP1 A:A14 3.2 86.7 1.0 O3' A:A13 3.6 76.6 1.0 O6 A:G4 3.8 55.0 1.0 P A:A14 4.1 73.5 1.0 N7 A:G4 4.2 57.0 1.0 H4' A:A13 4.3 97.8 1.0 O A:HOH203 4.3 64.0 1.0 N7 A:G3 4.4 49.1 1.0 O6 A:G3 4.4 48.9 1.0 HO2' A:A13 4.4 94.9 1.0 O2' A:A13 4.5 79.2 1.0 C6 A:G4 4.7 53.8 1.0 C3' A:A13 4.7 78.7 1.0 C5 A:G4 4.8 56.7 1.0 C4' A:A13 5.0 81.7 1.0 H42 A:C17 5.0 61.5 1.0

Manganese binding site 5 out of 6 in the Apo PREQ1 Riboswitch Aptamer Grown in MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Apo PREQ1 Riboswitch Aptamer Grown in MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn105 b:0.3 occ:1.00 O A:HOH227 2.3 64.2 1.0 OP2 A:A23 2.3 60.2 1.0 O A:HOH228 2.8 61.7 1.0 H5'' A:U22 3.5 62.5 1.0 H4' A:U22 3.7 76.6 1.0 P A:A23 3.7 60.2 1.0 H8 A:A23 4.0 69.3 1.0 C5' A:U22 4.2 52.1 1.0 C4' A:U22 4.3 63.8 1.0 N7 A:A23 4.3 52.5 1.0 O5' A:A23 4.4 52.3 1.0 H5' A:U22 4.4 62.5 1.0 H3' A:U22 4.4 62.2 1.0 OP1 A:A23 4.5 61.6 1.0 C8 A:A23 4.5 57.7 1.0 O3' A:U22 4.6 55.9 1.0 C3' A:U22 4.7 51.8 1.0

Manganese binding site 6 out of 6 in the Apo PREQ1 Riboswitch Aptamer Grown in MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Apo PREQ1 Riboswitch Aptamer Grown in MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn106 b:96.2 occ:1.00 O A:HOH213 2.3 62.9 1.0 O A:HOH216 2.4 86.3 1.0 H62 A:A19 3.7 61.5 1.0 O A:HOH232 4.0 83.6 1.0 N6 A:A19 4.4 51.2 1.0 H41 A:C1 4.5 66.1 1.0 O6 A:G20 4.6 49.7 1.0 H42 A:C1 4.6 66.1 1.0 H61 A:A19 4.7 61.5 1.0 N7 A:A19 4.7 50.8 1.0 N4 A:C1 4.9 55.1 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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