Manganese in PDB 6dlq: Prpp Riboswitch Bound to Prpp, Manganese Chloride Soaked Structure

The structure of Prpp Riboswitch Bound to Prpp, Manganese Chloride Soaked Structure, PDB code: 6dlq was solved by A.Peselis, A.Serganov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 2.80
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	85.321, 90.506, 73.482, 90.00, 122.52, 90.00
R / Rfree (%)	22.6 / 25.4

The structure of Prpp Riboswitch Bound to Prpp, Manganese Chloride Soaked Structure also contains other interesting chemical elements:

Potassium	(K)	1 atom
Sodium	(Na)	4 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Manganese atom in the Prpp Riboswitch Bound to Prpp, Manganese Chloride Soaked Structure (pdb code 6dlq). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 12 binding sites of Manganese where determined in the Prpp Riboswitch Bound to Prpp, Manganese Chloride Soaked Structure, PDB code: 6dlq:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Manganese binding site 1 out of 12 in the Prpp Riboswitch Bound to Prpp, Manganese Chloride Soaked Structure


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Prpp Riboswitch Bound to Prpp, Manganese Chloride Soaked Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn202 b:68.8 occ:1.00 OP2 A:C91 2.2 50.3 1.0 OP1 A:C90 2.3 73.5 1.0 OP1 A:G48 2.4 51.0 1.0 P A:C90 3.3 54.2 1.0 OP2 A:C90 3.5 49.3 1.0 P A:C91 3.6 63.2 1.0 P A:G48 3.8 60.8 1.0 O2' A:A93 4.0 54.1 1.0 O5' A:C90 4.2 51.8 1.0 N7 A:G48 4.3 55.0 1.0 OP1 A:C91 4.3 66.2 1.0 O5' A:C91 4.4 51.4 1.0 O3' A:A47 4.4 57.8 1.0 C8 A:G48 4.5 53.6 1.0 OP2 A:G48 4.6 66.8 1.0 O3' A:C90 4.6 67.7 1.0 O3' A:G89 4.6 55.3 1.0 C5' A:C90 4.7 50.4 1.0 O3' A:A93 4.8 50.9 1.0 C3' A:C90 4.8 47.9 1.0 O5' A:G48 4.8 54.9 1.0 OP2 A:C92 5.0 53.1 1.0

Manganese binding site 2 out of 12 in the Prpp Riboswitch Bound to Prpp, Manganese Chloride Soaked Structure


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Prpp Riboswitch Bound to Prpp, Manganese Chloride Soaked Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn203 b:83.2 occ:1.00 OP2 A:G48 2.3 66.8 1.0 OP1 A:C91 2.3 66.2 1.0 P A:C91 3.7 63.2 1.0 P A:G48 3.7 60.8 1.0 C5' A:G48 4.0 59.3 1.0 O3' A:C90 4.1 67.7 1.0 O5' A:G48 4.3 54.9 1.0 OP1 A:G48 4.4 51.0 1.0 OP2 A:C91 4.5 50.3 1.0 O5' A:A47 4.6 67.6 1.0 O5' A:C91 4.7 51.4 1.0 O3' A:A47 4.8 57.8 1.0 C5' A:C91 4.9 49.3 1.0

Manganese binding site 3 out of 12 in the Prpp Riboswitch Bound to Prpp, Manganese Chloride Soaked Structure


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Prpp Riboswitch Bound to Prpp, Manganese Chloride Soaked Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn204 b:91.9 occ:1.00 OP1 A:G94 2.4 80.2 1.0 P A:G94 3.8 53.4 1.0 OP2 A:G6 4.2 62.9 1.0 OP2 A:G94 4.4 47.8 1.0 C3' A:A93 4.7 49.8 1.0 O3' A:A93 4.7 50.9 1.0 O5' A:G94 4.7 53.3 1.0 C5' A:A93 4.8 52.3 1.0 OP1 A:C92 4.8 55.4 1.0 C4' A:A93 4.9 47.6 1.0

Manganese binding site 4 out of 12 in the Prpp Riboswitch Bound to Prpp, Manganese Chloride Soaked Structure


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Prpp Riboswitch Bound to Prpp, Manganese Chloride Soaked Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn205 b:0.5 occ:1.00 N7 A:G15 2.6 65.2 1.0 OP2 A:A14 2.6 68.7 1.0 C8 A:G15 3.5 60.1 1.0 C5 A:G15 3.6 57.6 1.0 O6 A:G15 3.6 74.6 1.0 P A:A14 3.8 88.9 1.0 C6 A:G15 3.9 59.4 1.0 OP1 A:A14 4.1 99.3 1.0 O5' A:A14 4.6 80.6 1.0 N9 A:G15 4.7 58.9 1.0 C4 A:G15 4.8 57.9 1.0 O6 A:G16 4.8 65.7 1.0 N7 A:G16 4.9 50.5 1.0 N1 A:A46 4.9 63.2 1.0

Manganese binding site 5 out of 12 in the Prpp Riboswitch Bound to Prpp, Manganese Chloride Soaked Structure


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Prpp Riboswitch Bound to Prpp, Manganese Chloride Soaked Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn206 b:77.8 occ:1.00 OP1 A:U49 4.0 57.7 1.0 O6 A:G50 4.0 78.8 1.0 N7 A:G50 4.1 90.6 1.0 C5' A:A47 4.5 63.9 1.0 C6 A:G50 4.5 77.6 1.0 C5 A:G50 4.5 79.9 1.0 N6 A:A51 4.7 68.5 1.0 N7 A:A51 4.8 74.2 1.0 P A:U49 4.9 59.5 1.0 O3' A:G48 4.9 56.7 1.0

Manganese binding site 6 out of 12 in the Prpp Riboswitch Bound to Prpp, Manganese Chloride Soaked Structure


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Prpp Riboswitch Bound to Prpp, Manganese Chloride Soaked Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn207 b:70.7 occ:1.00 OP2 A:C75 2.0 61.9 1.0 O2P A:PRP201 2.0 55.4 1.0 O2 A:U49 2.2 75.4 1.0 P A:PRP201 3.2 62.5 1.0 C2 A:U49 3.2 68.9 1.0 P A:C75 3.5 71.7 1.0 O3P A:PRP201 3.5 57.7 1.0 O1P A:PRP201 3.6 51.6 1.0 N3 A:U49 3.6 68.0 1.0 O5' A:C75 4.2 61.7 1.0 O3' A:A74 4.2 77.8 1.0 O2' A:A74 4.3 70.2 1.0 N1 A:U49 4.4 61.2 1.0 N1 A:G48 4.5 68.8 1.0 O5 A:PRP201 4.5 72.7 1.0 OP1 A:C75 4.5 59.0 1.0 C2' A:A74 4.6 57.9 1.0 N2 A:G48 4.7 49.2 1.0 C2' A:U49 4.8 78.5 1.0 C1' A:U49 4.8 60.3 1.0 OP2 A:C76 4.8 80.3 1.0 C2 A:G48 4.9 51.5 1.0 C3' A:A74 4.9 68.7 1.0 C5 A:C75 5.0 80.1 1.0

Manganese binding site 7 out of 12 in the Prpp Riboswitch Bound to Prpp, Manganese Chloride Soaked Structure


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of Prpp Riboswitch Bound to Prpp, Manganese Chloride Soaked Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn208 b:0.4 occ:1.00 N7 A:A46 3.0 61.2 1.0 OP2 A:A46 3.6 60.2 1.0 C8 A:A46 3.6 59.4 1.0 OP2 A:C45 3.7 84.9 1.0 C5 A:A46 4.2 59.5 1.0 O5' A:C45 4.4 62.7 1.0 C5 A:C45 4.4 64.7 1.0 C6 A:C45 4.6 60.9 1.0 N6 A:A46 4.6 78.2 1.0 P A:C45 4.6 76.0 1.0 P A:A46 4.8 64.2 1.0 C6 A:A46 4.8 64.3 1.0 O5' A:A46 4.9 57.0 1.0 N9 A:A46 4.9 56.7 1.0 C3' A:C45 5.0 58.1 1.0

Manganese binding site 8 out of 12 in the Prpp Riboswitch Bound to Prpp, Manganese Chloride Soaked Structure


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of Prpp Riboswitch Bound to Prpp, Manganese Chloride Soaked Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn209 b:0.7 occ:0.91 N7 A:A38 2.8 85.7 1.0 C8 A:A38 3.0 70.9 1.0 OP1 A:A38 3.6 66.0 1.0 C5 A:A38 4.1 58.6 1.0 C5' A:G37 4.2 77.0 1.0 N9 A:A38 4.3 50.7 1.0 OP1 A:G37 4.4 84.3 1.0 C4' A:G37 4.8 73.1 1.0 C4 A:A38 4.9 50.2 1.0

Manganese binding site 9 out of 12 in the Prpp Riboswitch Bound to Prpp, Manganese Chloride Soaked Structure


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 9 of Prpp Riboswitch Bound to Prpp, Manganese Chloride Soaked Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn210 b:81.5 occ:0.72 O4 A:U18 2.7 83.0 1.0 O6 A:G17 2.8 81.8 1.0 N7 A:G41 3.1 83.5 1.0 C4 A:U18 3.6 72.9 1.0 N2 A:G37 3.6 57.5 1.0 C8 A:G41 3.7 85.0 1.0 N3 A:U18 3.8 75.5 1.0 C5 A:G41 3.9 73.2 1.0 C6 A:G17 3.9 66.0 1.0 C2 A:G37 4.1 58.1 1.0 N1 A:G37 4.1 66.5 1.0 O6 A:G41 4.4 65.0 1.0 C6 A:G41 4.4 65.8 1.0 N9 A:G41 4.6 82.7 1.0 C4 A:G41 4.7 81.2 1.0 C5 A:G17 4.8 60.9 1.0 N1 A:G17 4.8 71.7 1.0 N7 A:G42 4.8 64.7 1.0 OP2 A:U40 4.8 74.0 1.0 O4 A:U43 4.8 84.4 1.0 O6 A:G42 4.8 86.9 1.0 N7 A:G17 4.9 59.4 1.0 C5 A:U18 5.0 60.5 1.0 N3 A:G37 5.0 61.7 1.0

Manganese binding site 10 out of 12 in the Prpp Riboswitch Bound to Prpp, Manganese Chloride Soaked Structure


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 10 of Prpp Riboswitch Bound to Prpp, Manganese Chloride Soaked Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn211 b:61.5 occ:1.00 O1P A:PRP201 2.5 51.6 1.0 O6 A:G48 2.5 64.0 1.0 C6 A:G48 3.5 57.3 1.0 P A:PRP201 3.7 62.5 1.0 O3P A:PRP201 3.7 57.7 1.0 N1 A:G48 3.9 68.8 1.0 N7 A:G95 4.1 51.9 1.0 O6 A:G77 4.3 72.0 1.0 O6 A:G95 4.3 51.6 1.0 C5 A:PRP201 4.4 59.8 1.0 N4 A:C96 4.5 49.7 1.0 O5 A:PRP201 4.6 72.7 1.0 O2P A:PRP201 4.8 55.4 1.0 C4' A:G94 4.8 62.1 1.0 C5 A:G48 4.8 45.4 1.0 O3' A:G94 4.9 54.1 1.0 OP2 A:G95 4.9 66.8 1.0 C5 A:G95 5.0 47.6 1.0

A.Peselis, A.Serganov. Ykkc Riboswitches Employ An Add-on Helix to Adjust Specificity For Polyanionic Ligands. Nat. Chem. Biol. V. 14 887 2018.
ISSN: ESSN 1552-4469
PubMed: 30120360
DOI: 10.1038/S41589-018-0114-4