Manganese in PDB 7tdb: Crystal Structure of the E. Coli Thim Riboswitch in Complex with Thiamine Bisphosphonate, Manganese Ions

The structure of Crystal Structure of the E. Coli Thim Riboswitch in Complex with Thiamine Bisphosphonate, Manganese Ions, PDB code: 7tdb 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)	56.26 / 2.56
Space group	P 32 1 2
Cell size a, b, c (Å), α, β, γ (°)	64.962, 64.962, 101.518, 90, 90, 120
R / Rfree (%)	21.7 / 24.6

The structure of Crystal Structure of the E. Coli Thim Riboswitch in Complex with Thiamine Bisphosphonate, Manganese Ions also contains other interesting chemical elements:

Magnesium

(Mg)

6 atoms

The binding sites of Manganese atom in the Crystal Structure of the E. Coli Thim Riboswitch in Complex with Thiamine Bisphosphonate, Manganese Ions (pdb code 7tdb). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 3 binding sites of Manganese where determined in the Crystal Structure of the E. Coli Thim Riboswitch in Complex with Thiamine Bisphosphonate, Manganese Ions, PDB code: 7tdb:
Jump to Manganese binding site number: 1; 2; 3;

Manganese binding site 1 out of 3 in the Crystal Structure of the E. Coli Thim Riboswitch in Complex with Thiamine Bisphosphonate, Manganese Ions


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of the E. Coli Thim Riboswitch in Complex with Thiamine Bisphosphonate, Manganese Ions within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn105 b:73.3 occ:1.00 O A:HOH210 2.1 82.0 1.0 O A:HOH202 2.2 89.3 1.0 O A:HOH204 2.2 79.6 1.0 O1B A:GMI101 2.4 83.0 1.0 O6 A:G60 2.5 85.6 1.0 O6 A:G78 2.5 84.1 1.0 O2A A:GMI101 2.5 85.0 1.0 C6 A:G78 3.3 81.7 1.0 N1 A:G78 3.4 85.9 1.0 C6 A:G60 3.5 80.0 1.0 PB A:GMI101 3.6 81.0 1.0 PA A:GMI101 3.6 86.7 1.0 C3A A:GMI101 3.7 73.8 1.0 N1 A:G60 3.9 80.6 1.0 O4 A:U59 4.0 75.4 1.0 O A:HOH209 4.2 86.1 1.0 N1 A:A61 4.2 79.0 1.0 N3 A:C77 4.3 85.7 1.0 N4 A:C77 4.4 81.5 1.0 O2B A:GMI101 4.4 83.1 1.0 C2 A:A61 4.5 78.7 1.0 O1A A:GMI101 4.6 86.1 1.0 C5 A:G78 4.7 86.6 1.0 O3B A:GMI101 4.7 97.2 1.0 C2 A:G78 4.7 87.9 1.0 O7 A:GMI101 4.7 82.8 1.0 C5 A:G60 4.8 76.8 1.0 C4 A:C77 4.8 86.5 1.0 C4 A:U59 4.8 75.6 1.0 N2 A:G72 4.9 84.4 1.0 N6 A:A80 5.0 78.8 1.0

Manganese binding site 2 out of 3 in the Crystal Structure of the E. Coli Thim Riboswitch in Complex with Thiamine Bisphosphonate, Manganese Ions


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structure of the E. Coli Thim Riboswitch in Complex with Thiamine Bisphosphonate, Manganese Ions within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn106 b:82.8 occ:1.00 O A:HOH201 2.1 86.2 1.0 O A:HOH217 2.2 85.4 1.0 O A:HOH209 2.2 86.1 1.0 O A:HOH203 2.2 89.1 1.0 O2B A:GMI101 2.4 83.1 1.0 O1A A:GMI101 2.5 86.1 1.0 PA A:GMI101 3.6 86.7 1.0 PB A:GMI101 3.7 81.0 1.0 O2' A:G72 4.0 83.9 1.0 C3A A:GMI101 4.1 73.8 1.0 O2A A:GMI101 4.1 85.0 1.0 N4 A:C77 4.2 81.5 1.0 N7 A:A75 4.2 83.3 1.0 O1B A:GMI101 4.4 83.0 1.0 O6 A:G76 4.6 89.8 1.0 N7 A:G76 4.7 86.8 1.0 O A:HOH204 4.7 79.6 1.0 N6 A:A75 4.9 80.9 1.0 O3B A:GMI101 4.9 97.2 1.0 O7 A:GMI101 4.9 82.8 1.0 C8 A:A75 4.9 82.3 1.0 C5 A:A75 4.9 82.8 1.0

Manganese binding site 3 out of 3 in the Crystal Structure of the E. Coli Thim Riboswitch in Complex with Thiamine Bisphosphonate, Manganese Ions


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Crystal Structure of the E. Coli Thim Riboswitch in Complex with Thiamine Bisphosphonate, Manganese Ions within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn107 b:81.5 occ:1.00 O A:HOH212 2.2 99.3 1.0 OP1 A:C63 2.5 81.2 1.0 OP2 A:U64 2.5 79.6 1.0 P A:U64 3.6 74.7 1.0 P A:C63 3.7 69.9 1.0 OP1 A:U64 3.8 79.0 1.0 OP2 A:C63 4.2 81.2 1.0 O3' A:U62 4.6 78.6 1.0 O5' A:U64 4.7 77.2 1.0 O3' A:C63 4.7 79.6 1.0 O5' A:C63 4.8 77.8 1.0 O A:HOH211 5.0 83.0 1.0 C3' A:C63 5.0 70.9 1.0

M.J.Zeller, A.Nuthanakanti, K.Li, J.Aube, A.Serganov, K.M.Weeks. Subsite Ligand Recognition and Cooperativity in the Tpp Riboswitch: Implications For Fragment-Linking in Rna Ligand Discovery. Acs Chem.Biol. V. 17 438 2022.
ISSN: ESSN 1554-8937
PubMed: 35060698
DOI: 10.1021/ACSCHEMBIO.1C00880