Magnesium in PDB 9c6k: Cryo-Em Structure of the Tpp Riboswitch Embedded in An Rna Scaffold Bound to Thiamine Pyrophosphate

The structure of Cryo-Em Structure of the Tpp Riboswitch Embedded in An Rna Scaffold Bound to Thiamine Pyrophosphate also contains other interesting chemical elements:

Sodium

(Na)

2 atoms

The binding sites of Magnesium atom in the Cryo-Em Structure of the Tpp Riboswitch Embedded in An Rna Scaffold Bound to Thiamine Pyrophosphate (pdb code 9c6k). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Cryo-Em Structure of the Tpp Riboswitch Embedded in An Rna Scaffold Bound to Thiamine Pyrophosphate, PDB code: 9c6k:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in the Cryo-Em Structure of the Tpp Riboswitch Embedded in An Rna Scaffold Bound to Thiamine Pyrophosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Cryo-Em Structure of the Tpp Riboswitch Embedded in An Rna Scaffold Bound to Thiamine Pyrophosphate within 5.0Å range: probe atom residue distance (Å) B Occ X:Mg201 b:93.1 occ:1.00 O2B X:TPP203 1.9 90.0 1.0 O6 X:G78 1.9 94.4 1.0 O6 X:G60 2.0 97.0 1.0 C6 X:G78 2.9 94.4 1.0 C6 X:G60 3.0 97.0 1.0 PB X:TPP203 3.3 90.0 1.0 N1 X:G78 3.3 94.4 1.0 N1 X:G60 3.4 97.0 1.0 N1 X:A61 3.4 99.7 1.0 O1B X:TPP203 3.8 90.0 1.0 O4 X:U59 4.0 93.8 1.0 C2 X:A61 4.1 99.7 1.0 O3A X:TPP203 4.2 90.0 1.0 C5 X:G78 4.2 94.4 1.0 O3B X:TPP203 4.2 90.0 1.0 C5 X:G60 4.3 97.0 1.0 C6 X:A61 4.4 99.7 1.0 N4 X:C77 4.4 93.7 1.0 N3 X:C77 4.4 93.7 1.0 N6 X:A61 4.4 99.7 1.0 C2 X:G78 4.7 94.4 1.0 C2 X:G60 4.7 97.0 1.0 C4 X:C77 4.7 93.7 1.0 C4 X:U59 4.8 93.8 1.0 MG X:MG204 4.9 89.3 1.0 N7 X:G60 4.9 97.0 1.0 N7 X:G78 4.9 94.4 1.0

Magnesium binding site 2 out of 6 in the Cryo-Em Structure of the Tpp Riboswitch Embedded in An Rna Scaffold Bound to Thiamine Pyrophosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Cryo-Em Structure of the Tpp Riboswitch Embedded in An Rna Scaffold Bound to Thiamine Pyrophosphate within 5.0Å range: probe atom residue distance (Å) B Occ X:Mg202 b:92.1 occ:1.00 O1A X:TPP203 2.1 90.0 1.0 O1B X:TPP203 2.8 90.0 1.0 PA X:TPP203 3.4 90.0 1.0 O3A X:TPP203 3.9 90.0 1.0 PB X:TPP203 3.9 90.0 1.0 O2A X:TPP203 4.0 90.0 1.0 O6 X:G76 4.2 94.7 1.0 N4 X:C77 4.3 93.7 1.0 MG X:MG204 4.4 89.3 1.0 N7 X:A75 4.4 92.8 1.0 O7 X:TPP203 4.6 90.0 1.0 N7 X:G76 4.6 94.7 1.0 N6 X:A75 4.9 92.8 1.0 O3B X:TPP203 4.9 90.0 1.0 O2B X:TPP203 4.9 90.0 1.0

Magnesium binding site 3 out of 6 in the Cryo-Em Structure of the Tpp Riboswitch Embedded in An Rna Scaffold Bound to Thiamine Pyrophosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Cryo-Em Structure of the Tpp Riboswitch Embedded in An Rna Scaffold Bound to Thiamine Pyrophosphate within 5.0Å range: probe atom residue distance (Å) B Occ X:Mg204 b:89.3 occ:1.00 O7 X:TPP203 2.9 90.0 1.0 O1A X:TPP203 3.0 90.0 1.0 O4' X:G72 3.3 91.5 1.0 PA X:TPP203 3.5 90.0 1.0 C1' X:G72 3.8 91.5 1.0 C4' X:G72 3.9 91.5 1.0 C7 X:TPP203 4.0 90.0 1.0 O3A X:TPP203 4.2 90.0 1.0 O2' X:G72 4.3 91.5 1.0 MG X:MG202 4.4 92.1 1.0 N4 X:C63 4.6 99.1 1.0 C2' X:G72 4.6 91.5 1.0 O2B X:TPP203 4.7 90.0 1.0 C5' X:G72 4.7 91.5 1.0 O1B X:TPP203 4.8 90.0 1.0 PB X:TPP203 4.8 90.0 1.0 O2A X:TPP203 4.9 90.0 1.0 C2 X:A61 4.9 99.7 1.0 MG X:MG201 4.9 93.1 1.0 N9 X:G72 5.0 91.5 1.0 C3' X:G72 5.0 91.5 1.0

Magnesium binding site 4 out of 6 in the Cryo-Em Structure of the Tpp Riboswitch Embedded in An Rna Scaffold Bound to Thiamine Pyrophosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Cryo-Em Structure of the Tpp Riboswitch Embedded in An Rna Scaffold Bound to Thiamine Pyrophosphate within 5.0Å range: probe atom residue distance (Å) B Occ X:Mg205 b:90.2 occ:1.00 O6 X:G65 3.6 94.9 1.0 O6 X:G66 4.0 94.8 1.0 O4 X:U64 4.2 96.9 1.0 N7 X:G65 4.3 94.9 1.0 C6 X:G65 4.4 94.9 1.0 C4 X:U64 4.6 96.9 1.0 C5 X:U64 4.6 96.9 1.0 C5 X:G65 4.7 94.9 1.0 OP2 X:G72 4.7 91.5 1.0 N4 X:C73 5.0 90.3 1.0

Magnesium binding site 5 out of 6 in the Cryo-Em Structure of the Tpp Riboswitch Embedded in An Rna Scaffold Bound to Thiamine Pyrophosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Cryo-Em Structure of the Tpp Riboswitch Embedded in An Rna Scaffold Bound to Thiamine Pyrophosphate within 5.0Å range: probe atom residue distance (Å) B Occ X:Mg206 b:79.9 occ:1.00 OP2 X:A80 3.5 94.0 1.0 O2' X:A53 3.8 92.7 1.0 OP1 X:A80 4.0 94.0 1.0 O6 X:G83 4.0 91.0 1.0 C4' X:U54 4.1 101.8 1.0 P X:A80 4.2 94.0 1.0 N7 X:G82 4.4 91.1 1.0 C5' X:U54 4.4 101.8 1.0 OP2 X:G81 4.5 91.9 1.0 O3' X:U54 4.5 101.8 1.0 OP2 X:C55 4.6 104.8 1.0 N7 X:G81 4.7 91.9 1.0 C3' X:U54 4.8 101.8 1.0 O6 X:G82 4.8 91.1 1.0 C6 X:G83 4.8 91.0 1.0 O5' X:A80 4.9 94.0 1.0 C2' X:A53 5.0 92.7 1.0

Magnesium binding site 6 out of 6 in the Cryo-Em Structure of the Tpp Riboswitch Embedded in An Rna Scaffold Bound to Thiamine Pyrophosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Cryo-Em Structure of the Tpp Riboswitch Embedded in An Rna Scaffold Bound to Thiamine Pyrophosphate within 5.0Å range: probe atom residue distance (Å) B Occ X:Mg207 b:85.4 occ:1.00 N7 X:G36 4.0 112.7 1.0 N7 X:G37 4.4 102.9 1.0 O6 X:G37 4.5 102.9 1.0 O6 X:G36 4.5 112.7 1.0 C5 X:G36 4.6 112.7 1.0 C8 X:G36 4.7 112.7 1.0 C6 X:G36 4.8 112.7 1.0

D.B.Haack, B.Rudolfs, S.Jin, K.M.Weeks, N.Toor. Scaffold-Enabled High-Resolution Cryo-Em Structure Determination of Rna. Biorxiv 2024.
ISSN: ISSN 2692-8205
PubMed: 38915706
DOI: 10.1101/2024.06.10.598011