Magnesium in PDB 8tju: Tetrahymena Ribozyme Scaffolded Tabv Xrrna

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 27;

Binding sites:

The binding sites of Magnesium atom in the Tetrahymena Ribozyme Scaffolded Tabv Xrrna (pdb code 8tju). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 27 binding sites of Magnesium where determined in the Tetrahymena Ribozyme Scaffolded Tabv Xrrna, PDB code: 8tju:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 27 in the Tetrahymena Ribozyme Scaffolded Tabv Xrrna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Tetrahymena Ribozyme Scaffolded Tabv Xrrna within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg501 b:88.8 occ:0.77 O6 A:G264 3.6 119.1 1.0 N7 A:G264 3.8 119.1 1.0 C6 A:G264 4.3 119.1 1.0 C5 A:G264 4.4 119.1 1.0 OP1 A:C28 4.5 114.5 1.0 C8 A:G264 4.8 119.1 1.0 O6 A:G265 5.0 132.0 1.0

Magnesium binding site 2 out of 27 in the Tetrahymena Ribozyme Scaffolded Tabv Xrrna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Tetrahymena Ribozyme Scaffolded Tabv Xrrna within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:136.9 occ:1.00 OP2 A:C30 2.0 128.4 1.0 OP1 A:A361 2.6 174.8 1.0 P A:C30 3.1 128.4 1.0 O5' A:C30 3.1 128.4 1.0 OP2 A:A31 3.7 123.8 1.0 P A:A361 4.0 174.8 1.0 C3' A:A29 4.0 120.0 1.0 O3' A:A29 4.1 120.0 1.0 OP1 A:C30 4.2 128.4 1.0 C5' A:C30 4.5 128.4 1.0 O2 A:U73 4.5 130.0 1.0 OP2 A:A361 4.5 174.8 1.0 O3' A:A360 4.9 176.4 1.0 O5' A:A361 5.0 174.8 1.0

Magnesium binding site 3 out of 27 in the Tetrahymena Ribozyme Scaffolded Tabv Xrrna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Tetrahymena Ribozyme Scaffolded Tabv Xrrna within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg503 b:159.5 occ:0.87 OP2 A:A269 3.1 183.0 1.0 OP2 A:A268 3.5 182.3 1.0 OP1 A:A268 3.6 182.3 1.0 P A:A268 3.8 182.3 1.0 O5' A:A268 3.9 182.3 1.0 N7 A:A269 4.0 183.0 1.0 O6 A:G270 4.0 178.9 1.0 C8 A:A269 4.2 183.0 1.0 N7 A:G270 4.3 178.9 1.0 P A:A269 4.5 183.0 1.0 C6 A:G270 4.8 178.9 1.0 O5' A:A269 4.8 183.0 1.0 C5 A:G270 5.0 178.9 1.0

Magnesium binding site 4 out of 27 in the Tetrahymena Ribozyme Scaffolded Tabv Xrrna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Tetrahymena Ribozyme Scaffolded Tabv Xrrna within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg504 b:108.6 occ:0.78 OP2 A:A341 1.9 120.6 1.0 OP1 A:A338 1.9 111.5 1.0 OP2 A:G342 2.0 115.0 1.0 OP1 A:A340 2.4 112.6 1.0 P A:A341 3.3 120.6 1.0 P A:A338 3.3 111.5 1.0 P A:G342 3.3 115.0 1.0 P A:A340 3.7 112.6 1.0 O5' A:A341 3.8 120.6 1.0 OP1 A:G342 3.9 115.0 1.0 C5' A:A341 3.9 120.6 1.0 OP2 A:A338 4.0 111.5 1.0 O3' A:A337 4.1 111.4 1.0 OP1 A:A341 4.2 120.6 1.0 O5' A:A338 4.3 111.5 1.0 O3' A:A341 4.3 120.6 1.0 O5' A:A340 4.3 112.6 1.0 O3' A:A340 4.3 112.6 1.0 O5' A:G342 4.4 115.0 1.0 C5' A:A340 4.4 112.6 1.0 OP2 A:A340 4.5 112.6 1.0 C3' A:A340 4.6 112.6 1.0 C4' A:A341 4.7 120.6 1.0 C5' A:A338 4.7 111.5 1.0 O3' A:U339 4.8 125.1 1.0 O5' A:A337 4.8 111.4 1.0 C3' A:A341 4.9 120.6 1.0

Magnesium binding site 5 out of 27 in the Tetrahymena Ribozyme Scaffolded Tabv Xrrna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Tetrahymena Ribozyme Scaffolded Tabv Xrrna within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg505 b:109.7 occ:0.85 OP2 A:A338 1.9 111.5 1.0 OP1 A:A337 1.9 111.4 1.0 OP2 A:A340 2.0 112.6 1.0 P A:A337 3.1 111.4 1.0 O5' A:A337 3.3 111.4 1.0 P A:A338 3.3 111.5 1.0 P A:A340 3.4 112.6 1.0 OP2 A:A337 4.0 111.4 1.0 OP1 A:A340 4.0 112.6 1.0 O5' A:A338 4.1 111.5 1.0 OP1 A:A338 4.2 111.5 1.0 O5' A:A340 4.2 112.6 1.0 C3' A:A337 4.3 111.4 1.0 O3' A:A337 4.3 111.4 1.0 O3' A:U336 4.3 113.0 1.0 O3' A:U339 4.4 125.1 1.0 C5' A:A337 4.6 111.4 1.0 C3' A:U339 4.7 125.1 1.0 N7 A:A340 4.9 112.6 1.0 C8 A:A340 5.0 112.6 1.0

Magnesium binding site 6 out of 27 in the Tetrahymena Ribozyme Scaffolded Tabv Xrrna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Tetrahymena Ribozyme Scaffolded Tabv Xrrna within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg506 b:88.9 occ:0.81 O6 A:G342 2.8 115.0 1.0 N7 A:G342 3.0 115.0 1.0 C6 A:G342 3.5 115.0 1.0 C5 A:G342 3.5 115.0 1.0 C8 A:G342 4.2 115.0 1.0 OP1 A:U322 4.3 128.8 1.0 OP2 A:A337 4.4 111.4 1.0 C5 A:U322 4.5 128.8 1.0 OP2 A:C320 4.8 127.1 1.0 N1 A:G342 4.8 115.0 1.0 OP1 A:C319 4.8 122.0 1.0 OP2 A:U322 4.8 128.8 1.0 OP1 A:U336 4.8 113.0 1.0 C4 A:G342 4.9 115.0 1.0 OP1 A:C320 4.9 127.1 1.0 N7 A:A337 4.9 111.4 1.0

Magnesium binding site 7 out of 27 in the Tetrahymena Ribozyme Scaffolded Tabv Xrrna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Tetrahymena Ribozyme Scaffolded Tabv Xrrna within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg507 b:123.3 occ:0.84 N1 A:G318 2.0 122.0 1.0 O6 A:G318 2.0 122.0 1.0 N7 A:G317 2.0 129.9 1.0 C6 A:G318 2.1 122.0 1.0 C5 A:G317 2.1 129.9 1.0 C6 A:G317 2.3 129.9 1.0 O6 A:G317 2.3 129.9 1.0 C8 A:G317 3.1 129.9 1.0 C2 A:G318 3.1 122.0 1.0 C5 A:G318 3.2 122.0 1.0 C4 A:G317 3.2 129.9 1.0 N1 A:G317 3.4 129.9 1.0 N9 A:G317 3.7 129.9 1.0 N2 A:G318 3.8 122.0 1.0 C4 A:G318 3.9 122.0 1.0 N3 A:G318 4.0 122.0 1.0 C2 A:G317 4.2 129.9 1.0 N7 A:G318 4.2 122.0 1.0 N3 A:G317 4.2 129.9 1.0 OP2 A:G317 4.8 129.9 1.0 C5 A:U316 4.9 139.6 1.0 N6 A:A332 4.9 132.8 1.0

Magnesium binding site 8 out of 27 in the Tetrahymena Ribozyme Scaffolded Tabv Xrrna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Tetrahymena Ribozyme Scaffolded Tabv Xrrna within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg508 b:104.2 occ:0.78 OP1 A:A293 4.2 121.1 1.0 O4 A:U316 4.4 139.6 1.0 OP2 A:A315 4.8 146.6 1.0 OP2 A:G314 4.9 150.0 1.0 OP2 A:A293 4.9 121.1 1.0 O6 A:G317 5.0 129.9 1.0

Magnesium binding site 9 out of 27 in the Tetrahymena Ribozyme Scaffolded Tabv Xrrna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Tetrahymena Ribozyme Scaffolded Tabv Xrrna within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg509 b:155.9 occ:0.80 N7 A:G302 2.0 157.3 1.0 O6 A:G302 2.1 157.3 1.0 C5 A:G302 2.3 157.3 1.0 C6 A:G302 2.4 157.3 1.0 C8 A:G302 3.2 157.3 1.0 O6 A:G303 3.6 154.5 1.0 C4 A:G302 3.6 157.3 1.0 N7 A:G303 3.7 154.5 1.0 N1 A:G302 3.7 157.3 1.0 O6 A:G301 3.8 158.5 1.0 C6 A:G301 3.9 158.5 1.0 N9 A:G302 4.0 157.3 1.0 C5 A:G301 4.1 158.5 1.0 C6 A:G303 4.2 154.5 1.0 C5 A:G303 4.3 154.5 1.0 N7 A:G301 4.3 158.5 1.0 N1 A:G301 4.4 158.5 1.0 C2 A:G302 4.6 157.3 1.0 N3 A:G302 4.6 157.3 1.0 O4 A:U309 4.7 150.1 1.0 O6 A:G304 4.7 149.7 1.0 C8 A:G303 4.8 154.5 1.0 C4 A:G301 4.8 158.5 1.0 N3 A:U309 5.0 150.1 1.0 N3 A:U310 5.0 153.8 1.0

Magnesium binding site 10 out of 27 in the Tetrahymena Ribozyme Scaffolded Tabv Xrrna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Tetrahymena Ribozyme Scaffolded Tabv Xrrna within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg510 b:126.6 occ:0.87 O6 A:G304 3.8 149.7 1.0 OP2 A:G303 4.0 154.5 1.0 N7 A:G304 4.2 149.7 1.0 C6 A:G304 4.5 149.7 1.0 C5 A:G304 4.7 149.7 1.0

C.J.Langeberg, J.S.Kieft. A Generalizable Scaffold-Based Approach For Structure Determination of Rnas By Cryo-Em. Nucleic Acids Res. 2023.
ISSN: ESSN 1362-4962
PubMed: 37791881
DOI: 10.1093/NAR/GKAD784