Magnesium in PDB 9c6j: Group Iic Intron Embedded with the Tpp Riboswitch

Pages:

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

Binding sites:

The binding sites of Magnesium atom in the Group Iic Intron Embedded with the Tpp Riboswitch (pdb code 9c6j). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 21 binding sites of Magnesium where determined in the Group Iic Intron Embedded with the Tpp Riboswitch, PDB code: 9c6j:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 21 in the Group Iic Intron Embedded with the Tpp Riboswitch


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Group Iic Intron Embedded with the Tpp Riboswitch within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg501 b:51.3 occ:1.00 OP1 A:A184 3.0 50.4 1.0 N1 A:A371 4.0 44.1 1.0 OP2 A:U176 4.0 44.7 1.0 OP2 A:C185 4.0 53.4 1.0 C2 A:A371 4.2 44.1 1.0 P A:A184 4.2 50.4 1.0 OP1 A:C185 4.3 53.4 1.0 O5' A:A184 4.4 50.4 1.0 C5' A:A184 4.4 50.4 1.0 P A:C185 4.5 53.4 1.0 N6 A:A370 4.6 44.0 1.0 OP1 A:G175 4.6 42.5 1.0 O3' A:A184 4.9 50.4 1.0 OP1 A:U176 5.0 44.7 1.0 P A:U176 5.0 44.7 1.0

Magnesium binding site 2 out of 21 in the Group Iic Intron Embedded with the Tpp Riboswitch


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Group Iic Intron Embedded with the Tpp Riboswitch within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:55.0 occ:1.00 OP2 A:A186 2.4 56.9 1.0 P A:A186 3.6 56.9 1.0 N7 A:A187 3.7 55.7 1.0 O5' A:A186 3.8 56.9 1.0 N6 A:A187 4.2 55.7 1.0 C8 A:A186 4.3 56.9 1.0 OP2 A:A187 4.3 55.7 1.0 N7 A:A186 4.4 56.9 1.0 OP1 A:A186 4.6 56.9 1.0 C5 A:A187 4.6 55.7 1.0 C8 A:A187 4.7 55.7 1.0 O3' A:C185 4.8 53.4 1.0 C6 A:A187 4.9 55.7 1.0 C3' A:C185 4.9 53.4 1.0

Magnesium binding site 3 out of 21 in the Group Iic Intron Embedded with the Tpp Riboswitch


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Group Iic Intron Embedded with the Tpp Riboswitch within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg503 b:54.6 occ:1.00 N7 A:G5 2.5 52.2 1.0 OP2 A:U4 2.6 52.3 1.0 O6 A:G5 3.5 52.2 1.0 C5 A:G5 3.5 52.2 1.0 C8 A:G5 3.5 52.2 1.0 O5' A:U4 3.6 52.3 1.0 P A:U4 3.6 52.3 1.0 C6 A:G5 3.8 52.2 1.0 OP1 A:G3 3.9 53.6 1.0 N1 A:A376 4.0 56.8 1.0 C6 A:U4 4.1 52.3 1.0 C5 A:U4 4.2 52.3 1.0 C2 A:A376 4.4 56.8 1.0 OP1 A:U4 4.5 52.3 1.0 C6 A:A376 4.7 56.8 1.0 C4 A:G5 4.7 52.2 1.0 N9 A:G5 4.7 52.2 1.0 O3' A:G3 4.9 53.6 1.0 N6 A:A376 4.9 56.8 1.0 OP2 A:G5 4.9 52.2 1.0 N1 A:U4 5.0 52.3 1.0 C5' A:U4 5.0 52.3 1.0

Magnesium binding site 4 out of 21 in the Group Iic Intron Embedded with the Tpp Riboswitch


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Group Iic Intron Embedded with the Tpp Riboswitch within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg504 b:48.3 occ:1.00 O6 A:G265 3.4 48.6 1.0 O6 A:G264 3.8 48.2 1.0 N4 A:C7 4.3 49.2 1.0 N4 A:C263 4.4 48.0 1.0 C6 A:G265 4.5 48.6 1.0 C6 A:G264 4.7 48.2 1.0 N7 A:G264 4.7 48.2 1.0 N7 A:G265 4.8 48.6 1.0 C4 A:C263 5.0 48.0 1.0

Magnesium binding site 5 out of 21 in the Group Iic Intron Embedded with the Tpp Riboswitch


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Group Iic Intron Embedded with the Tpp Riboswitch within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg505 b:49.2 occ:1.00 OP1 A:G111 2.1 47.1 1.0 P A:G111 3.4 47.1 1.0 O5' A:G111 3.7 47.1 1.0 OP1 A:C112 3.9 48.5 1.0 O2 A:U13 4.1 55.5 1.0 OP2 A:C112 4.1 48.5 1.0 C3' A:A110 4.2 49.4 1.0 O2' A:A110 4.2 49.4 1.0 O3' A:A110 4.2 49.4 1.0 P A:C112 4.3 48.5 1.0 OP1 A:G14 4.4 58.0 1.0 OP2 A:G111 4.6 47.1 1.0 O3' A:G111 4.6 47.1 1.0 C2' A:A110 4.6 49.4 1.0 O3' A:U13 4.6 55.5 1.0

Magnesium binding site 6 out of 21 in the Group Iic Intron Embedded with the Tpp Riboswitch


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Group Iic Intron Embedded with the Tpp Riboswitch within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg506 b:56.6 occ:1.00 O6 A:G46 3.7 48.9 1.0 O4 A:U47 3.8 51.8 1.0 OP2 A:U59 3.8 59.0 1.0 OP1 A:U59 4.3 59.0 1.0 N7 A:G46 4.3 48.9 1.0 O4 A:U45 4.4 49.1 1.0 N6 A:A61 4.5 51.1 1.0 C6 A:G46 4.5 48.9 1.0 O2' A:G58 4.5 61.8 1.0 P A:U59 4.6 59.0 1.0 N1 A:G48 4.8 55.1 1.0 C5 A:G46 4.8 48.9 1.0 C4 A:U47 4.9 51.8 1.0 O6 A:G48 4.9 55.1 1.0 C4 A:U45 4.9 49.1 1.0

Magnesium binding site 7 out of 21 in the Group Iic Intron Embedded with the Tpp Riboswitch


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Group Iic Intron Embedded with the Tpp Riboswitch within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg507 b:43.6 occ:1.00 OP2 A:U66 1.9 44.7 1.0 OP1 A:A67 2.2 44.2 1.0 P A:U66 3.3 44.7 1.0 P A:A67 3.6 44.2 1.0 O3' A:U66 3.8 44.7 1.0 O5' A:U66 4.1 44.7 1.0 OP1 A:U66 4.1 44.7 1.0 O3' A:U65 4.3 45.9 1.0 O5' A:A67 4.5 44.2 1.0 C5' A:A67 4.6 44.2 1.0 OP2 A:A67 4.6 44.2 1.0

Magnesium binding site 8 out of 21 in the Group Iic Intron Embedded with the Tpp Riboswitch


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Group Iic Intron Embedded with the Tpp Riboswitch within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg508 b:49.1 occ:1.00 N7 A:G242 3.9 47.6 1.0 O6 A:G242 4.1 47.6 1.0 O6 A:G244 4.3 48.1 1.0 O6 A:G243 4.4 48.1 1.0 N7 A:G243 4.5 48.1 1.0 C5 A:G242 4.6 47.6 1.0 C6 A:G242 4.6 47.6 1.0 C8 A:G242 4.8 47.6 1.0

Magnesium binding site 9 out of 21 in the Group Iic Intron Embedded with the Tpp Riboswitch


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Group Iic Intron Embedded with the Tpp Riboswitch within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg509 b:57.6 occ:1.00 OP1 A:C39 3.6 54.1 1.0 OP2 A:G243 4.3 48.1 1.0 O3' A:C38 4.3 51.9 1.0 P A:C39 4.5 54.1 1.0 N7 A:G244 4.6 48.1 1.0 C5' A:C38 4.8 51.9 1.0 OP1 A:C38 4.8 51.9 1.0

Magnesium binding site 10 out of 21 in the Group Iic Intron Embedded with the Tpp Riboswitch


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Group Iic Intron Embedded with the Tpp Riboswitch within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg510 b:50.1 occ:1.00 OP1 A:A120 2.5 42.0 1.0 P A:A120 3.9 42.0 1.0 OP2 A:G239 3.9 41.4 1.0 O2' A:A237 4.1 43.9 1.0 OP2 A:U238 4.2 41.5 1.0 OP2 A:A120 4.4 42.0 1.0 OP1 A:A121 4.5 44.0 1.0 OP1 A:U238 4.5 41.5 1.0 P A:U238 4.8 41.5 1.0 O5' A:A120 4.9 42.0 1.0 O3' A:C119 4.9 42.7 1.0 P A:G239 5.0 41.4 1.0 OP1 A:G239 5.0 41.4 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