Magnesium in PDB 7yg9: Cryo-Em Structure of Tetrahymena Ribozyme Conformation 1 Undergoing the Second-Step Self-Splicing

The binding sites of Magnesium atom in the Cryo-Em Structure of Tetrahymena Ribozyme Conformation 1 Undergoing the Second-Step Self-Splicing (pdb code 7yg9). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Cryo-Em Structure of Tetrahymena Ribozyme Conformation 1 Undergoing the Second-Step Self-Splicing, PDB code: 7yg9:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in the Cryo-Em Structure of Tetrahymena Ribozyme Conformation 1 Undergoing the Second-Step Self-Splicing


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 Tetrahymena Ribozyme Conformation 1 Undergoing the Second-Step Self-Splicing within 5.0Å range: probe atom residue distance (Å) B Occ N:Mg501 b:30.0 occ:1.00 OP1 N:A304 1.8 17.0 1.0 OP2 A:SSU4 1.9 45.1 1.0 OP1 N:A306 2.0 18.5 1.0 OP1 N:C208 2.3 23.4 1.0 P A:SSU4 3.0 45.1 1.0 P N:A304 3.1 17.0 1.0 P N:A306 3.3 18.5 1.0 O3' B:U6 3.4 33.4 1.0 S1P A:SSU4 3.4 45.1 1.0 C5' B:U6 3.5 33.4 1.0 OP1 N:U307 3.7 17.6 1.0 OP2 N:A304 3.7 17.0 1.0 P N:C208 3.8 23.4 1.0 C4' B:U6 3.8 33.4 1.0 OP2 N:A306 3.9 18.5 1.0 O5' A:SSU4 3.9 45.1 1.0 O5' N:A304 4.0 17.0 1.0 O5' N:A306 4.0 18.5 1.0 C3' B:U6 4.1 33.4 1.0 O5' B:U6 4.2 33.4 1.0 O3' N:G303 4.3 18.2 1.0 C5' N:A304 4.3 17.0 1.0 O3' A:G3 4.3 29.7 0.2 O3' N:A207 4.3 28.8 1.0 O3' N:U305 4.4 17.7 1.0 OP2 N:C208 4.6 23.4 1.0 C3' A:G3 4.7 29.7 0.7 O5' N:C208 4.7 23.4 1.0 O2' N:U305 4.9 17.7 1.0 O2' A:G3 4.9 29.7 0.5 C3' N:U305 5.0 17.7 1.0

Magnesium binding site 2 out of 8 in the Cryo-Em Structure of Tetrahymena Ribozyme Conformation 1 Undergoing the Second-Step Self-Splicing


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 Tetrahymena Ribozyme Conformation 1 Undergoing the Second-Step Self-Splicing within 5.0Å range: probe atom residue distance (Å) B Occ N:Mg502 b:30.0 occ:1.00 OP2 N:C262 1.9 31.0 1.0 OP1 N:A207 2.0 28.8 1.0 O2 N:U305 3.3 17.7 1.0 P N:C262 3.3 31.0 1.0 P N:A207 3.4 28.8 1.0 O5' N:C262 4.0 31.0 1.0 O5' N:A207 4.1 28.8 1.0 C3' N:A261 4.1 20.5 1.0 OP2 N:A207 4.1 28.8 1.0 O3' N:A261 4.2 20.5 1.0 OP1 N:C262 4.2 31.0 1.0 C2 N:U305 4.4 17.7 1.0 O3' N:A206 4.4 28.3 1.0 C5' N:A207 4.6 28.8 1.0 O2' N:U305 4.7 17.7 1.0 C5' N:A261 4.8 20.5 1.0 C4' N:A261 4.8 20.5 1.0 C1' N:U305 4.8 17.7 1.0 S1P A:SSU4 4.8 45.1 1.0 OP2 N:A263 4.9 28.6 1.0

Magnesium binding site 3 out of 8 in the Cryo-Em Structure of Tetrahymena Ribozyme Conformation 1 Undergoing the Second-Step Self-Splicing


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 Tetrahymena Ribozyme Conformation 1 Undergoing the Second-Step Self-Splicing within 5.0Å range: probe atom residue distance (Å) B Occ N:Mg503 b:30.0 occ:1.00 OP2 N:A308 2.5 19.3 1.0 OP2 N:U307 2.7 17.6 1.0 N7 A:G3 3.3 29.7 0.8 O3' N:A306 3.5 18.5 1.0 P N:U307 3.7 17.6 1.0 C8 A:G3 3.9 29.7 0.8 P N:A308 3.9 19.3 1.0 C5 A:G3 4.0 29.7 0.8 O2' N:A306 4.2 18.5 1.0 O5' N:U307 4.3 17.6 1.0 C3' N:U307 4.4 17.6 1.0 O6 A:G3 4.4 29.7 0.8 C6 A:G3 4.5 29.7 0.8 O5' N:A308 4.6 19.3 1.0 O3' N:U307 4.6 17.6 1.0 N7 N:A308 4.7 19.3 1.0 C3' N:A306 4.8 18.5 1.0 N7 N:G309 4.8 22.4 1.0 N9 A:G3 4.8 29.7 0.8 C4 A:G3 4.9 29.7 0.8 C6 N:U307 4.9 17.6 1.0 OP1 N:A308 5.0 19.3 1.0 C2' N:A306 5.0 18.5 1.0 OP1 N:U307 5.0 17.6 1.0

Magnesium binding site 4 out of 8 in the Cryo-Em Structure of Tetrahymena Ribozyme Conformation 1 Undergoing the Second-Step Self-Splicing


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 Tetrahymena Ribozyme Conformation 1 Undergoing the Second-Step Self-Splicing within 5.0Å range: probe atom residue distance (Å) B Occ N:Mg504 b:30.0 occ:1.00 OP2 N:U258 1.8 11.8 1.0 OP2 N:U305 2.4 17.7 1.0 OP1 N:G257 2.4 11.6 1.0 P N:U258 3.1 11.8 1.0 O2 N:C260 3.6 14.4 1.0 O4 N:U259 3.6 12.7 1.0 OP1 N:U258 3.6 11.8 1.0 P N:U305 3.7 17.7 1.0 P N:G257 3.7 11.6 1.0 C5' N:U305 4.0 17.7 1.0 O5' N:U305 4.1 17.7 1.0 O5' N:U258 4.1 11.8 1.0 C5 N:U259 4.1 12.7 1.0 O2' N:C260 4.1 14.4 1.0 O3' N:G257 4.2 11.6 1.0 O3' N:A304 4.2 17.0 1.0 C4 N:U259 4.2 12.7 1.0 OP2 N:G257 4.4 11.6 1.0 O5' N:G257 4.5 11.6 1.0 C2 N:C260 4.5 14.4 1.0 C3' N:G257 4.6 11.6 1.0 C5' N:G257 4.7 11.6 1.0 O3' N:A256 4.8 13.1 1.0 OP1 N:U305 4.9 17.7 1.0

Magnesium binding site 5 out of 8 in the Cryo-Em Structure of Tetrahymena Ribozyme Conformation 1 Undergoing the Second-Step Self-Splicing


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 Tetrahymena Ribozyme Conformation 1 Undergoing the Second-Step Self-Splicing within 5.0Å range: probe atom residue distance (Å) B Occ N:Mg505 b:30.0 occ:1.00 OP1 N:U258 2.0 11.8 1.0 P N:U258 3.5 11.8 1.0 OP2 N:A261 3.6 20.5 1.0 O5' N:U258 4.2 11.8 1.0 C5' N:U258 4.2 11.8 1.0 MG N:MG508 4.3 30.0 1.0 O3' N:G257 4.3 11.6 1.0 O4' N:A306 4.3 18.5 1.0 OP2 N:U259 4.3 12.7 1.0 C8 N:A306 4.5 18.5 1.0 OP2 N:U258 4.5 11.8 1.0 N3 N:A304 4.5 17.0 1.0 C5' N:U305 4.7 17.7 1.0 N7 N:A306 4.7 18.5 1.0 N9 N:A306 4.8 18.5 1.0 P N:A261 4.8 20.5 1.0 C5' N:A306 4.9 18.5 1.0

Magnesium binding site 6 out of 8 in the Cryo-Em Structure of Tetrahymena Ribozyme Conformation 1 Undergoing the Second-Step Self-Splicing


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 Tetrahymena Ribozyme Conformation 1 Undergoing the Second-Step Self-Splicing within 5.0Å range: probe atom residue distance (Å) B Occ N:Mg506 b:30.0 occ:1.00 OP1 N:U305 2.8 17.7 1.0 OP1 N:G303 3.3 18.2 1.0 P N:U305 3.6 17.7 1.0 OP2 N:U305 3.8 17.7 1.0 O2' N:A304 4.0 17.0 1.0 O3' N:A304 4.1 17.0 1.0 C3' N:A304 4.2 17.0 1.0 P N:G303 4.3 18.2 1.0 N3 N:A256 4.5 13.1 1.0 C2' N:A304 4.5 17.0 1.0 O5' N:G303 4.6 18.2 1.0 O3' N:A256 4.7 13.1 1.0 C1' N:A256 4.7 13.1 1.0 OP2 N:G303 4.8 18.2 1.0 OP1 N:G257 5.0 11.6 1.0

Magnesium binding site 7 out of 8 in the Cryo-Em Structure of Tetrahymena Ribozyme Conformation 1 Undergoing the Second-Step Self-Splicing


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Cryo-Em Structure of Tetrahymena Ribozyme Conformation 1 Undergoing the Second-Step Self-Splicing within 5.0Å range: probe atom residue distance (Å) B Occ N:Mg507 b:30.0 occ:1.00 OP1 N:U259 2.0 12.7 1.0 OP1 N:A261 3.3 20.5 1.0 P N:U259 3.5 12.7 1.0 N7 N:A261 4.0 20.5 1.0 O3' N:U258 4.0 11.8 1.0 OP2 N:A265 4.1 23.8 1.0 N7 N:A306 4.2 18.5 1.0 OP2 N:U259 4.3 12.7 1.0 O2' N:U106 4.3 15.2 1.0 N6 N:A306 4.3 18.5 1.0 C8 N:A261 4.5 20.5 1.0 O5' N:U259 4.5 12.7 1.0 P N:A261 4.7 20.5 1.0 C5' N:U259 4.7 12.7 1.0 C2' N:U106 4.8 15.2 1.0 O2 N:U106 4.8 15.2 1.0

Magnesium binding site 8 out of 8 in the Cryo-Em Structure of Tetrahymena Ribozyme Conformation 1 Undergoing the Second-Step Self-Splicing


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Cryo-Em Structure of Tetrahymena Ribozyme Conformation 1 Undergoing the Second-Step Self-Splicing within 5.0Å range: probe atom residue distance (Å) B Occ N:Mg508 b:30.0 occ:1.00 O4 N:U307 2.5 17.6 1.0 C4 N:U307 3.3 17.6 1.0 N3 N:A306 3.4 18.5 1.0 C2 N:A306 3.6 18.5 1.0 C4 N:A306 3.6 18.5 1.0 C2 N:A304 3.7 17.0 1.0 C5 N:U307 3.8 17.6 1.0 N6 N:A268 3.9 17.4 1.0 N1 N:A306 4.0 18.5 1.0 C5 N:A306 4.1 18.5 1.0 N3 N:A304 4.2 17.0 1.0 N9 N:A306 4.2 18.5 1.0 N3 N:U307 4.2 17.6 1.0 MG N:MG505 4.3 30.0 1.0 C6 N:A306 4.3 18.5 1.0 N1 N:A304 4.5 17.0 1.0 O4' N:A306 4.5 18.5 1.0 N1 N:A269 4.7 16.2 1.0 C1' N:A306 4.7 18.5 1.0 N7 N:A306 4.9 18.5 1.0 C8 N:A306 4.9 18.5 1.0 C6 N:U307 5.0 17.6 1.0

S.Li, M.Z.Palo, X.Zhang, G.Pintilie, K.Zhang. Snapshots of the Second-Step Self-Splicing of Tetrahymena Ribozyme Revealed By Cryo-Em. Nat Commun V. 14 1294 2023.
ISSN: ESSN 2041-1723
PubMed: 36928031
DOI: 10.1038/S41467-023-36724-5