Magnesium in PDB 7yga: Cryo-Em Structure of Tetrahymena Ribozyme Conformation 2 Undergoing the Second-Step Self-Splicing

The binding sites of Magnesium atom in the Cryo-Em Structure of Tetrahymena Ribozyme Conformation 2 Undergoing the Second-Step Self-Splicing (pdb code 7yga). 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 2 Undergoing the Second-Step Self-Splicing, PDB code: 7yga:
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 2 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 2 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:A306 1.8 41.6 1.0 OP1 N:A304 1.8 39.4 1.0 S1P A:SSU4 1.8 61.8 1.0 OP1 N:C208 2.0 46.0 1.0 O3' B:U6 3.0 51.5 1.0 P N:A304 3.2 39.4 1.0 P N:A306 3.2 41.6 1.0 P A:SSU4 3.5 61.8 1.0 P N:C208 3.5 46.0 1.0 C5' B:U6 3.6 51.5 1.0 C4' B:U6 3.7 51.5 1.0 C3' B:U6 3.8 51.5 1.0 O5' N:A304 3.9 39.4 1.0 OP2 N:A306 3.9 41.6 1.0 OP1 N:U307 4.0 40.7 1.0 OP2 N:A304 4.0 39.4 1.0 O5' A:SSU4 4.0 61.8 1.0 O5' N:A306 4.1 41.6 1.0 O3' N:A207 4.1 50.6 1.0 O3' N:U305 4.1 40.6 1.0 O3' A:G3 4.2 53.4 0.2 C5' N:A304 4.2 39.4 1.0 O3' N:G303 4.2 40.0 1.0 O5' N:C208 4.3 46.0 1.0 O2' A:G3 4.4 53.4 0.5 OP2 N:C208 4.4 46.0 1.0 O5' B:U6 4.6 51.5 1.0 C3' N:U305 4.7 40.6 1.0 OP2 A:SSU4 4.7 61.8 1.0 O2' N:U305 5.0 40.6 1.0

Magnesium binding site 2 out of 8 in the Cryo-Em Structure of Tetrahymena Ribozyme Conformation 2 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 2 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 OP1 N:A207 1.8 50.6 1.0 OP2 N:C262 1.8 54.6 1.0 P N:A207 3.2 50.6 1.0 P N:C262 3.3 54.6 1.0 O2 N:U305 3.7 40.6 1.0 OP2 N:A207 3.8 50.6 1.0 O5' N:C262 3.8 54.6 1.0 C3' N:A261 4.1 44.1 1.0 O3' N:A206 4.1 51.9 1.0 O5' N:A207 4.2 50.6 1.0 O3' N:A261 4.2 44.1 1.0 OP1 N:C262 4.2 54.6 1.0 C5' N:A261 4.8 44.1 1.0 C2 N:U305 4.8 40.6 1.0 C5' N:A207 4.8 50.6 1.0 C4' N:A261 4.8 44.1 1.0

Magnesium binding site 3 out of 8 in the Cryo-Em Structure of Tetrahymena Ribozyme Conformation 2 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 2 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 OP1 N:U259 1.9 37.5 1.0 P N:U259 3.4 37.5 1.0 OP1 N:A261 3.5 44.1 1.0 N7 N:A261 4.0 44.1 1.0 OP2 N:A265 4.2 45.1 1.0 N6 N:A306 4.2 41.6 1.0 O3' N:U258 4.2 37.0 1.0 N7 N:A306 4.2 41.6 1.0 OP2 N:U259 4.3 37.5 1.0 O5' N:U259 4.3 37.5 1.0 C8 N:A261 4.4 44.1 1.0 O2' N:U106 4.5 41.2 1.0 C5' N:U259 4.6 37.5 1.0 O2 N:U106 4.8 41.2 1.0 P N:A261 4.9 44.1 1.0 C2' N:U106 4.9 41.2 1.0 C5 N:A306 5.0 41.6 1.0

Magnesium binding site 4 out of 8 in the Cryo-Em Structure of Tetrahymena Ribozyme Conformation 2 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 2 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:A308 2.0 42.1 1.0 OP2 N:U307 2.4 40.7 1.0 P N:A308 3.4 42.1 1.0 P N:U307 3.6 40.7 1.0 O3' N:A306 3.6 41.6 1.0 N7 A:G3 3.8 53.4 0.8 C8 A:G3 4.1 53.4 0.8 C3' N:U307 4.2 40.7 1.0 O3' N:U307 4.3 40.7 1.0 O5' N:A308 4.3 42.1 1.0 OP1 N:A308 4.3 42.1 1.0 O5' N:U307 4.3 40.7 1.0 N7 N:A308 4.5 42.1 1.0 O2' N:A306 4.5 41.6 1.0 C8 N:A308 4.7 42.1 1.0 C5 A:G3 4.7 53.4 0.8 N7 N:G309 4.8 44.6 1.0 OP1 N:U307 4.8 40.7 1.0 C3' N:A306 4.9 41.6 1.0 C5' N:U307 5.0 40.7 1.0

Magnesium binding site 5 out of 8 in the Cryo-Em Structure of Tetrahymena Ribozyme Conformation 2 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 2 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 OP2 N:U258 2.0 37.0 1.0 OP1 N:G257 2.1 36.9 1.0 OP2 N:U305 2.1 40.6 1.0 P N:U258 3.3 37.0 1.0 P N:G257 3.4 36.9 1.0 P N:U305 3.6 40.6 1.0 O2 N:C260 3.7 38.8 1.0 O4 N:U259 3.7 37.5 1.0 OP2 N:G257 3.8 36.9 1.0 OP1 N:U258 4.0 37.0 1.0 C5 N:U259 4.1 37.5 1.0 O3' N:G257 4.2 36.9 1.0 O5' N:U305 4.2 40.6 1.0 O5' N:G257 4.3 36.9 1.0 O3' N:A304 4.3 39.4 1.0 C4 N:U259 4.3 37.5 1.0 O2' N:C260 4.3 38.8 1.0 O5' N:U258 4.4 37.0 1.0 C5' N:U305 4.4 40.6 1.0 O3' N:A256 4.4 37.3 1.0 OP1 N:U305 4.5 40.6 1.0 C2 N:C260 4.5 38.8 1.0 C3' N:G257 4.5 36.9 1.0 C5' N:G257 4.6 36.9 1.0 N3 N:C260 5.0 38.8 1.0

Magnesium binding site 6 out of 8 in the Cryo-Em Structure of Tetrahymena Ribozyme Conformation 2 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 2 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:U258 2.0 37.0 1.0 P N:U258 3.5 37.0 1.0 OP2 N:A261 4.0 44.1 1.0 MG N:MG507 4.0 30.0 1.0 O3' N:G257 4.2 36.9 1.0 O5' N:U258 4.3 37.0 1.0 C5' N:U258 4.3 37.0 1.0 C8 N:A306 4.4 41.6 1.0 O4' N:A306 4.4 41.6 1.0 OP2 N:U259 4.4 37.5 1.0 OP2 N:U258 4.4 37.0 1.0 N3 N:A304 4.5 39.4 1.0 N7 N:A306 4.6 41.6 1.0 N9 N:A306 4.8 41.6 1.0 C5' N:U305 4.9 40.6 1.0 O3' N:A304 5.0 39.4 1.0

Magnesium binding site 7 out of 8 in the Cryo-Em Structure of Tetrahymena Ribozyme Conformation 2 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 2 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 O4 N:U307 2.5 40.7 1.0 C4 N:U307 3.4 40.7 1.0 N3 N:A306 3.6 41.6 1.0 C4 N:A306 3.7 41.6 1.0 C2 N:A306 3.7 41.6 1.0 C5 N:U307 3.9 40.7 1.0 C2 N:A304 3.9 39.4 1.0 C5 N:A306 3.9 41.6 1.0 N6 N:A268 3.9 40.7 1.0 N1 N:A306 4.0 41.6 1.0 MG N:MG506 4.0 30.0 1.0 C6 N:A306 4.0 41.6 1.0 N9 N:A306 4.2 41.6 1.0 N3 N:A304 4.3 39.4 1.0 N3 N:U307 4.5 40.7 1.0 N7 N:A306 4.6 41.6 1.0 C8 N:A306 4.7 41.6 1.0 O4' N:A306 4.7 41.6 1.0 N1 N:A304 4.7 39.4 1.0 C1' N:A306 4.8 41.6 1.0 N6 N:A306 4.8 41.6 1.0 N1 N:A269 4.9 39.6 1.0

Magnesium binding site 8 out of 8 in the Cryo-Em Structure of Tetrahymena Ribozyme Conformation 2 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 2 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 OP1 N:U305 2.3 40.6 1.0 P N:U305 3.5 40.6 1.0 OP1 N:G303 3.8 40.0 1.0 OP2 N:U305 4.0 40.6 1.0 O2' N:A304 4.0 39.4 1.0 O3' N:A304 4.0 39.4 1.0 C3' N:A304 4.1 39.4 1.0 N3 N:A256 4.2 37.3 1.0 C2' N:A304 4.5 39.4 1.0 P N:G303 4.5 40.0 1.0 O3' N:A256 4.6 37.3 1.0 OP2 N:G303 4.6 40.0 1.0 C1' N:A256 4.6 37.3 1.0 O5' N:G303 4.7 40.0 1.0 O5' N:U305 4.8 40.6 1.0 OP1 N:G257 4.8 36.9 1.0 C2 N:A256 5.0 37.3 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