Magnesium in PDB 7ygc: Cryo-Em Structure of Tetrahymena Ribozyme Conformation 4 Undergoing the Second-Step Self-Splicing

The binding sites of Magnesium atom in the Cryo-Em Structure of Tetrahymena Ribozyme Conformation 4 Undergoing the Second-Step Self-Splicing (pdb code 7ygc). 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 Tetrahymena Ribozyme Conformation 4 Undergoing the Second-Step Self-Splicing, PDB code: 7ygc:
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 Tetrahymena Ribozyme Conformation 4 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 4 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 34.1 1.0 OP1 N:A306 1.9 35.6 1.0 P N:A304 3.2 34.1 1.0 P N:A306 3.3 35.6 1.0 OP1 N:C208 3.4 58.0 1.0 OP1 N:U307 3.8 33.9 1.0 O5' N:A306 3.9 35.6 1.0 O5' N:A304 4.0 34.1 1.0 OP2 N:A306 4.0 35.6 1.0 OP2 N:A304 4.1 34.1 1.0 O2' A:G3 4.1 51.7 1.0 C5' N:A304 4.1 34.1 1.0 O3' N:G303 4.2 39.1 1.0 O3' A:G3 4.4 51.7 1.0 O3' N:U305 4.4 37.8 1.0 O2' N:U305 4.6 37.8 1.0 P N:C208 4.7 58.0 1.0 C3' N:U305 4.8 37.8 1.0

Magnesium binding site 2 out of 6 in the Cryo-Em Structure of Tetrahymena Ribozyme Conformation 4 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 4 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:A308 2.7 35.5 1.0 OP2 N:U307 2.8 33.9 1.0 O3' N:A306 3.5 35.6 1.0 P N:U307 3.7 33.9 1.0 P N:A308 4.1 35.5 1.0 O2' N:A306 4.2 35.6 1.0 N7 A:G3 4.2 51.7 1.0 C8 A:G3 4.3 51.7 1.0 O5' N:U307 4.3 33.9 1.0 C3' N:U307 4.5 33.9 1.0 O5' N:A308 4.6 35.5 1.0 N7 N:A308 4.7 35.5 1.0 C3' N:A306 4.7 35.6 1.0 O3' N:U307 4.8 33.9 1.0 C6 N:U307 4.9 33.9 1.0 N7 N:G309 4.9 37.9 1.0 C2' N:A306 5.0 35.6 1.0 C5 N:U307 5.0 33.9 1.0

Magnesium binding site 3 out of 6 in the Cryo-Em Structure of Tetrahymena Ribozyme Conformation 4 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 4 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:U305 3.1 37.8 1.0 OP1 N:G303 3.5 39.1 1.0 OP2 N:U305 3.6 37.8 1.0 P N:U305 3.7 37.8 1.0 O2' N:A304 4.2 34.1 1.0 O3' N:A304 4.2 34.1 1.0 O5' N:G303 4.4 39.1 1.0 C3' N:A304 4.4 34.1 1.0 P N:G303 4.5 39.1 1.0 O3' N:A256 4.5 31.3 1.0 C1' N:A256 4.5 31.3 1.0 N3 N:A256 4.5 31.3 1.0 O4' N:A256 4.7 31.3 1.0 C2' N:A304 4.8 34.1 1.0 OP1 N:G257 4.8 19.1 1.0

Magnesium binding site 4 out of 6 in the Cryo-Em Structure of Tetrahymena Ribozyme Conformation 4 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 4 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 2.0 31.4 1.0 OP1 N:G257 2.2 19.1 1.0 OP2 N:U305 2.4 37.8 1.0 P N:U258 3.3 31.4 1.0 P N:U305 3.6 37.8 1.0 P N:G257 3.7 19.1 1.0 O2 N:C260 3.7 31.5 1.0 O4 N:U259 3.8 33.9 1.0 OP1 N:U258 3.8 31.4 1.0 C5' N:U305 4.0 37.8 1.0 O3' N:A304 4.0 34.1 1.0 O5' N:U305 4.0 37.8 1.0 O2' N:C260 4.0 31.5 1.0 C5 N:U259 4.2 33.9 1.0 O3' N:G257 4.3 19.1 1.0 O5' N:U258 4.3 31.4 1.0 C4 N:U259 4.4 33.9 1.0 OP2 N:G257 4.4 19.1 1.0 O5' N:G257 4.4 19.1 1.0 C2 N:C260 4.6 31.5 1.0 C5' N:G257 4.7 19.1 1.0 O3' N:A256 4.7 31.3 1.0 C3' N:G257 4.7 19.1 1.0 OP1 N:U305 4.9 37.8 1.0

Magnesium binding site 5 out of 6 in the Cryo-Em Structure of Tetrahymena Ribozyme Conformation 4 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 4 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 2.1 31.4 1.0 OP2 N:A261 3.0 38.9 1.0 P N:U258 3.5 31.4 1.0 C5' N:U258 4.3 31.4 1.0 O5' N:U258 4.3 31.4 1.0 O3' N:G257 4.3 19.1 1.0 OP2 N:U259 4.3 33.9 1.0 O4' N:A306 4.3 35.6 1.0 C8 N:A306 4.4 35.6 1.0 N3 N:A304 4.4 34.1 1.0 P N:A261 4.4 38.9 1.0 OP2 N:U258 4.5 31.4 1.0 N7 N:A306 4.6 35.6 1.0 N9 N:A306 4.7 35.6 1.0 C5' N:U305 4.9 37.8 1.0 O5' N:A261 5.0 38.9 1.0

Magnesium binding site 6 out of 6 in the Cryo-Em Structure of Tetrahymena Ribozyme Conformation 4 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 4 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:U259 2.3 33.9 1.0 P N:U259 3.5 33.9 1.0 OP1 N:A261 3.9 38.9 1.0 N7 N:A261 3.9 38.9 1.0 OP2 N:A265 3.9 37.7 1.0 O3' N:U258 3.9 31.4 1.0 N6 N:A306 4.0 35.6 1.0 N7 N:A306 4.1 35.6 1.0 O2' N:U106 4.3 31.8 1.0 OP2 N:U259 4.3 33.9 1.0 C8 N:A261 4.4 38.9 1.0 O2 N:U106 4.6 31.8 1.0 O5' N:U259 4.7 33.9 1.0 C2' N:U106 4.7 31.8 1.0 OP2 N:A261 4.8 38.9 1.0 C5 N:A306 4.9 35.6 1.0 C6 N:A306 4.9 35.6 1.0 P N:A261 4.9 38.9 1.0 C5 N:A261 4.9 38.9 1.0 P N:A265 4.9 37.7 1.0 C5' N:U259 5.0 33.9 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