Magnesium in PDB 7yg8: Cryo-Em Structure of Tetrahymena Ribozyme Conformation 5 Undergoing the Second-Step Self-Splicing

The binding sites of Magnesium atom in the Cryo-Em Structure of Tetrahymena Ribozyme Conformation 5 Undergoing the Second-Step Self-Splicing (pdb code 7yg8). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Cryo-Em Structure of Tetrahymena Ribozyme Conformation 5 Undergoing the Second-Step Self-Splicing, PDB code: 7yg8:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Cryo-Em Structure of Tetrahymena Ribozyme Conformation 5 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 5 Undergoing the Second-Step Self-Splicing within 5.0Å range: probe atom residue distance (Å) B Occ N:Mg501 b:67.2 occ:1.00 OP1 N:A304 2.1 62.2 1.0 OP1 N:A306 2.6 61.5 1.0 OP1 N:C208 3.3 78.2 1.0 P N:A304 3.4 62.2 1.0 OP2 N:A304 3.8 62.2 1.0 P N:A306 3.9 61.5 1.0 O3' A:G3 4.0 75.9 1.0 OP1 N:U307 4.0 60.9 1.0 O3' N:G303 4.3 65.8 1.0 O2' A:G3 4.3 75.9 1.0 O5' N:A304 4.5 62.2 1.0 OP2 N:A306 4.5 61.5 1.0 O5' N:A306 4.6 61.5 1.0 P N:C208 4.7 78.2 1.0 C5' N:A304 4.8 62.2 1.0

Magnesium binding site 2 out of 5 in the Cryo-Em Structure of Tetrahymena Ribozyme Conformation 5 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 5 Undergoing the Second-Step Self-Splicing within 5.0Å range: probe atom residue distance (Å) B Occ N:Mg502 b:58.7 occ:1.00 OP2 N:A308 2.6 62.4 1.0 OP2 N:U307 2.8 60.9 1.0 O3' N:A306 3.4 61.5 1.0 P N:U307 3.7 60.9 1.0 P N:A308 4.1 62.4 1.0 N7 A:G3 4.1 75.9 1.0 O2' N:A306 4.2 61.5 1.0 C8 A:G3 4.2 75.9 1.0 O5' N:U307 4.2 60.9 1.0 C3' N:U307 4.5 60.9 1.0 O5' N:A308 4.6 62.4 1.0 N7 N:A308 4.7 62.4 1.0 C3' N:A306 4.7 61.5 1.0 O3' N:U307 4.7 60.9 1.0 C6 N:U307 4.9 60.9 1.0 C5 A:G3 5.0 75.9 1.0 C2' N:A306 5.0 61.5 1.0

Magnesium binding site 3 out of 5 in the Cryo-Em Structure of Tetrahymena Ribozyme Conformation 5 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 5 Undergoing the Second-Step Self-Splicing within 5.0Å range: probe atom residue distance (Å) B Occ N:Mg503 b:54.4 occ:1.00 OP1 N:U305 2.9 62.0 1.0 OP1 N:G303 3.3 65.8 1.0 OP2 N:U305 3.4 62.0 1.0 P N:U305 3.6 62.0 1.0 O3' N:A304 4.2 62.2 1.0 O2' N:A304 4.3 62.2 1.0 C3' N:A304 4.6 62.2 1.0 P N:G303 4.7 65.8 1.0 O3' N:A256 4.7 54.0 1.0 C1' N:A256 4.8 54.0 1.0 OP1 N:G257 4.8 52.0 1.0 O4' N:A256 4.8 54.0 1.0 N3 N:A256 5.0 54.0 1.0 C2' N:A304 5.0 62.2 1.0 O5' N:G303 5.0 65.8 1.0

Magnesium binding site 4 out of 5 in the Cryo-Em Structure of Tetrahymena Ribozyme Conformation 5 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 5 Undergoing the Second-Step Self-Splicing within 5.0Å range: probe atom residue distance (Å) B Occ N:Mg504 b:56.5 occ:1.00 OP2 N:U258 2.3 52.4 1.0 OP1 N:G257 2.3 52.0 1.0 OP2 N:U305 2.5 62.0 1.0 O2 N:C260 3.4 58.5 1.0 P N:U258 3.6 52.4 1.0 P N:G257 3.7 52.0 1.0 O4 N:U259 3.8 55.0 1.0 P N:U305 3.8 62.0 1.0 O2' N:C260 4.0 58.5 1.0 OP1 N:U258 4.1 52.4 1.0 O5' N:U305 4.2 62.0 1.0 C5' N:U305 4.2 62.0 1.0 C5 N:U259 4.2 55.0 1.0 C2 N:C260 4.2 58.5 1.0 OP2 N:G257 4.3 52.0 1.0 C4 N:U259 4.4 55.0 1.0 O3' N:A304 4.4 62.2 1.0 O5' N:U258 4.5 52.4 1.0 O5' N:G257 4.5 52.0 1.0 O3' N:G257 4.7 52.0 1.0 O3' N:A256 4.8 54.0 1.0 N3 N:C260 4.9 58.5 1.0 C5' N:G257 4.9 52.0 1.0 C3' N:G257 5.0 52.0 1.0

Magnesium binding site 5 out of 5 in the Cryo-Em Structure of Tetrahymena Ribozyme Conformation 5 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 5 Undergoing the Second-Step Self-Splicing within 5.0Å range: probe atom residue distance (Å) B Occ N:Mg505 b:42.2 occ:1.00 OP1 N:U258 2.4 52.4 1.0 OP2 N:A261 2.7 64.3 1.0 P N:U258 3.8 52.4 1.0 O4' N:A306 4.1 61.5 1.0 P N:A261 4.1 64.3 1.0 C8 N:A306 4.1 61.5 1.0 OP2 N:U259 4.2 55.0 1.0 C5' N:U258 4.4 52.4 1.0 N7 N:A306 4.4 61.5 1.0 O5' N:U258 4.4 52.4 1.0 N9 N:A306 4.5 61.5 1.0 N3 N:A304 4.6 62.2 1.0 O3' N:G257 4.6 52.0 1.0 O5' N:A261 4.7 64.3 1.0 C5' N:U305 4.7 62.0 1.0 C5' N:A306 4.7 61.5 1.0 OP2 N:U258 4.8 52.4 1.0 O3' N:C260 4.9 58.5 1.0 C5 N:A306 4.9 61.5 1.0 C1' N:A306 5.0 61.5 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