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

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

Magnesium binding site 1 out of 3 in the Cryo-Em Structure of Tetrahymena Ribozyme Conformation 2 Undergoing the First-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 First-Step Self-Splicing within 5.0Å range: probe atom residue distance (Å) B Occ N:Mg502 b:30.0 occ:1.00 OP1 N:A306 2.3 185.4 1.0 OP1 N:A304 2.7 177.3 1.0 O3' N:GTP501 3.1 216.5 1.0 P N:A306 3.4 185.4 1.0 OP1 N:C208 3.5 190.6 1.0 OP2 N:A306 3.7 185.4 1.0 P N:A304 3.7 177.3 1.0 OP1 N:U307 3.9 179.3 1.0 OP2 N:A304 3.9 177.3 1.0 O5' N:A306 4.2 185.4 1.0 C3' N:GTP501 4.4 216.5 1.0 O3' N:U305 4.7 179.0 1.0 P N:C208 4.7 190.6 1.0 O3' N:G303 4.8 183.7 1.0 O5' N:A304 4.8 177.3 1.0 O2' N:U305 4.9 179.0 1.0

Magnesium binding site 2 out of 3 in the Cryo-Em Structure of Tetrahymena Ribozyme Conformation 2 Undergoing the First-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 First-Step Self-Splicing within 5.0Å range: probe atom residue distance (Å) B Occ N:Mg503 b:30.0 occ:1.00 OP2 N:C262 1.9 208.5 1.0 OP1 N:A207 2.0 195.4 1.0 P N:C262 2.9 208.5 1.0 O5' N:C262 3.2 208.5 1.0 P N:A207 3.3 195.4 1.0 OP1 N:C262 3.6 208.5 1.0 C5' N:A207 3.6 195.4 1.0 O5' N:A207 3.6 195.4 1.0 O3' N:A206 4.1 193.6 1.0 O3' N:A261 4.3 191.5 1.0 O2 N:U305 4.3 179.0 1.0 C5' N:C262 4.5 208.5 1.0 OP2 N:A207 4.5 195.4 1.0 C3' N:A261 4.7 191.5 1.0 OP2 N:C208 4.8 190.6 1.0 OP2 N:A263 4.8 202.1 1.0

Magnesium binding site 3 out of 3 in the Cryo-Em Structure of Tetrahymena Ribozyme Conformation 2 Undergoing the First-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 First-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 2.5 180.9 1.0 OP2 N:U307 3.3 179.3 1.0 O1G N:GTP501 3.7 216.5 1.0 N7 N:GTP501 3.9 216.5 1.0 P N:A308 4.0 180.9 1.0 O3' N:A306 4.0 185.4 1.0 C8 N:GTP501 4.1 216.5 1.0 P N:U307 4.3 179.3 1.0 O2' N:A306 4.5 185.4 1.0 O5' N:A308 4.6 180.9 1.0 OP1 N:A308 4.8 180.9 1.0 C5 N:GTP501 4.9 216.5 1.0 PG N:GTP501 4.9 216.5 1.0 O3' N:U307 4.9 179.3 1.0 C3' N:U307 4.9 179.3 1.0 N7 N:G309 4.9 187.6 1.0 N7 N:A308 4.9 180.9 1.0 O5' N:U307 5.0 179.3 1.0

X.Zhang, S.Li, P.Greg, Z.P.Michael, K.Zhang. Snapshots of the First-Step Self-Splicing of Tetrahymena Ribozyme Revealed By Cryo-Em To Be Published.