Magnesium in PDB 7ych: Cryo-Em Structure of Tetrahymena Ribozyme Conformation 3 Undergoing the First-Step Self-Splicing

The binding sites of Magnesium atom in the Cryo-Em Structure of Tetrahymena Ribozyme Conformation 3 Undergoing the First-Step Self-Splicing (pdb code 7ych). 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 3 Undergoing the First-Step Self-Splicing, PDB code: 7ych:
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 3 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 3 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 1.4 152.0 1.0 OP1 N:A304 2.0 144.0 1.0 OP1 N:C208 2.4 155.0 1.0 O3' B:U6 2.6 172.1 1.0 P N:A306 2.9 152.0 1.0 P B:A7 3.2 209.0 1.0 P N:A304 3.3 144.0 1.0 O5' N:A306 3.6 152.0 1.0 OP1 N:U307 3.6 148.4 1.0 OP2 N:A306 3.7 152.0 1.0 P N:C208 3.7 155.0 1.0 C3' B:U6 3.8 172.1 1.0 O3' N:U305 3.9 145.5 1.0 C4' B:U6 3.9 172.1 1.0 O5' N:A304 4.0 144.0 1.0 OP2 N:A304 4.0 144.0 1.0 C5' B:U6 4.2 172.1 1.0 OP2 B:A7 4.2 209.0 1.0 C5' N:A304 4.2 144.0 1.0 O3' N:A207 4.4 161.1 1.0 C3' N:U305 4.4 145.5 1.0 O5' B:A7 4.4 209.0 1.0 O2' N:U305 4.4 145.5 1.0 OP2 N:C208 4.5 155.0 1.0 O3' N:G303 4.5 145.8 1.0 O2' B:U6 4.5 172.1 1.0 O2' N:GTP501 4.6 187.3 1.0 O3' N:GTP501 4.7 187.3 1.0 C2' B:U6 4.8 172.1 1.0 O5' N:C208 4.8 155.0 1.0 C2' N:U305 5.0 145.5 1.0 C5' N:A306 5.0 152.0 1.0

Magnesium binding site 2 out of 3 in the Cryo-Em Structure of Tetrahymena Ribozyme Conformation 3 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 3 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 1.5 173.2 1.0 OP1 N:A207 1.8 161.1 1.0 P N:C262 2.5 173.2 1.0 O5' N:C262 2.9 173.2 1.0 P N:A207 3.2 161.1 1.0 OP1 N:C262 3.2 173.2 1.0 O3' N:A261 3.8 155.8 1.0 O5' N:A207 3.9 161.1 1.0 O3' N:A206 3.9 155.2 1.0 C5' N:A207 4.1 161.1 1.0 C5' N:C262 4.2 173.2 1.0 C3' N:A261 4.2 155.8 1.0 OP2 N:A207 4.3 161.1 1.0 O2 N:U305 4.4 145.5 1.0 OP2 N:A263 4.7 163.3 1.0 C4' N:A261 4.9 155.8 1.0 C3' N:A206 4.9 155.2 1.0 C5' N:A206 5.0 155.2 1.0

Magnesium binding site 3 out of 3 in the Cryo-Em Structure of Tetrahymena Ribozyme Conformation 3 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 3 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 2.5 151.2 1.0 OP2 N:U307 2.6 148.4 1.0 N7 N:GTP501 3.2 187.3 1.0 O3' N:A306 3.4 152.0 1.0 P N:U307 3.6 148.4 1.0 C8 N:GTP501 3.8 187.3 1.0 P N:A308 4.0 151.2 1.0 O2' N:A306 4.1 152.0 1.0 O5' N:U307 4.1 148.4 1.0 C5 N:GTP501 4.2 187.3 1.0 O6 N:GTP501 4.4 187.3 1.0 C3' N:U307 4.5 148.4 1.0 N7 N:A308 4.5 151.2 1.0 C3' N:A306 4.6 152.0 1.0 O5' N:A308 4.7 151.2 1.0 C6 N:GTP501 4.7 187.3 1.0 O3' N:U307 4.7 148.4 1.0 C2' N:A306 4.9 152.0 1.0 N9 N:GTP501 4.9 187.3 1.0 OP1 N:U307 4.9 148.4 1.0 N7 N:G309 4.9 156.1 1.0 C8 N:A308 4.9 151.2 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.