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

The binding sites of Magnesium atom in the Cryo-Em Structure of Tetrahymena Ribozyme Conformation 4 Undergoing the First-Step Self-Splicing (pdb code 7yci). 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 4 Undergoing the First-Step Self-Splicing, PDB code: 7yci:
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 4 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 4 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:A304 1.6 133.0 1.0 OP1 N:A306 1.7 137.0 1.0 OP1 N:C208 1.9 139.5 1.0 P N:A304 2.9 133.0 1.0 O3' B:U6 3.0 158.7 1.0 P N:A306 3.2 137.0 1.0 P N:C208 3.4 139.5 1.0 C4' B:U6 3.4 158.7 1.0 OP2 N:A304 3.4 133.0 1.0 O5' N:A304 3.7 133.0 1.0 C3' B:U6 3.7 158.7 1.0 O2' B:U6 3.9 158.7 1.0 O5' N:A306 3.9 137.0 1.0 C5' B:U6 4.0 158.7 1.0 O3' N:U305 4.0 132.2 1.0 O3' N:A207 4.0 143.0 1.0 O3' N:G303 4.1 139.6 1.0 C5' N:A304 4.1 133.0 1.0 O3' N:GTP501 4.1 168.0 1.0 OP1 N:U307 4.2 134.3 1.0 OP2 N:A306 4.2 137.0 1.0 OP2 N:C208 4.2 139.5 1.0 O2' N:U305 4.3 132.2 1.0 O5' N:C208 4.3 139.5 1.0 C3' N:U305 4.4 132.2 1.0 C2' B:U6 4.4 158.7 1.0 O4' B:U6 4.6 158.7 1.0 C2' N:U305 4.8 132.2 1.0 O2' N:GTP501 4.9 168.0 1.0

Magnesium binding site 2 out of 3 in the Cryo-Em Structure of Tetrahymena Ribozyme Conformation 4 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 4 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 1.5 157.5 1.0 OP1 N:A207 2.1 143.0 1.0 P N:C262 2.7 157.5 1.0 O5' N:C262 3.1 157.5 1.0 P N:A207 3.4 143.0 1.0 OP1 N:C262 3.6 157.5 1.0 O5' N:A207 3.8 143.0 1.0 O3' N:A261 3.9 141.4 1.0 O2 N:U305 4.0 132.2 1.0 C3' N:A261 4.2 141.4 1.0 OP2 N:A207 4.2 143.0 1.0 C5' N:A207 4.2 143.0 1.0 C5' N:C262 4.5 157.5 1.0 OP2 N:A263 4.5 150.6 1.0 O3' N:A206 4.6 143.9 1.0 C4' N:A261 4.9 141.4 1.0

Magnesium binding site 3 out of 3 in the Cryo-Em Structure of Tetrahymena Ribozyme Conformation 4 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 4 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 2.1 137.3 1.0 OP2 N:U307 2.9 134.3 1.0 P N:A308 3.5 137.3 1.0 N7 N:GTP501 4.0 168.0 1.0 P N:U307 4.1 134.3 1.0 O3' N:A306 4.2 137.0 1.0 O5' N:A308 4.2 137.3 1.0 O1A N:GTP501 4.2 168.0 1.0 C8 N:GTP501 4.3 168.0 1.0 OP1 N:A308 4.4 137.3 1.0 O3' N:U307 4.5 134.3 1.0 C3' N:U307 4.6 134.3 1.0 O5' N:U307 4.7 134.3 1.0 N7 N:A308 4.8 137.3 1.0 O2' N:A306 4.9 137.0 1.0 C8 N:A308 4.9 137.3 1.0 C5 N:GTP501 5.0 168.0 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.