Magnesium in PDB 7ygd: Cryo-Em Structure of Tetrahymena Ribozyme Conformation 6 Undergoing the Second-Step Self-Splicing

The binding sites of Magnesium atom in the Cryo-Em Structure of Tetrahymena Ribozyme Conformation 6 Undergoing the Second-Step Self-Splicing (pdb code 7ygd). 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 6 Undergoing the Second-Step Self-Splicing, PDB code: 7ygd:
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 6 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 6 Undergoing the Second-Step Self-Splicing within 5.0Å range: probe atom residue distance (Å) B Occ N:Mg501 b:124.4 occ:1.00 OP1 N:A304 2.2 123.5 1.0 OP1 N:A306 2.5 129.4 1.0 P N:A304 3.4 123.5 1.0 OP1 N:C208 3.4 132.2 1.0 O3' A:G3 3.5 141.4 1.0 OP2 N:A304 3.7 123.5 1.0 OP1 N:U307 3.7 120.1 1.0 P N:A306 3.8 129.4 1.0 O2' A:G3 4.2 141.4 1.0 OP2 N:A306 4.3 129.4 1.0 O3' N:G303 4.4 127.7 1.0 O5' N:A306 4.4 129.4 1.0 O5' N:A304 4.4 123.5 1.0 C3' A:G3 4.7 141.4 1.0 P N:C208 4.8 132.2 1.0 C5' N:A304 4.8 123.5 1.0 C2' A:G3 4.9 141.4 1.0 O3' N:U305 5.0 128.2 1.0

Magnesium binding site 2 out of 6 in the Cryo-Em Structure of Tetrahymena Ribozyme Conformation 6 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 6 Undergoing the Second-Step Self-Splicing within 5.0Å range: probe atom residue distance (Å) B Occ N:Mg502 b:109.8 occ:1.00 OP2 N:A308 2.5 117.0 1.0 OP2 N:U307 2.8 120.1 1.0 O3' N:A306 3.4 129.4 1.0 C8 A:G3 3.7 141.4 1.0 P N:U307 3.7 120.1 1.0 N7 A:G3 3.7 141.4 1.0 O2' N:A306 3.8 129.4 1.0 P N:A308 4.0 117.0 1.0 O5' N:U307 4.4 120.1 1.0 C3' N:U307 4.5 120.1 1.0 N9 A:G3 4.5 141.4 1.0 C3' N:A306 4.5 129.4 1.0 C5 A:G3 4.6 141.4 1.0 O5' N:A308 4.7 117.0 1.0 C2' N:A306 4.7 129.4 1.0 O3' N:U307 4.7 120.1 1.0 C2' A:G3 4.8 141.4 1.0 N7 N:A308 4.8 117.0 1.0 OP1 N:A308 5.0 117.0 1.0 OP1 N:U307 5.0 120.1 1.0

Magnesium binding site 3 out of 6 in the Cryo-Em Structure of Tetrahymena Ribozyme Conformation 6 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 6 Undergoing the Second-Step Self-Splicing within 5.0Å range: probe atom residue distance (Å) B Occ N:Mg503 b:118.3 occ:1.00 OP1 N:U305 2.4 128.2 1.0 OP2 N:U305 2.9 128.2 1.0 P N:U305 3.0 128.2 1.0 OP1 N:G303 3.0 127.7 1.0 O3' N:A304 3.7 123.5 1.0 O2' N:A304 4.1 123.5 1.0 C3' N:A304 4.1 123.5 1.0 P N:G303 4.4 127.7 1.0 O5' N:U305 4.4 128.2 1.0 C2' N:A304 4.7 123.5 1.0 O5' N:G303 4.9 127.7 1.0

Magnesium binding site 4 out of 6 in the Cryo-Em Structure of Tetrahymena Ribozyme Conformation 6 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 6 Undergoing the Second-Step Self-Splicing within 5.0Å range: probe atom residue distance (Å) B Occ N:Mg504 b:114.0 occ:1.00 OP2 N:U305 2.7 128.2 1.0 OP2 N:U258 2.8 107.2 1.0 OP1 N:G257 2.8 105.4 1.0 O2 N:C260 3.3 117.3 1.0 P N:U258 3.7 107.2 1.0 OP1 N:U258 3.7 107.2 1.0 P N:U305 3.8 128.2 1.0 C5' N:U305 4.0 128.2 1.0 O3' N:A304 4.0 123.5 1.0 O2' N:C260 4.2 117.3 1.0 O5' N:U305 4.2 128.2 1.0 P N:G257 4.3 105.4 1.0 C2 N:C260 4.5 117.3 1.0 O3' N:G257 4.8 105.4 1.0 O5' N:U258 4.8 107.2 1.0 MG N:MG505 4.9 91.8 1.0 C1' N:C260 4.9 117.3 1.0 O3' N:A256 5.0 105.9 1.0

Magnesium binding site 5 out of 6 in the Cryo-Em Structure of Tetrahymena Ribozyme Conformation 6 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 6 Undergoing the Second-Step Self-Splicing within 5.0Å range: probe atom residue distance (Å) B Occ N:Mg505 b:91.8 occ:1.00 OP1 N:U258 2.5 107.2 1.0 OP2 N:A261 2.9 130.7 1.0 P N:U258 4.0 107.2 1.0 O4' N:A306 4.1 129.4 1.0 OP2 N:U259 4.2 113.4 1.0 N3 N:A304 4.3 123.5 1.0 C8 N:A306 4.4 129.4 1.0 P N:A261 4.4 130.7 1.0 C5' N:U258 4.5 107.2 1.0 N9 N:A306 4.6 129.4 1.0 N7 N:A306 4.6 129.4 1.0 O5' N:U258 4.7 107.2 1.0 O3' N:G257 4.8 105.4 1.0 OP2 N:U258 4.9 107.2 1.0 C2 N:A304 4.9 123.5 1.0 MG N:MG504 4.9 114.0 1.0 C4 N:A306 4.9 129.4 1.0 C5 N:A306 5.0 129.4 1.0 C1' N:A306 5.0 129.4 1.0

Magnesium binding site 6 out of 6 in the Cryo-Em Structure of Tetrahymena Ribozyme Conformation 6 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 6 Undergoing the Second-Step Self-Splicing within 5.0Å range: probe atom residue distance (Å) B Occ N:Mg506 b:88.8 occ:1.00 OP1 N:U259 2.5 113.4 1.0 N6 N:A306 3.5 129.4 1.0 O2' N:U106 3.6 106.7 1.0 O3' N:U258 3.6 107.2 1.0 P N:U259 3.6 113.4 1.0 OP2 N:A265 3.8 125.6 1.0 N7 N:A261 4.1 130.7 1.0 N7 N:A306 4.1 129.4 1.0 C2' N:U106 4.2 106.7 1.0 O2 N:U106 4.4 106.7 1.0 C6 N:A306 4.5 129.4 1.0 OP2 N:U259 4.6 113.4 1.0 OP1 N:A261 4.6 130.7 1.0 C5 N:A306 4.7 129.4 1.0 C8 N:A261 4.7 130.7 1.0 O5' N:U259 4.7 113.4 1.0 C5' N:U259 4.8 113.4 1.0 P N:A265 4.9 125.6 1.0 C3' N:U258 4.9 107.2 1.0 C5 N:A261 5.0 130.7 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