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

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 40; Page 5, Binding sites: 41 - 50; Page 6, Binding sites: 51 - 54;

Binding sites:

The binding sites of Magnesium atom in the Cryo-Em Structure of Tetrahymena Ribozyme Conformation 3 Undergoing the Second-Step Self-Splicing (pdb code 7ygb). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 54 binding sites of Magnesium where determined in the Cryo-Em Structure of Tetrahymena Ribozyme Conformation 3 Undergoing the Second-Step Self-Splicing, PDB code: 7ygb:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 54 in the Cryo-Em Structure of Tetrahymena Ribozyme Conformation 3 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 3 Undergoing the Second-Step Self-Splicing within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg101 b:19.1 occ:1.00 OP1 N:A304 2.1 18.9 1.0 O3' B:U6 2.1 27.5 1.0 OP1 N:A306 2.3 18.4 1.0 OP1 N:C208 2.5 22.5 1.0 P B:SSU7 2.7 38.2 1.0 OP2 B:SSU7 2.9 38.2 1.0 S1P B:SSU7 2.9 38.2 1.0 C3' B:U6 3.3 27.5 1.0 C4' B:U6 3.5 27.5 1.0 P N:A304 3.5 18.9 1.0 OP1 N:U307 3.6 17.9 1.0 C5' B:U6 3.6 27.5 1.0 P N:A306 3.6 18.4 1.0 P N:C208 3.9 22.5 1.0 OP2 N:A304 4.1 18.9 1.0 O5' B:SSU7 4.2 38.2 1.0 OP2 N:A306 4.2 18.4 1.0 O5' N:A306 4.3 18.4 1.0 O2' A:G3 4.3 35.1 1.0 O3' N:A207 4.3 25.5 1.0 O5' N:A304 4.4 18.9 1.0 O3' N:G303 4.5 19.1 1.0 O2' B:U6 4.5 27.5 1.0 C2' B:U6 4.5 27.5 1.0 O3' A:G3 4.5 35.1 1.0 O5' B:U6 4.5 27.5 1.0 C5' N:A304 4.7 18.9 1.0 OP2 N:C208 4.8 22.5 1.0 C3' A:G3 4.8 35.1 1.0 O3' N:U305 4.8 21.0 1.0 O5' N:C208 4.9 22.5 1.0 O4' B:U6 4.9 27.5 1.0 P N:U307 5.0 17.9 1.0

Magnesium binding site 2 out of 54 in the Cryo-Em Structure of Tetrahymena Ribozyme Conformation 3 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 3 Undergoing the Second-Step Self-Splicing within 5.0Å range: probe atom residue distance (Å) B Occ N:Mg501 b:25.1 occ:1.00 N7 N:G111 3.9 18.8 1.0 O6 N:G111 4.0 18.8 1.0 N7 N:G112 4.3 22.8 1.0 O6 N:G112 4.3 22.8 1.0 O6 N:G110 4.6 18.3 1.0 C5 N:G111 4.6 18.8 1.0 C6 N:G111 4.6 18.8 1.0 N7 N:G110 4.6 18.3 1.0 C6 N:G110 4.7 18.3 1.0 C5 N:G110 4.8 18.3 1.0 C8 N:G111 4.9 18.8 1.0

Magnesium binding site 3 out of 54 in the Cryo-Em Structure of Tetrahymena Ribozyme Conformation 3 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 3 Undergoing the Second-Step Self-Splicing within 5.0Å range: probe atom residue distance (Å) B Occ N:Mg502 b:31.4 occ:1.00 OP2 N:C262 2.1 33.0 1.0 OP1 N:A207 2.2 25.5 1.0 P N:C262 3.4 33.0 1.0 P N:A207 3.6 25.5 1.0 O5' N:C262 3.7 33.0 1.0 O2 N:U305 4.1 21.0 1.0 OP2 N:A207 4.2 25.5 1.0 O3' N:A206 4.3 25.2 1.0 OP1 N:C262 4.4 33.0 1.0 O3' N:A261 4.4 20.6 1.0 C3' N:A261 4.4 20.6 1.0 OP2 N:A263 4.4 28.5 1.0 O5' N:A207 4.7 25.5 1.0 OP1 N:A206 4.8 25.2 1.0 O5' N:A206 4.9 25.2 1.0

Magnesium binding site 4 out of 54 in the Cryo-Em Structure of Tetrahymena Ribozyme Conformation 3 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 3 Undergoing the Second-Step Self-Splicing within 5.0Å range: probe atom residue distance (Å) B Occ N:Mg503 b:34.2 occ:1.00 O6 N:G116 3.7 31.7 1.0 O6 N:G117 4.1 32.4 1.0 N4 N:C204 4.1 30.9 1.0 O4 N:U205 4.3 28.1 1.0 OP2 N:A114 4.4 27.1 1.0 N7 N:G116 4.5 31.7 1.0 OP2 N:A115 4.5 30.0 1.0 C6 N:G116 4.7 31.7 1.0 N7 N:A115 4.9 30.0 1.0 C5 N:G116 5.0 31.7 1.0

Magnesium binding site 5 out of 54 in the Cryo-Em Structure of Tetrahymena Ribozyme Conformation 3 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 3 Undergoing the Second-Step Self-Splicing within 5.0Å range: probe atom residue distance (Å) B Occ N:Mg504 b:16.4 occ:1.00 OP2 N:A187 2.1 23.0 1.0 OP1 N:A184 2.1 16.1 1.0 OP2 N:G188 2.4 20.7 1.0 OP1 N:A186 2.4 18.8 1.0 C5' N:A187 3.4 23.0 1.0 P N:A187 3.4 23.0 1.0 P N:A184 3.6 16.1 1.0 P N:A186 3.7 18.8 1.0 O5' N:A187 3.8 23.0 1.0 P N:G188 3.8 20.7 1.0 OP2 N:A186 4.1 18.8 1.0 C4' N:A187 4.2 23.0 1.0 OP1 N:A187 4.3 23.0 1.0 O5' N:A184 4.4 16.1 1.0 O3' N:A183 4.4 16.7 1.0 O5' N:A186 4.4 18.8 1.0 OP1 N:A183 4.4 16.7 1.0 O3' N:A187 4.5 23.0 1.0 O3' N:A186 4.5 18.8 1.0 OP2 N:A184 4.5 16.1 1.0 C3' N:A186 4.5 18.8 1.0 O5' N:G188 4.6 20.7 1.0 C5' N:A186 4.6 18.8 1.0 OP1 N:G188 4.8 20.7 1.0 C5' N:A183 4.8 16.7 1.0 O3' N:U185 4.8 23.7 1.0 C3' N:A187 4.9 23.0 1.0 C5' N:A184 4.9 16.1 1.0

Magnesium binding site 6 out of 54 in the Cryo-Em Structure of Tetrahymena Ribozyme Conformation 3 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 3 Undergoing the Second-Step Self-Splicing within 5.0Å range: probe atom residue distance (Å) B Occ N:Mg505 b:14.1 occ:1.00 OP1 N:A183 2.3 16.7 1.0 OP2 N:A184 2.3 16.1 1.0 OP2 N:A186 2.4 18.8 1.0 P N:A183 3.4 16.7 1.0 OP2 N:A183 3.7 16.7 1.0 P N:A184 3.7 16.1 1.0 N7 N:A184 3.9 16.1 1.0 P N:A186 3.9 18.8 1.0 C8 N:A184 4.2 16.1 1.0 OP1 N:A184 4.2 16.1 1.0 O5' N:A183 4.3 16.7 1.0 N7 N:A186 4.4 18.8 1.0 C3' N:A183 4.5 16.7 1.0 N3 N:A139 4.6 20.2 1.0 O3' N:U182 4.6 20.2 1.0 O3' N:A183 4.6 16.7 1.0 C8 N:A186 4.6 18.8 1.0 O3' N:U185 4.6 23.7 1.0 C2 N:A139 4.6 20.2 1.0 O5' N:A184 4.7 16.1 1.0 C3' N:U185 4.8 23.7 1.0 O5' N:A186 4.8 18.8 1.0 OP1 N:A186 4.8 18.8 1.0 C5' N:A183 5.0 16.7 1.0

Magnesium binding site 7 out of 54 in the Cryo-Em Structure of Tetrahymena Ribozyme Conformation 3 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 7 of Cryo-Em Structure of Tetrahymena Ribozyme Conformation 3 Undergoing the Second-Step Self-Splicing within 5.0Å range: probe atom residue distance (Å) B Occ N:Mg506 b:16.2 occ:1.00 O6 N:G188 3.4 20.7 1.0 N7 N:G188 3.5 20.7 1.0 OP1 N:C165 3.8 23.0 1.0 N7 N:A183 4.0 16.7 1.0 OP2 N:C166 4.0 23.6 1.0 C6 N:G188 4.0 20.7 1.0 C5 N:G188 4.1 20.7 1.0 OP1 N:U168 4.3 21.7 1.0 OP1 N:C166 4.3 23.6 1.0 C8 N:A183 4.3 16.7 1.0 OP2 N:A183 4.4 16.7 1.0 P N:C166 4.5 23.6 1.0 C8 N:G188 4.6 20.7 1.0 C5' N:C165 4.7 23.0 1.0 OP1 N:U182 4.8 20.2 1.0 O3' N:U167 4.8 24.3 1.0 P N:C165 4.8 23.0 1.0 O3' N:C165 4.9 23.0 1.0 C5' N:U182 4.9 20.2 1.0 O5' N:C165 4.9 23.0 1.0 C5 N:U168 5.0 21.7 1.0

Magnesium binding site 8 out of 54 in the Cryo-Em Structure of Tetrahymena Ribozyme Conformation 3 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 8 of Cryo-Em Structure of Tetrahymena Ribozyme Conformation 3 Undergoing the Second-Step Self-Splicing within 5.0Å range: probe atom residue distance (Å) B Occ N:Mg507 b:21.3 occ:1.00 O6 N:G164 2.1 22.4 1.0 N7 N:G163 2.7 22.5 1.0 C6 N:G164 3.1 22.4 1.0 C8 N:G163 3.3 22.5 1.0 C5 N:G163 3.5 22.5 1.0 C5 N:G164 3.8 22.4 1.0 N7 N:G164 3.9 22.4 1.0 O6 N:G163 3.9 22.5 1.0 C6 N:G163 4.0 22.5 1.0 OP2 N:G163 4.1 22.5 1.0 N1 N:G164 4.2 22.4 1.0 N9 N:G163 4.3 22.5 1.0 N6 N:A178 4.4 32.0 1.0 N7 N:A178 4.4 32.0 1.0 C4 N:G163 4.4 22.5 1.0 OP2 N:U162 4.6 27.0 1.0 O2' N:U177 4.7 31.0 1.0 O5' N:U162 4.9 27.0 1.0 C5 N:U162 4.9 27.0 1.0

Magnesium binding site 9 out of 54 in the Cryo-Em Structure of Tetrahymena Ribozyme Conformation 3 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 9 of Cryo-Em Structure of Tetrahymena Ribozyme Conformation 3 Undergoing the Second-Step Self-Splicing within 5.0Å range: probe atom residue distance (Å) B Occ N:Mg508 b:33.2 occ:1.00 OP1 N:A139 3.0 20.2 1.0 OP2 N:A139 3.5 20.2 1.0 P N:A139 3.7 20.2 1.0 O6 N:G163 3.7 22.5 1.0 O4 N:U162 3.9 27.0 1.0 O2' N:C138 4.4 24.5 1.0 C6 N:G163 4.5 22.5 1.0 O3' N:C138 4.5 24.5 1.0 N1 N:G163 4.6 22.5 1.0 C3' N:C138 4.8 24.5 1.0

Magnesium binding site 10 out of 54 in the Cryo-Em Structure of Tetrahymena Ribozyme Conformation 3 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 10 of Cryo-Em Structure of Tetrahymena Ribozyme Conformation 3 Undergoing the Second-Step Self-Splicing within 5.0Å range: probe atom residue distance (Å) B Occ N:Mg509 b:43.4 occ:1.00 O6 N:G149 3.7 37.5 1.0 O6 N:G148 3.9 39.4 1.0 O6 N:G150 4.0 36.2 1.0 N7 N:G148 4.1 39.4 1.0 C6 N:G148 4.5 39.4 1.0 C5 N:G148 4.6 39.4 1.0 C6 N:G149 4.8 37.5 1.0 N7 N:G149 4.8 37.5 1.0 O4 N:U155 4.8 33.4 1.0 C6 N:G150 5.0 36.2 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