Magnesium in PDB 7ez0: Apo L-21 Scai Tetrahymena Ribozyme

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>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 27;

Binding sites:

The binding sites of Magnesium atom in the Apo L-21 Scai Tetrahymena Ribozyme (pdb code 7ez0). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 27 binding sites of Magnesium where determined in the Apo L-21 Scai Tetrahymena Ribozyme, PDB code: 7ez0:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 27 in the Apo L-21 Scai Tetrahymena Ribozyme


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Apo L-21 Scai Tetrahymena Ribozyme within 5.0Å range: probe atom residue distance (Å) B Occ N:Mg501 b:25.1 occ:0.77 O6 N:G111 4.2 33.2 1.0 N7 N:G111 4.4 33.2 1.0 O6 N:G110 4.5 28.9 1.0 N7 N:G110 4.8 28.9 1.0 C6 N:G110 4.8 28.9 1.0 C6 N:G111 4.9 33.2 1.0 C5 N:G110 4.9 28.9 1.0

Magnesium binding site 2 out of 27 in the Apo L-21 Scai Tetrahymena Ribozyme


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Apo L-21 Scai Tetrahymena Ribozyme within 5.0Å range: probe atom residue distance (Å) B Occ N:Mg502 b:43.6 occ:1.00 OP1 N:A207 2.0 51.6 1.0 OP2 N:C262 2.5 50.8 1.0 P N:A207 3.5 51.6 1.0 P N:C262 3.7 50.8 1.0 O2 N:U305 3.9 30.9 1.0 OP1 N:C262 4.1 50.8 1.0 O2' N:U305 4.2 30.9 1.0 O3' N:A206 4.3 53.2 1.0 O5' N:A207 4.3 51.6 1.0 OP2 N:A207 4.5 51.6 1.0 C5' N:A207 4.5 51.6 1.0 O3' N:A261 4.7 37.2 1.0 C3' N:A261 4.8 37.2 1.0 O5' N:C262 4.8 50.8 1.0 C2 N:U305 4.9 30.9 1.0 OP2 N:C208 5.0 45.4 1.0 C5' N:C262 5.0 50.8 1.0

Magnesium binding site 3 out of 27 in the Apo L-21 Scai Tetrahymena Ribozyme


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Apo L-21 Scai Tetrahymena Ribozyme within 5.0Å range: probe atom residue distance (Å) B Occ N:Mg503 b:45.3 occ:0.87 OP2 N:A114 3.0 55.0 1.0 OP1 N:A114 3.8 55.0 1.0 P N:A114 3.8 55.0 1.0 O6 N:G116 4.0 59.9 1.0 OP2 N:A115 4.4 57.7 1.0 O4 N:U205 4.4 54.0 1.0 O5' N:A114 4.5 55.0 1.0 N7 N:G116 4.5 59.9 1.0 N1 N:A206 4.7 53.2 1.0 N7 N:A115 4.7 57.7 1.0 C2 N:A206 4.8 53.2 1.0 O6 N:G117 4.8 59.9 1.0 C6 N:G116 4.9 59.9 1.0

Magnesium binding site 4 out of 27 in the Apo L-21 Scai Tetrahymena Ribozyme


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Apo L-21 Scai Tetrahymena Ribozyme within 5.0Å range: probe atom residue distance (Å) B Occ N:Mg504 b:34.2 occ:0.78 OP1 N:A184 1.8 27.2 1.0 OP1 N:A186 1.8 34.3 1.0 OP2 N:A187 1.9 43.3 1.0 P N:A186 3.2 34.3 1.0 P N:A184 3.2 27.2 1.0 P N:A187 3.4 43.3 1.0 OP2 N:G188 3.5 34.8 1.0 OP2 N:A184 3.8 27.2 1.0 O5' N:A186 3.8 34.3 1.0 OP2 N:A186 3.9 34.3 1.0 C5' N:A187 4.0 43.3 1.0 O5' N:A187 4.1 43.3 1.0 O5' N:A184 4.1 27.2 1.0 C5' N:A186 4.1 34.3 1.0 C3' N:A186 4.1 34.3 1.0 O3' N:A186 4.2 34.3 1.0 O3' N:A183 4.2 28.9 1.0 O3' N:U185 4.3 32.4 1.0 OP1 N:A187 4.4 43.3 1.0 P N:G188 4.4 34.8 1.0 O3' N:A187 4.6 43.3 1.0 C4' N:A186 4.7 34.3 1.0 C5' N:A184 4.7 27.2 1.0 OP1 N:G188 4.7 34.8 1.0 OP1 N:A183 4.8 28.9 1.0 C3' N:U185 4.9 32.4 1.0 C4' N:A187 4.9 43.3 1.0 C4' N:U185 4.9 32.4 1.0

Magnesium binding site 5 out of 27 in the Apo L-21 Scai Tetrahymena Ribozyme


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Apo L-21 Scai Tetrahymena Ribozyme within 5.0Å range: probe atom residue distance (Å) B Occ N:Mg505 b:24.0 occ:0.85 OP1 N:A183 2.2 28.9 1.0 OP2 N:A184 2.2 27.2 1.0 OP2 N:A186 2.2 34.3 1.0 P N:A183 3.5 28.9 1.0 P N:A186 3.7 34.3 1.0 P N:A184 3.7 27.2 1.0 O5' N:A183 3.9 28.9 1.0 N7 N:A184 4.0 27.2 1.0 C8 N:A184 4.3 27.2 1.0 OP2 N:A183 4.3 28.9 1.0 C2 N:A139 4.4 36.4 1.0 N7 N:A186 4.4 34.3 1.0 OP1 N:A186 4.4 34.3 1.0 O5' N:A184 4.5 27.2 1.0 OP1 N:A184 4.5 27.2 1.0 O5' N:A186 4.5 34.3 1.0 C3' N:A183 4.5 28.9 1.0 C8 N:A186 4.6 34.3 1.0 N3 N:A139 4.6 36.4 1.0 O3' N:U185 4.6 32.4 1.0 O3' N:A183 4.6 28.9 1.0 O3' N:U182 4.7 34.6 1.0 C3' N:U185 4.7 32.4 1.0 C5' N:A183 4.8 28.9 1.0 N1 N:A139 5.0 36.4 1.0

Magnesium binding site 6 out of 27 in the Apo L-21 Scai Tetrahymena Ribozyme


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Apo L-21 Scai Tetrahymena Ribozyme within 5.0Å range: probe atom residue distance (Å) B Occ N:Mg506 b:53.4 occ:0.81 N7 N:G188 3.0 34.8 1.0 C8 N:G188 3.7 34.8 1.0 OP1 N:U168 3.9 34.3 1.0 N7 N:A183 4.1 28.9 1.0 C5 N:G188 4.2 34.8 1.0 C8 N:A183 4.2 28.9 1.0 OP1 N:C165 4.4 35.8 1.0 OP2 N:U168 4.4 34.3 1.0 O6 N:G188 4.5 34.8 1.0 OP2 N:A183 4.5 28.9 1.0 OP2 N:C166 4.7 37.1 1.0 OP1 N:C166 4.7 37.1 1.0 OP1 N:U182 4.7 34.6 1.0 P N:U168 4.7 34.3 1.0 C6 N:G188 4.7 34.8 1.0 O3' N:C165 4.9 35.8 1.0 C5' N:C165 4.9 35.8 1.0 N9 N:G188 4.9 34.8 1.0 P N:C166 4.9 37.1 1.0

Magnesium binding site 7 out of 27 in the Apo L-21 Scai Tetrahymena Ribozyme


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Apo L-21 Scai Tetrahymena Ribozyme within 5.0Å range: probe atom residue distance (Å) B Occ N:Mg507 b:29.6 occ:0.84 O6 N:G164 1.8 36.7 1.0 N7 N:G163 2.8 39.7 1.0 C6 N:G164 2.8 36.7 1.0 C5 N:G164 3.5 36.7 1.0 C5 N:G163 3.5 39.7 1.0 C8 N:G163 3.6 39.7 1.0 N7 N:G164 3.6 36.7 1.0 O6 N:G163 3.8 39.7 1.0 N1 N:G164 3.9 36.7 1.0 C6 N:G163 3.9 39.7 1.0 OP2 N:G163 4.0 39.7 1.0 N7 N:A178 4.5 43.9 1.0 N9 N:G163 4.6 39.7 1.0 C4 N:G163 4.6 39.7 1.0 N6 N:A178 4.7 43.9 1.0 OP2 N:U162 4.7 45.9 1.0 O2' N:U177 4.8 42.1 1.0 C4 N:G164 4.8 36.7 1.0 C8 N:G164 4.9 36.7 1.0

Magnesium binding site 8 out of 27 in the Apo L-21 Scai Tetrahymena Ribozyme


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Apo L-21 Scai Tetrahymena Ribozyme within 5.0Å range: probe atom residue distance (Å) B Occ N:Mg508 b:37.6 occ:0.78 OP1 N:A139 3.8 36.4 1.0 O4 N:U162 4.2 45.9 1.0 OP2 N:A139 4.5 36.4 1.0 O6 N:G163 4.6 39.7 1.0 P N:A139 4.6 36.4 1.0 N7 N:A161 4.9 53.1 1.0

Magnesium binding site 9 out of 27 in the Apo L-21 Scai Tetrahymena Ribozyme


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Apo L-21 Scai Tetrahymena Ribozyme within 5.0Å range: probe atom residue distance (Å) B Occ N:Mg509 b:49.2 occ:0.80 O6 N:G148 3.7 60.7 1.0 O6 N:G149 4.0 58.5 1.0 N7 N:G148 4.2 60.7 1.0 O4 N:U155 4.4 55.7 1.0 O6 N:G150 4.4 58.4 1.0 C6 N:G148 4.5 60.7 1.0 C5 N:G148 4.7 60.7 1.0 O6 N:G147 4.9 62.6 1.0 N4 N:C154 5.0 53.1 1.0

Magnesium binding site 10 out of 27 in the Apo L-21 Scai Tetrahymena Ribozyme


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Apo L-21 Scai Tetrahymena Ribozyme within 5.0Å range: probe atom residue distance (Å) B Occ N:Mg510 b:52.0 occ:0.87 OP2 N:G149 2.5 58.5 1.0 P N:G149 3.6 58.5 1.0 OP2 N:G150 3.6 58.4 1.0 O5' N:G149 3.8 58.5 1.0 N7 N:G150 3.9 58.4 1.0 OP1 N:G149 4.2 58.5 1.0 C8 N:G150 4.6 58.4 1.0 C8 N:G149 4.8 58.5 1.0 O3' N:G148 4.9 60.7 1.0 N7 N:G149 5.0 58.5 1.0

Z.Su, K.Zhang, K.Kappel, S.Li, M.Z.Palo, G.D.Pintilie, R.Rangan, B.Luo, Y.Wei, R.Das, W.Chiu. Cryo-Em Structures of Full-Length Tetrahymena Ribozyme at 3.1 Angstrom Resolution. Nature 2021.
ISSN: ESSN 1476-4687
PubMed: 34381213
DOI: 10.1038/S41586-021-03803-W