Magnesium in PDB 7ez2: Holo L-16 Scai Tetrahymena Ribozyme

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>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 31;

Binding sites:

The binding sites of Magnesium atom in the Holo L-16 Scai Tetrahymena Ribozyme (pdb code 7ez2). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 31 binding sites of Magnesium where determined in the Holo L-16 Scai Tetrahymena Ribozyme, PDB code: 7ez2:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 31 in the Holo L-16 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 Holo L-16 Scai Tetrahymena Ribozyme within 5.0Å range: probe atom residue distance (Å) B Occ N:Mg501 b:12.9 occ:0.77 N7 N:G111 3.7 19.5 1.0 O6 N:G111 4.1 19.5 1.0 N7 N:G110 4.6 19.5 1.0 C5 N:G111 4.6 19.5 1.0 O6 N:G110 4.6 19.5 1.0 C5 N:G110 4.7 19.5 1.0 C8 N:G111 4.7 19.5 1.0 C6 N:G111 4.7 19.5 1.0 C6 N:G110 4.7 19.5 1.0 N7 N:G112 4.8 19.5 1.0

Magnesium binding site 2 out of 31 in the Holo L-16 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 Holo L-16 Scai Tetrahymena Ribozyme within 5.0Å range: probe atom residue distance (Å) B Occ N:Mg502 b:12.4 occ:1.00 OP1 N:A207 2.0 19.5 1.0 OP2 N:C262 2.1 19.5 1.0 P N:C262 3.4 19.5 1.0 P N:A207 3.5 19.5 1.0 O5' N:C262 3.8 19.5 1.0 O5' N:A207 4.1 19.5 1.0 O3' N:A206 4.2 19.5 1.0 OP1 N:C262 4.2 19.5 1.0 C5' N:A207 4.3 19.5 1.0 OP2 N:A207 4.5 19.5 1.0 O2 N:U305 4.6 19.5 1.0 O3' N:A261 4.6 19.5 1.0 O2' N:U305 4.6 19.5 1.0 OP2 N:A263 4.7 19.5 1.0 C3' N:A261 4.8 19.5 1.0 MG N:MG527 5.0 30.0 1.0

Magnesium binding site 3 out of 31 in the Holo L-16 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 Holo L-16 Scai Tetrahymena Ribozyme within 5.0Å range: probe atom residue distance (Å) B Occ N:Mg503 b:15.1 occ:0.87 O6 N:G116 3.6 19.5 1.0 O4 N:U205 4.1 19.5 1.0 O6 N:G117 4.1 22.8 1.0 N7 N:G116 4.2 19.5 1.0 C6 N:G116 4.5 19.5 1.0 N7 N:A115 4.5 19.5 1.0 N4 N:C204 4.5 19.5 1.0 OP2 N:A115 4.7 19.5 1.0 C5 N:G116 4.7 19.5 1.0 OP2 N:A114 4.8 19.5 1.0

Magnesium binding site 4 out of 31 in the Holo L-16 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 Holo L-16 Scai Tetrahymena Ribozyme within 5.0Å range: probe atom residue distance (Å) B Occ N:Mg504 b:11.4 occ:0.78 OP2 N:A187 1.8 8.8 1.0 OP1 N:A184 1.9 19.5 1.0 OP1 N:A186 2.2 13.7 1.0 OP2 N:G188 2.3 19.5 1.0 P N:A187 3.2 8.8 1.0 P N:A184 3.3 19.5 1.0 P N:G188 3.5 19.5 1.0 P N:A186 3.5 13.7 1.0 OP1 N:A187 3.8 8.8 1.0 OP1 N:G188 3.9 19.5 1.0 O5' N:A187 3.9 8.8 1.0 O3' N:A183 4.0 19.5 1.0 OP2 N:A186 4.0 13.7 1.0 OP2 N:A184 4.2 19.5 1.0 C5' N:A187 4.2 8.8 1.0 O5' N:A184 4.3 19.5 1.0 O5' N:A186 4.3 13.7 1.0 O3' N:A186 4.3 13.7 1.0 O3' N:A187 4.3 8.8 1.0 C3' N:A186 4.5 13.7 1.0 C5' N:A186 4.6 13.7 1.0 C5' N:A184 4.7 19.5 1.0 O3' N:U185 4.7 19.5 1.0 O5' N:G188 4.7 19.5 1.0 OP1 N:A183 4.8 19.5 1.0 C4' N:A187 4.9 8.8 1.0 C4' N:U185 5.0 19.5 1.0

Magnesium binding site 5 out of 31 in the Holo L-16 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 Holo L-16 Scai Tetrahymena Ribozyme within 5.0Å range: probe atom residue distance (Å) B Occ N:Mg505 b:9.1 occ:0.85 OP2 N:A184 2.1 19.5 1.0 OP1 N:A183 2.3 19.5 1.0 OP2 N:A186 2.5 13.7 1.0 P N:A184 3.6 19.5 1.0 P N:A183 3.6 19.5 1.0 P N:A186 4.0 13.7 1.0 OP2 N:A183 4.2 19.5 1.0 OP1 N:A184 4.3 19.5 1.0 O5' N:A183 4.4 19.5 1.0 C3' N:A183 4.4 19.5 1.0 N7 N:A184 4.4 19.5 1.0 O5' N:A184 4.4 19.5 1.0 O3' N:A183 4.5 19.5 1.0 N7 N:A186 4.5 13.7 1.0 C8 N:A186 4.6 13.7 1.0 O5' N:A186 4.7 13.7 1.0 C8 N:A184 4.7 19.5 1.0 O3' N:U182 4.8 19.5 1.0 OP1 N:A186 4.8 13.7 1.0 O3' N:U185 4.9 19.5 1.0

Magnesium binding site 6 out of 31 in the Holo L-16 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 Holo L-16 Scai Tetrahymena Ribozyme within 5.0Å range: probe atom residue distance (Å) B Occ N:Mg506 b:6.5 occ:0.81 O6 N:G188 2.0 19.5 1.0 C6 N:G188 3.2 19.5 1.0 OP1 N:U168 4.0 19.5 1.0 OP2 N:U168 4.0 19.5 1.0 N1 N:G188 4.1 19.5 1.0 C5 N:G188 4.1 19.5 1.0 N7 N:G188 4.4 19.5 1.0 OP1 N:C165 4.4 19.5 1.0 P N:U168 4.5 19.5 1.0 OP1 N:C166 4.6 19.5 1.0 OP2 N:C166 4.7 19.5 1.0 N7 N:A183 4.7 19.5 1.0 OP2 N:A183 4.7 19.5 1.0 C5 N:U168 4.8 19.5 1.0 OP1 N:U182 4.9 19.5 1.0 C8 N:A183 4.9 19.5 1.0

Magnesium binding site 7 out of 31 in the Holo L-16 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 Holo L-16 Scai Tetrahymena Ribozyme within 5.0Å range: probe atom residue distance (Å) B Occ N:Mg507 b:12.7 occ:0.84 O6 N:G164 2.5 19.5 1.0 N7 N:G163 3.1 17.9 1.0 C6 N:G164 3.5 19.5 1.0 C8 N:G163 3.8 17.9 1.0 C5 N:G163 3.9 17.9 1.0 N7 N:G164 4.0 19.5 1.0 O6 N:G163 4.1 17.9 1.0 C5 N:G164 4.1 19.5 1.0 OP2 N:G163 4.2 17.9 1.0 C6 N:G163 4.3 17.9 1.0 N6 N:A178 4.4 32.4 1.0 N7 N:A178 4.5 32.4 1.0 OP2 N:U162 4.6 29.3 1.0 N1 N:G164 4.7 19.5 1.0 O2' N:U177 4.8 24.6 1.0 N9 N:G163 4.9 17.9 1.0 C4 N:G163 5.0 17.9 1.0

Magnesium binding site 8 out of 31 in the Holo L-16 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 Holo L-16 Scai Tetrahymena Ribozyme within 5.0Å range: probe atom residue distance (Å) B Occ N:Mg508 b:16.8 occ:0.78 O6 N:G160 4.2 42.6 1.0 N7 N:G160 4.5 42.6 1.0 N6 N:A161 4.8 31.0 1.0 N7 N:A159 4.9 55.5 1.0 C6 N:G160 5.0 42.6 1.0

Magnesium binding site 9 out of 31 in the Holo L-16 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 Holo L-16 Scai Tetrahymena Ribozyme within 5.0Å range: probe atom residue distance (Å) B Occ N:Mg509 b:19.4 occ:0.80 N7 N:G148 3.0 51.5 1.0 C8 N:G148 3.9 51.5 1.0 C5 N:G148 3.9 51.5 1.0 O6 N:G148 4.0 51.5 1.0 C6 N:G148 4.3 51.5 1.0 N7 N:G147 4.7 58.3 1.0 N7 N:G149 4.7 43.8 1.0 O6 N:G150 4.7 38.3 1.0 O6 N:G149 4.8 43.8 1.0 C5 N:G147 4.9 58.3 1.0 OP2 N:G148 4.9 51.5 1.0 O6 N:G147 4.9 58.3 1.0 C6 N:G147 5.0 58.3 1.0

Magnesium binding site 10 out of 31 in the Holo L-16 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 Holo L-16 Scai Tetrahymena Ribozyme within 5.0Å range: probe atom residue distance (Å) B Occ N:Mg510 b:25.7 occ:0.87 OP2 N:G150 2.3 38.3 1.0 P N:G150 3.5 38.3 1.0 O5' N:G150 3.7 38.3 1.0 OP2 N:A151 4.2 33.3 1.0 OP1 N:G150 4.3 38.3 1.0 C8 N:G150 4.4 38.3 1.0 N7 N:G150 4.4 38.3 1.0 O3' N:G149 4.8 43.8 1.0 OP2 N:G149 4.8 43.8 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