Magnesium in PDB 7r6l: 5 Prime Exon-Free Pre-2S Intermediate of the Tetrahymena Group I Intron, Symmetry-Expanded Monomer From A Synthetic Dimeric Construct

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Binding sites:

The binding sites of Magnesium atom in the 5 Prime Exon-Free Pre-2S Intermediate of the Tetrahymena Group I Intron, Symmetry-Expanded Monomer From A Synthetic Dimeric Construct (pdb code 7r6l). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 20 binding sites of Magnesium where determined in the 5 Prime Exon-Free Pre-2S Intermediate of the Tetrahymena Group I Intron, Symmetry-Expanded Monomer From A Synthetic Dimeric Construct, PDB code: 7r6l:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 20 in the 5 Prime Exon-Free Pre-2S Intermediate of the Tetrahymena Group I Intron, Symmetry-Expanded Monomer From A Synthetic Dimeric Construct


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of 5 Prime Exon-Free Pre-2S Intermediate of the Tetrahymena Group I Intron, Symmetry-Expanded Monomer From A Synthetic Dimeric Construct within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg401 b:25.9 occ:1.00 O6 A:G164 2.3 20.1 1.0 N7 A:G163 2.7 23.9 1.0 C8 A:G163 3.3 23.9 1.0 C6 A:G164 3.3 20.1 1.0 OP2 A:G163 3.7 23.9 1.0 C5 A:G163 3.8 23.9 1.0 N7 A:G164 3.9 20.1 1.0 C5 A:G164 4.0 20.1 1.0 OP2 A:U162 4.2 30.6 1.0 O6 A:G163 4.4 23.9 1.0 N1 A:G164 4.4 20.1 1.0 O2' A:U177 4.4 27.4 1.0 N9 A:G163 4.5 23.9 1.0 C6 A:G163 4.5 23.9 1.0 N7 A:A178 4.6 29.0 1.0 O5' A:U162 4.6 30.6 1.0 O2 A:U177 4.6 27.4 1.0 C5 A:U162 4.7 30.6 1.0 O5' A:G163 4.7 23.9 1.0 C4 A:G163 4.8 23.9 1.0 C6 A:U162 4.8 30.6 1.0 P A:G163 4.9 23.9 1.0 P A:U162 5.0 30.6 1.0

Magnesium binding site 2 out of 20 in the 5 Prime Exon-Free Pre-2S Intermediate of the Tetrahymena Group I Intron, Symmetry-Expanded Monomer From A Synthetic Dimeric Construct


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of 5 Prime Exon-Free Pre-2S Intermediate of the Tetrahymena Group I Intron, Symmetry-Expanded Monomer From A Synthetic Dimeric Construct within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:19.8 occ:1.00 OP2 A:A171 2.2 20.7 1.0 P A:A171 3.6 20.7 1.0 O5' A:A171 4.2 20.7 1.0 OP1 A:C170 4.3 19.8 1.0 OP1 A:A171 4.4 20.7 1.0 C8 A:A171 4.4 20.7 1.0 O3' A:U167 4.5 20.4 1.0 N7 A:A171 4.6 20.7 1.0 OP2 A:C165 4.6 19.6 1.0 OP2 A:C170 4.7 19.8 1.0 O3' A:C170 4.7 19.8 1.0 OP2 A:U168 4.8 18.4 1.0 O2' A:U167 4.8 20.4 1.0 O5' A:U168 4.8 18.4 1.0 P A:C170 4.9 19.8 1.0 O2 A:U167 4.9 20.4 1.0

Magnesium binding site 3 out of 20 in the 5 Prime Exon-Free Pre-2S Intermediate of the Tetrahymena Group I Intron, Symmetry-Expanded Monomer From A Synthetic Dimeric Construct


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of 5 Prime Exon-Free Pre-2S Intermediate of the Tetrahymena Group I Intron, Symmetry-Expanded Monomer From A Synthetic Dimeric Construct within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg403 b:15.3 occ:1.00 O4 A:U177 4.1 27.4 1.0 O6 A:G176 4.2 25.7 1.0 N7 A:G176 4.5 25.7 1.0 OP2 A:G175 4.6 26.6 1.0 N7 A:G175 4.7 26.6 1.0 OP2 A:G174 4.9 27.8 1.0

Magnesium binding site 4 out of 20 in the 5 Prime Exon-Free Pre-2S Intermediate of the Tetrahymena Group I Intron, Symmetry-Expanded Monomer From A Synthetic Dimeric Construct


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of 5 Prime Exon-Free Pre-2S Intermediate of the Tetrahymena Group I Intron, Symmetry-Expanded Monomer From A Synthetic Dimeric Construct within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg404 b:19.8 occ:1.00 OP1 A:U273 2.3 19.8 1.0 OP1 A:A256 2.3 19.8 1.0 P A:U273 3.7 19.8 1.0 P A:A256 3.7 19.8 1.0 OP2 A:C274 4.0 19.8 1.0 O5' A:U273 4.3 19.8 1.0 N7 A:A256 4.3 19.8 1.0 C8 A:A256 4.4 19.8 1.0 OP2 A:A256 4.5 19.8 1.0 OP2 A:U273 4.5 19.8 1.0 O3' A:C255 4.5 11.2 1.0 C5' A:U273 4.5 19.8 1.0 O5' A:A256 4.6 19.8 1.0 O3' A:G272 4.7 12.7 1.0

Magnesium binding site 5 out of 20 in the 5 Prime Exon-Free Pre-2S Intermediate of the Tetrahymena Group I Intron, Symmetry-Expanded Monomer From A Synthetic Dimeric Construct


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of 5 Prime Exon-Free Pre-2S Intermediate of the Tetrahymena Group I Intron, Symmetry-Expanded Monomer From A Synthetic Dimeric Construct within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg405 b:19.8 occ:1.00 OP1 A:U258 2.2 9.6 1.0 P A:U258 3.7 9.6 1.0 OP2 A:A261 3.9 19.8 1.0 O4' A:A306 4.1 14.6 1.0 C8 A:A306 4.2 14.6 1.0 N3 A:A304 4.4 11.8 1.0 N7 A:A306 4.4 14.6 1.0 OP2 A:U258 4.5 9.6 1.0 O3' A:G257 4.5 19.8 1.0 N9 A:A306 4.5 14.6 1.0 O5' A:U258 4.5 9.6 1.0 C5' A:U258 4.6 9.6 1.0 C5 A:A306 4.9 14.6 1.0 O3' A:A304 4.9 11.8 1.0 C1' A:A306 4.9 14.6 1.0 C5' A:A306 4.9 14.6 1.0 C4 A:A306 5.0 14.6 1.0 C2 A:A304 5.0 11.8 1.0 C1' A:A304 5.0 11.8 1.0

Magnesium binding site 6 out of 20 in the 5 Prime Exon-Free Pre-2S Intermediate of the Tetrahymena Group I Intron, Symmetry-Expanded Monomer From A Synthetic Dimeric Construct


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of 5 Prime Exon-Free Pre-2S Intermediate of the Tetrahymena Group I Intron, Symmetry-Expanded Monomer From A Synthetic Dimeric Construct within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg406 b:19.8 occ:1.00 OP1 A:U259 2.1 9.1 1.0 P A:U259 3.4 9.1 1.0 O5' A:U259 3.7 9.1 1.0 OP2 A:A265 4.0 23.2 1.0 N7 A:A261 4.0 19.8 1.0 OP1 A:A261 4.1 19.8 1.0 N7 A:A306 4.4 14.6 1.0 C8 A:A261 4.4 19.8 1.0 OP2 A:A261 4.4 19.8 1.0 O3' A:U258 4.4 9.6 1.0 OP2 A:U259 4.4 9.1 1.0 C5' A:U259 4.5 9.1 1.0 O2' A:U106 4.7 2.0 1.0 P A:A261 4.8 19.8 1.0 N6 A:A306 4.8 14.6 1.0 O2 A:U106 4.8 2.0 1.0 C5' A:G264 4.9 27.6 1.0 P A:A265 4.9 23.2 1.0

Magnesium binding site 7 out of 20 in the 5 Prime Exon-Free Pre-2S Intermediate of the Tetrahymena Group I Intron, Symmetry-Expanded Monomer From A Synthetic Dimeric Construct


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of 5 Prime Exon-Free Pre-2S Intermediate of the Tetrahymena Group I Intron, Symmetry-Expanded Monomer From A Synthetic Dimeric Construct within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg407 b:19.8 occ:1.00 OP1 A:A301 2.3 17.7 1.0 OP2 A:A302 2.4 15.0 1.0 OP1 A:G272 3.4 12.7 1.0 P A:A301 3.6 17.7 1.0 O5' A:A301 3.7 17.7 1.0 P A:A302 3.8 15.0 1.0 C3' A:U300 4.2 16.5 1.0 N2 A:G303 4.2 12.3 1.0 O2' A:U300 4.2 16.5 1.0 N1 A:A256 4.3 19.8 1.0 N6 A:A256 4.3 19.8 1.0 OP1 A:A302 4.3 15.0 1.0 C4' A:U271 4.3 10.5 1.0 O3' A:U300 4.3 16.5 1.0 O3' A:U271 4.5 10.5 1.0 N1 A:G303 4.5 12.3 1.0 P A:G272 4.5 12.7 1.0 C2' A:U300 4.5 16.5 1.0 O4' A:U271 4.6 10.5 1.0 OP1 A:U300 4.7 16.5 1.0 O3' A:A301 4.7 17.7 1.0 O5' A:A302 4.8 15.0 1.0 C6 A:A256 4.8 19.8 1.0 OP2 A:A301 4.8 17.7 1.0 C2 A:G303 4.9 12.3 1.0 C3' A:A301 5.0 17.7 1.0

Magnesium binding site 8 out of 20 in the 5 Prime Exon-Free Pre-2S Intermediate of the Tetrahymena Group I Intron, Symmetry-Expanded Monomer From A Synthetic Dimeric Construct


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of 5 Prime Exon-Free Pre-2S Intermediate of the Tetrahymena Group I Intron, Symmetry-Expanded Monomer From A Synthetic Dimeric Construct within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg408 b:19.8 occ:1.00 OP1 A:A306 2.0 14.6 1.0 OP1 A:A304 2.1 11.8 1.0 OP1 A:C208 2.7 21.0 1.0 P A:A306 3.5 14.6 1.0 P A:A304 3.5 11.8 1.0 P A:C208 3.7 21.0 1.0 OP2 B:DA415 4.0 71.3 1.0 OP2 A:C208 4.0 21.0 1.0 OP2 A:A304 4.1 11.8 1.0 OP2 A:A306 4.2 14.6 1.0 O3' A:A207 4.2 31.7 1.0 O5' A:A306 4.2 14.6 1.0 OP1 A:U307 4.4 14.0 1.0 O3' A:G303 4.4 12.3 1.0 O5' A:A304 4.4 11.8 1.0 O3' A:U305 4.5 13.8 1.0 C3' A:U305 4.6 13.8 1.0 C5' A:A304 4.6 11.8 1.0 O3' B:DG414 4.7 42.1 1.0 P B:DA415 4.9 71.3 1.0

Magnesium binding site 9 out of 20 in the 5 Prime Exon-Free Pre-2S Intermediate of the Tetrahymena Group I Intron, Symmetry-Expanded Monomer From A Synthetic Dimeric Construct


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of 5 Prime Exon-Free Pre-2S Intermediate of the Tetrahymena Group I Intron, Symmetry-Expanded Monomer From A Synthetic Dimeric Construct within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg409 b:19.8 occ:1.00 OP1 A:U305 2.1 13.8 1.0 P A:U305 3.4 13.8 1.0 OP2 A:U305 4.0 13.8 1.0 OP1 A:G303 4.2 12.3 1.0 O3' A:A304 4.3 11.8 1.0 C3' A:A304 4.4 11.8 1.0 O2' A:A304 4.4 11.8 1.0 O5' A:U305 4.5 13.8 1.0 N3 A:A256 4.7 19.8 1.0 O3' A:A256 4.8 19.8 1.0 OP1 A:G257 4.8 19.8 1.0 C2' A:A304 4.9 11.8 1.0 P A:G303 4.9 12.3 1.0 O5' A:G303 4.9 12.3 1.0 C5' A:U305 5.0 13.8 1.0

Magnesium binding site 10 out of 20 in the 5 Prime Exon-Free Pre-2S Intermediate of the Tetrahymena Group I Intron, Symmetry-Expanded Monomer From A Synthetic Dimeric Construct


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of 5 Prime Exon-Free Pre-2S Intermediate of the Tetrahymena Group I Intron, Symmetry-Expanded Monomer From A Synthetic Dimeric Construct within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg410 b:9.5 occ:1.00 N7 A:G276 4.0 11.2 1.0 O6 A:G276 4.1 11.2 1.0 O4 A:U300 4.3 16.5 1.0 N7 A:G275 4.6 8.0 1.0 C5 A:G276 4.8 11.2 1.0 C6 A:G276 4.8 11.2 1.0

D.Liu, F.A.Thelot, J.A.Piccirilli, M.Liao, P.Yin. Sub-3- Angstrom Cryo-Em Structure of Rna Enabled By Engineered Homomeric Self-Assembly. Nat.Methods V. 19 576 2022.
ISSN: ESSN 1548-7105
PubMed: 35501384
DOI: 10.1038/S41592-022-01455-W