Magnesium in PDB 7r6n: Exon-Free State of the Tetrahymena Group I Intron, Symmetry-Expanded Monomer From A Synthetic Trimeric Construct

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Binding sites:

The binding sites of Magnesium atom in the Exon-Free State of the Tetrahymena Group I Intron, Symmetry-Expanded Monomer From A Synthetic Trimeric Construct (pdb code 7r6n). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 12 binding sites of Magnesium where determined in the Exon-Free State of the Tetrahymena Group I Intron, Symmetry-Expanded Monomer From A Synthetic Trimeric Construct, PDB code: 7r6n:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 12 in the Exon-Free State of the Tetrahymena Group I Intron, Symmetry-Expanded Monomer From A Synthetic Trimeric Construct


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Exon-Free State of the Tetrahymena Group I Intron, Symmetry-Expanded Monomer From A Synthetic Trimeric Construct within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg501 b:55.0 occ:1.00 O6 A:G164 2.1 73.4 1.0 C6 A:G164 3.2 73.4 1.0 N7 A:G163 3.6 77.8 1.0 C5 A:G164 4.1 73.4 1.0 N7 A:G164 4.1 73.4 1.0 N7 A:A178 4.2 75.1 1.0 O6 A:G163 4.2 77.8 1.0 N1 A:G164 4.3 73.4 1.0 C5 A:G163 4.3 77.8 1.0 OP2 A:U162 4.3 82.8 1.0 C8 A:G163 4.3 77.8 1.0 OP2 A:G163 4.4 77.8 1.0 C6 A:G163 4.6 77.8 1.0 N6 A:A178 4.7 75.1 1.0 O2' A:U177 4.7 74.0 1.0 O5' A:U162 4.8 82.8 1.0

Magnesium binding site 2 out of 12 in the Exon-Free State of the Tetrahymena Group I Intron, Symmetry-Expanded Monomer From A Synthetic Trimeric Construct


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Exon-Free State of the Tetrahymena Group I Intron, Symmetry-Expanded Monomer From A Synthetic Trimeric Construct within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:41.3 occ:1.00 OP2 A:A171 2.1 69.7 1.0 P A:A171 3.3 69.7 1.0 OP1 A:A171 3.9 69.7 1.0 O5' A:A171 3.9 69.7 1.0 O3' A:C170 4.6 68.8 1.0 C8 A:A171 4.6 69.7 1.0 OP1 A:C170 4.7 68.8 1.0 N7 A:A171 4.7 69.7 1.0 O3' A:U167 4.8 68.7 1.0 OP2 A:C170 4.9 68.8 1.0

Magnesium binding site 3 out of 12 in the Exon-Free State of the Tetrahymena Group I Intron, Symmetry-Expanded Monomer From A Synthetic Trimeric Construct


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Exon-Free State of the Tetrahymena Group I Intron, Symmetry-Expanded Monomer From A Synthetic Trimeric Construct within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg503 b:52.0 occ:1.00 O6 A:G176 3.3 75.8 1.0 O4 A:U177 4.4 74.0 1.0 C6 A:G176 4.5 75.8 1.0 N7 A:G175 4.9 76.5 1.0

Magnesium binding site 4 out of 12 in the Exon-Free State of the Tetrahymena Group I Intron, Symmetry-Expanded Monomer From A Synthetic Trimeric Construct


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Exon-Free State of the Tetrahymena Group I Intron, Symmetry-Expanded Monomer From A Synthetic Trimeric Construct within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg504 b:40.8 occ:1.00 OP1 A:A256 2.2 86.8 1.0 OP1 A:U273 2.2 56.9 1.0 P A:A256 3.5 86.8 1.0 P A:U273 3.6 56.9 1.0 O3' A:C255 3.9 63.4 1.0 C5' A:U273 4.0 56.9 1.0 O5' A:U273 4.0 56.9 1.0 O5' A:A256 4.3 86.8 1.0 O3' A:G272 4.4 61.3 1.0 O3' A:U273 4.5 56.9 1.0 OP2 A:U273 4.6 56.9 1.0 OP2 A:A256 4.7 86.8 1.0 C8 A:A256 4.9 86.8 1.0

Magnesium binding site 5 out of 12 in the Exon-Free State of the Tetrahymena Group I Intron, Symmetry-Expanded Monomer From A Synthetic Trimeric Construct


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Exon-Free State of the Tetrahymena Group I Intron, Symmetry-Expanded Monomer From A Synthetic Trimeric Construct within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg505 b:28.6 occ:1.00 OP1 A:U258 2.1 54.3 1.0 P A:U258 3.5 54.3 1.0 N3 A:A304 3.9 57.7 1.0 O3' A:G257 4.0 58.4 1.0 C5' A:U258 4.1 54.3 1.0 O5' A:U258 4.2 54.3 1.0 OP2 A:A261 4.2 60.8 1.0 C2 A:A304 4.4 57.7 1.0 O4' A:A306 4.6 57.4 1.0 OP2 A:U258 4.6 54.3 1.0 N9 A:A306 4.9 57.4 1.0 C8 A:A306 5.0 57.4 1.0

Magnesium binding site 6 out of 12 in the Exon-Free State of the Tetrahymena Group I Intron, Symmetry-Expanded Monomer From A Synthetic Trimeric Construct


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Exon-Free State of the Tetrahymena Group I Intron, Symmetry-Expanded Monomer From A Synthetic Trimeric Construct within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg506 b:37.8 occ:1.00 OP1 A:U259 2.1 55.4 1.0 OP1 A:A261 3.4 60.8 1.0 P A:U259 3.5 55.4 1.0 OP2 A:A265 4.0 64.9 1.0 N7 A:A261 4.1 60.8 1.0 O3' A:U258 4.2 54.3 1.0 N7 A:A306 4.2 57.4 1.0 O2' A:U106 4.2 54.2 1.0 OP2 A:U259 4.4 55.4 1.0 N6 A:A306 4.4 57.4 1.0 O5' A:U259 4.5 55.4 1.0 P A:A261 4.6 60.8 1.0 C5' A:G264 4.7 66.0 1.0 C8 A:A261 4.7 60.8 1.0 C5' A:U259 4.7 55.4 1.0 O2 A:U106 4.8 54.2 1.0 C5 A:A261 4.8 60.8 1.0 OP2 A:A261 5.0 60.8 1.0

Magnesium binding site 7 out of 12 in the Exon-Free State of the Tetrahymena Group I Intron, Symmetry-Expanded Monomer From A Synthetic Trimeric Construct


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Exon-Free State of the Tetrahymena Group I Intron, Symmetry-Expanded Monomer From A Synthetic Trimeric Construct within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg507 b:61.7 occ:1.00 OP1 A:A301 2.1 64.9 1.0 OP2 A:A302 2.1 64.1 1.0 P A:A302 3.4 64.1 1.0 N6 A:A256 3.4 86.8 1.0 P A:A301 3.4 64.9 1.0 N2 A:G303 3.7 61.8 1.0 N1 A:A256 3.8 86.8 1.0 OP1 A:A302 3.9 64.1 1.0 O5' A:A301 3.9 64.9 1.0 C3' A:U300 4.1 70.7 1.0 OP1 A:G272 4.1 61.3 1.0 C6 A:A256 4.1 86.8 1.0 O3' A:A301 4.1 64.9 1.0 O3' A:U300 4.2 70.7 1.0 OP1 A:U300 4.2 70.7 1.0 O3' A:U271 4.3 60.3 1.0 O5' A:A302 4.6 64.1 1.0 OP2 A:A301 4.6 64.9 1.0 O2' A:U300 4.7 70.7 1.0 C2' A:U300 4.8 70.7 1.0 C3' A:A301 4.9 64.9 1.0 C2 A:G303 4.9 61.8 1.0 C5' A:A301 4.9 64.9 1.0 P A:G272 4.9 61.3 1.0 C4' A:U271 4.9 60.3 1.0

Magnesium binding site 8 out of 12 in the Exon-Free State of the Tetrahymena Group I Intron, Symmetry-Expanded Monomer From A Synthetic Trimeric Construct


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Exon-Free State of the Tetrahymena Group I Intron, Symmetry-Expanded Monomer From A Synthetic Trimeric Construct within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg508 b:42.2 occ:1.00 OP1 A:A304 2.1 57.7 1.0 OP1 A:A306 2.6 57.4 1.0 OP1 A:C208 2.9 70.2 1.0 P A:A304 3.3 57.7 1.0 OP2 A:A304 3.7 57.7 1.0 P A:C208 3.9 70.2 1.0 O3' A:G303 3.9 61.8 1.0 OP2 A:C208 3.9 70.2 1.0 P A:A306 3.9 57.4 1.0 O3' A:G414 4.5 68.8 1.0 O5' A:A306 4.5 57.4 1.0 O5' A:A304 4.6 57.7 1.0 OP2 A:A306 4.7 57.4 1.0 O3' A:A207 4.7 74.2 1.0 C5' A:A304 4.8 57.7 1.0 O2' A:G303 5.0 61.8 1.0

Magnesium binding site 9 out of 12 in the Exon-Free State of the Tetrahymena Group I Intron, Symmetry-Expanded Monomer From A Synthetic Trimeric Construct


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Exon-Free State of the Tetrahymena Group I Intron, Symmetry-Expanded Monomer From A Synthetic Trimeric Construct within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg509 b:42.2 occ:1.00 OP1 A:U305 2.0 58.5 1.0 P A:U305 3.5 58.5 1.0 OP1 A:G303 4.0 61.8 1.0 O5' A:U305 4.0 58.5 1.0 C3' A:A304 4.4 57.7 1.0 C5' A:G303 4.4 61.8 1.0 O3' A:A304 4.4 57.7 1.0 OP2 A:U305 4.4 58.5 1.0 N3 A:A256 4.5 86.8 1.0 O5' A:G303 4.5 61.8 1.0 O2' A:A304 4.6 57.7 1.0 C1' A:A256 4.7 86.8 1.0 P A:G303 4.8 61.8 1.0 O3' A:A256 4.8 86.8 1.0 C2' A:A304 4.9 57.7 1.0 MG A:MG512 5.0 47.0 1.0

Magnesium binding site 10 out of 12 in the Exon-Free State of the Tetrahymena Group I Intron, Symmetry-Expanded Monomer From A Synthetic Trimeric Construct


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Exon-Free State of the Tetrahymena Group I Intron, Symmetry-Expanded Monomer From A Synthetic Trimeric Construct within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg510 b:39.2 occ:1.00 OP2 A:U307 2.1 56.4 1.0 OP2 A:A308 2.2 58.5 1.0 P A:U307 3.3 56.4 1.0 O5' A:U307 3.5 56.4 1.0 P A:A308 3.6 58.5 1.0 OP1 A:U307 4.2 56.4 1.0 O2' A:A306 4.3 57.4 1.0 O5' A:A308 4.3 58.5 1.0 OP1 A:A308 4.3 58.5 1.0 N7 A:G414 4.4 68.8 1.0 O3' A:A306 4.5 57.4 1.0 C8 A:G414 4.6 68.8 1.0 O3' A:U307 4.6 56.4 1.0 C3' A:U307 4.7 56.4 1.0 C5' A:U307 4.8 56.4 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