Magnesium in PDB 7r6m: Post-2S Intermediate of the Tetrahymena Group I Intron, Symmetry- Expanded Monomer From A Synthetic Dimeric Construct

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>>> Page 1 <<< Page 2, Binding sites: 11 - 13;

Binding sites:

The binding sites of Magnesium atom in the Post-2S Intermediate of the Tetrahymena Group I Intron, Symmetry- Expanded Monomer From A Synthetic Dimeric Construct (pdb code 7r6m). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 13 binding sites of Magnesium where determined in the Post-2S Intermediate of the Tetrahymena Group I Intron, Symmetry- Expanded Monomer From A Synthetic Dimeric Construct, PDB code: 7r6m:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 13 in the Post-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 Post-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:Mg501 b:34.9 occ:1.00 OP2 A:G160 4.2 78.4 1.0 O4 A:U162 4.4 66.1 1.0 OP1 A:A139 4.6 55.8 1.0 OP2 A:A161 4.8 73.1 1.0

Magnesium binding site 2 out of 13 in the Post-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 Post-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:Mg502 b:56.6 occ:1.00 O6 A:G164 2.0 56.8 1.0 C6 A:G164 3.2 56.8 1.0 N7 A:G163 3.5 61.3 1.0 OP2 A:G163 3.7 61.3 1.0 OP2 A:U162 3.9 66.1 1.0 C8 A:G163 4.1 61.3 1.0 N1 A:G164 4.1 56.8 1.0 O5' A:U162 4.2 66.1 1.0 O2' A:U177 4.2 65.0 1.0 C5 A:G164 4.2 56.8 1.0 N7 A:G164 4.5 56.8 1.0 C5 A:G163 4.6 61.3 1.0 P A:U162 4.6 66.1 1.0 N7 A:A178 4.6 63.3 1.0 C6 A:U162 4.8 66.1 1.0 C5 A:U162 4.8 66.1 1.0 O6 A:G163 4.9 61.3 1.0 C3' A:U162 4.9 66.1 1.0 P A:G163 5.0 61.3 1.0

Magnesium binding site 3 out of 13 in the Post-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 Post-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:Mg503 b:81.8 occ:1.00 OP1 A:U273 2.0 56.6 1.0 OP1 A:A256 2.5 57.8 1.0 OP2 A:C274 3.4 56.2 1.0 P A:U273 3.5 56.6 1.0 C5' A:U273 4.0 56.6 1.0 P A:A256 4.0 57.8 1.0 O5' A:U273 4.0 56.6 1.0 OP2 A:U273 4.4 56.6 1.0 O3' A:G272 4.5 58.1 1.0 P A:C274 4.6 56.2 1.0 O3' A:C255 4.7 52.9 1.0 OP2 A:A256 4.7 57.8 1.0 C8 A:A256 4.8 57.8 1.0 N7 A:A256 4.8 57.8 1.0 OP1 A:C274 4.9 56.2 1.0 O5' A:A256 4.9 57.8 1.0

Magnesium binding site 4 out of 13 in the Post-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 Post-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:Mg504 b:81.8 occ:1.00 OP1 A:U258 2.0 44.8 1.0 P A:U258 3.4 44.8 1.0 O3' A:G257 3.9 46.4 1.0 C5' A:U258 4.0 44.8 1.0 O5' A:U258 4.2 44.8 1.0 N3 A:A304 4.2 71.8 1.0 O4' A:A306 4.5 62.4 1.0 OP2 A:A261 4.5 65.4 1.0 OP2 A:U258 4.5 44.8 1.0 OP2 A:U259 4.6 46.4 1.0 C8 A:A306 4.7 62.4 1.0 C2 A:A304 4.8 71.8 1.0 N7 A:A306 4.9 62.4 1.0 N9 A:A306 4.9 62.4 1.0 C1' A:A304 5.0 71.8 1.0

Magnesium binding site 5 out of 13 in the Post-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 Post-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:Mg505 b:33.0 occ:1.00 OP1 A:U259 2.0 46.4 1.0 P A:U259 3.5 46.4 1.0 OP1 A:A261 3.8 65.4 1.0 O2' A:U106 3.9 44.5 1.0 O3' A:U258 4.0 44.8 1.0 OP2 A:A265 4.1 73.3 1.0 N7 A:A261 4.2 65.4 1.0 N6 A:A306 4.3 62.4 1.0 OP2 A:U259 4.4 46.4 1.0 O5' A:U259 4.4 46.4 1.0 C5' A:U259 4.4 46.4 1.0 O2 A:U106 4.5 44.5 1.0 C2' A:U106 4.6 44.5 1.0 N7 A:A306 4.6 62.4 1.0 C8 A:A261 4.8 65.4 1.0 P A:A265 4.9 73.3 1.0 OP1 A:A265 4.9 73.3 1.0 C5' A:G264 4.9 70.8 1.0

Magnesium binding site 6 out of 13 in the Post-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 Post-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:Mg506 b:58.1 occ:1.00 OP1 A:U305 2.1 62.9 1.0 P A:U305 3.6 62.9 1.0 OP1 A:G303 3.9 85.0 1.0 C3' A:A304 4.3 71.8 1.0 OP2 A:U305 4.3 62.9 1.0 O5' A:G303 4.4 85.0 1.0 O5' A:U305 4.5 62.9 1.0 O3' A:A304 4.5 71.8 1.0 C5' A:G303 4.6 85.0 1.0 P A:G303 4.7 85.0 1.0 O2' A:A304 4.7 71.8 1.0 C5' A:U305 4.7 62.9 1.0 C2' A:A304 4.9 71.8 1.0 N3 A:A256 4.9 57.8 1.0 C3' A:G303 5.0 85.0 1.0 O5' A:A304 5.0 71.8 1.0

Magnesium binding site 7 out of 13 in the Post-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 Post-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:Mg507 b:55.2 occ:1.00 O6 A:G276 3.4 65.3 1.0 O4 A:U300 3.9 75.5 1.0 N7 A:G276 3.9 65.3 1.0 O6 A:G275 4.1 59.5 1.0 C6 A:G276 4.2 65.3 1.0 N7 A:G275 4.3 59.5 1.0 C5 A:G276 4.4 65.3 1.0 C6 A:G275 4.5 59.5 1.0 C5 A:G275 4.6 59.5 1.0 C4 A:U300 4.8 75.5 1.0

Magnesium binding site 8 out of 13 in the Post-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 Post-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:Mg508 b:77.8 occ:1.00 O4 A:U43 3.4 82.9 1.0 N7 A:A42 3.5 97.8 1.0 C8 A:A42 3.5 97.8 1.0 C5 A:A42 3.7 97.8 1.0 N9 A:A42 3.7 97.8 1.0 C4 A:A42 3.8 97.8 1.0 C4 A:U43 4.2 82.9 1.0 C5 A:U43 4.2 82.9 1.0 C6 A:A42 4.4 97.8 1.0 N1 A:A171 4.5 69.3 1.0 C1' A:A42 4.5 97.8 1.0 N3 A:A42 4.6 97.8 1.0 O6 A:G44 4.6 79.2 1.0 C2' A:A42 4.6 97.8 1.0 N6 A:A171 4.8 69.3 1.0 N6 A:A42 4.9 97.8 1.0 N1 A:A42 5.0 97.8 1.0

Magnesium binding site 9 out of 13 in the Post-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 Post-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:Mg509 b:40.6 occ:1.00 O6 A:G188 2.0 55.4 1.0 C6 A:G188 3.1 55.4 1.0 OP2 A:U168 3.4 61.7 1.0 OP1 A:C165 3.7 57.9 1.0 N7 A:A183 3.8 53.9 1.0 OP2 A:A183 3.8 53.9 1.0 N1 A:G188 3.9 55.4 1.0 C8 A:A183 4.1 53.9 1.0 C5 A:G188 4.2 55.4 1.0 O2 A:U168 4.3 61.7 1.0 OP2 A:C166 4.3 61.9 1.0 P A:U168 4.5 61.7 1.0 N7 A:G188 4.5 55.4 1.0 C5 A:A183 4.6 53.9 1.0 C5' A:C165 4.6 57.9 1.0 OP1 A:U168 4.7 61.7 1.0 OP1 A:U182 4.7 55.1 1.0 P A:C165 4.9 57.9 1.0 O5' A:C165 4.9 57.9 1.0 N3 A:U168 5.0 61.7 1.0

Magnesium binding site 10 out of 13 in the Post-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 Post-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:Mg510 b:28.5 occ:1.00 OP2 A:U253 3.5 57.0 1.0 OP2 A:C216 3.9 46.4 1.0 P A:U253 4.2 57.0 1.0 O5' A:U253 4.2 57.0 1.0 OP1 A:U253 4.4 57.0 1.0 OP2 A:G254 4.6 52.0 1.0 OP2 A:C217 4.7 47.7 1.0 N7 A:G254 4.7 52.0 1.0 P A:C216 5.0 46.4 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