Magnesium in PDB 7u87: Product of 13MER Primer with Activated G Monomer Diastereomer 1

The structure of Product of 13MER Primer with Activated G Monomer Diastereomer 1, PDB code: 7u87 was solved by Z.Fang, J.W.Szostak, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.68 / 1.70
Space group	P 3 2 1
Cell size a, b, c (Å), α, β, γ (°)	42.741, 42.741, 83.28, 90, 90, 120
R / Rfree (%)	18.8 / 24

The binding sites of Magnesium atom in the Product of 13MER Primer with Activated G Monomer Diastereomer 1 (pdb code 7u87). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Product of 13MER Primer with Activated G Monomer Diastereomer 1, PDB code: 7u87:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Product of 13MER Primer with Activated G Monomer Diastereomer 1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Product of 13MER Primer with Activated G Monomer Diastereomer 1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg102 b:18.9 occ:1.00 O B:HOH256 2.1 11.9 1.0 O A:HOH228 2.1 11.0 1.0 O A:HOH202 2.1 26.3 1.0 O B:HOH252 2.3 20.2 1.0 O B:HOH218 2.3 19.0 1.0 OP2 A:A5 4.0 11.1 1.0 O B:HOH212 4.1 12.1 1.0 OP1 A:LCG4 4.3 9.8 1.0 O B:HOH259 4.3 27.7 1.0 OP1 A:A5 4.3 12.2 1.0 OP2 B:U7 4.4 10.4 1.0 P A:A5 4.7 11.8 1.0 OP1 B:C6 4.7 8.5 1.0 OP2 A:LCG4 4.8 8.0 1.0 OP1 B:U7 4.9 14.1 1.0 P A:LCG4 5.0 10.1 1.0

Magnesium binding site 2 out of 3 in the Product of 13MER Primer with Activated G Monomer Diastereomer 1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Product of 13MER Primer with Activated G Monomer Diastereomer 1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg102 b:15.4 occ:1.00 O A:HOH244 2.0 17.8 1.0 O A:HOH241 2.0 17.9 1.0 O B:HOH210 2.0 15.7 1.0 O A:HOH246 2.1 14.3 1.0 O B:HOH235 2.2 15.4 1.0 OP2 B:A5 4.1 8.0 1.0 O A:HOH206 4.1 11.5 1.0 O B:HOH258 4.2 31.6 1.0 O A:HOH205 4.3 16.8 1.0 OP2 A:U7 4.3 9.4 1.0 OP1 B:A5 4.4 9.9 1.0 OP1 B:LCG4 4.4 8.8 1.0 OP1 A:C6 4.5 9.8 1.0 P B:A5 4.8 9.0 1.0 OP1 A:U7 4.9 12.8 1.0

Magnesium binding site 3 out of 3 in the Product of 13MER Primer with Activated G Monomer Diastereomer 1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Product of 13MER Primer with Activated G Monomer Diastereomer 1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg103 b:27.3 occ:1.00 O B:HOH257 1.9 32.1 1.0 O B:HOH221 2.1 16.2 1.0 O B:HOH260 2.1 26.1 1.0 O B:HOH261 2.2 24.5 1.0 O B:HOH220 2.3 15.2 1.0 O B:HOH202 2.3 19.2 1.0 O B:HOH206 3.9 27.2 1.0 O B:HOH203 4.1 26.0 1.0 O B:HOH251 4.1 21.9 1.0 N7 B:A10 4.2 9.2 1.0 O B:HOH226 4.2 17.6 1.0 O6 B:G11 4.3 8.2 1.0 O A:HOH239 4.4 17.6 1.0 N6 B:A10 4.5 8.3 1.0 N7 B:G11 4.5 7.6 1.0 C5 B:A10 5.0 8.8 1.0

L.T.Pazienza, Z.Fang, J.W.Szostak. Understanding the Metal Ion Function in the Rna Non-Enzymatic Extesion with Phosphorothioates To Be Published.