Magnesium in PDB 7u8a: Product of 14MER Primer with Activated G Monomer Diastereomer 2

The structure of Product of 14MER Primer with Activated G Monomer Diastereomer 2, PDB code: 7u8a 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)	41.42 / 2.10
Space group	P 3 2 1
Cell size a, b, c (Å), α, β, γ (°)	42.873, 42.873, 82.763, 90, 90, 120
R / Rfree (%)	19.9 / 28.2

The binding sites of Magnesium atom in the Product of 14MER Primer with Activated G Monomer Diastereomer 2 (pdb code 7u8a). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Product of 14MER Primer with Activated G Monomer Diastereomer 2, PDB code: 7u8a:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Product of 14MER Primer with Activated G Monomer Diastereomer 2


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Product of 14MER Primer with Activated G Monomer Diastereomer 2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg102 b:33.6 occ:0.33 O3' A:G4615 2.3 29.2 1.0 O2' A:G4615 2.4 21.1 1.0 C3' A:G4615 3.2 26.4 1.0 C2' A:G4615 3.3 25.6 1.0 C4' A:G4615 3.5 27.4 1.0 C5' A:G4615 4.3 30.3 1.0 C1' A:G4615 4.6 23.9 1.0 O4' A:G4615 4.7 25.3 1.0

Magnesium binding site 2 out of 5 in the Product of 14MER Primer with Activated G Monomer Diastereomer 2


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Product of 14MER Primer with Activated G Monomer Diastereomer 2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg103 b:28.5 occ:1.00 O A:HOH215 1.9 18.6 1.0 O B:HOH228 2.1 31.9 1.0 O B:HOH230 2.1 13.9 1.0 O B:HOH206 2.2 28.4 1.0 OP2 A:A5 4.0 17.0 1.0 OP1 A:A5 4.2 18.2 1.0 O B:HOH202 4.2 24.4 1.0 OP1 A:LCG4 4.3 16.6 1.0 OP2 B:U7 4.5 18.2 1.0 OP2 A:LCG4 4.5 16.4 1.0 OP1 B:C6 4.6 18.7 1.0 P A:A5 4.6 19.6 1.0 P A:LCG4 4.8 17.3 1.0 OP1 B:U7 4.9 23.0 1.0

Magnesium binding site 3 out of 5 in the Product of 14MER Primer with Activated G Monomer Diastereomer 2


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Product of 14MER Primer with Activated G Monomer Diastereomer 2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg104 b:30.3 occ:1.00 O A:HOH224 2.6 13.8 1.0 OP1 A:C6 2.7 17.4 1.0 C5' A:C6 3.3 15.2 1.0 P A:C6 3.8 17.9 1.0 O5' A:C6 3.8 15.2 1.0 O A:HOH220 3.8 19.8 1.0 O A:HOH212 3.9 9.9 1.0 MG B:MG103 4.0 22.2 1.0 O3' A:A5 4.2 18.3 1.0 O A:HOH207 4.5 23.9 1.0 C4' A:C6 4.6 15.9 1.0

Magnesium binding site 4 out of 5 in the Product of 14MER Primer with Activated G Monomer Diastereomer 2


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Product of 14MER Primer with Activated G Monomer Diastereomer 2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg102 b:39.9 occ:0.33 O3' B:G4615 2.5 28.2 1.0 O2' B:G4615 2.5 22.4 1.0 C3' B:G4615 3.4 26.2 1.0 C2' B:G4615 3.4 25.4 1.0 C4' B:G4615 3.7 26.5 1.0 C1' B:G4615 4.6 24.5 1.0 O4' B:G4615 4.7 25.5 1.0 C5' B:G4615 4.9 27.4 1.0

Magnesium binding site 5 out of 5 in the Product of 14MER Primer with Activated G Monomer Diastereomer 2


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Product of 14MER Primer with Activated G Monomer Diastereomer 2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg103 b:22.2 occ:1.00 O A:HOH224 2.0 13.8 1.0 O A:HOH220 2.0 19.8 1.0 O A:HOH209 2.0 21.3 1.0 O B:HOH205 2.0 17.7 1.0 O B:HOH223 2.0 24.4 1.0 MG A:MG104 4.0 30.3 1.0 OP2 B:A5 4.1 15.6 1.0 OP2 A:U7 4.3 16.1 1.0 OP1 B:A5 4.4 18.1 1.0 OP1 A:C6 4.4 17.4 1.0 O A:HOH207 4.4 23.9 1.0 OP1 B:LCG4 4.5 16.0 1.0 P B:A5 4.8 18.2 1.0 OP1 A:U7 4.9 18.2 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.