Magnesium in PDB 8vaw: Magnesium Catalyzed Primer Extension Product with 14MER Primer and Mixed Phosphorothioate Activated G Monomer

The structure of Magnesium Catalyzed Primer Extension Product with 14MER Primer and Mixed Phosphorothioate Activated G Monomer, PDB code: 8vaw 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)	37.73 / 1.25
Space group	P 3 2 1
Cell size a, b, c (Å), α, β, γ (°)	43.57, 43.57, 84.342, 90, 90, 120
R / Rfree (%)	18.8 / 19.1

The binding sites of Magnesium atom in the Magnesium Catalyzed Primer Extension Product with 14MER Primer and Mixed Phosphorothioate Activated G Monomer (pdb code 8vaw). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Magnesium Catalyzed Primer Extension Product with 14MER Primer and Mixed Phosphorothioate Activated G Monomer, PDB code: 8vaw:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Magnesium Catalyzed Primer Extension Product with 14MER Primer and Mixed Phosphorothioate Activated G Monomer


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Magnesium Catalyzed Primer Extension Product with 14MER Primer and Mixed Phosphorothioate Activated G Monomer within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg201 b:11.7 occ:1.00 O B:HOH379 2.0 11.9 1.0 O A:HOH337 2.1 14.4 1.0 O A:HOH345 2.1 11.9 1.0 O B:HOH336 2.1 13.3 1.0 O A:HOH311 2.1 14.9 1.0 O B:HOH342 2.1 14.0 1.0 O B:HOH310 4.1 11.2 1.0 OP2 A:A5 4.2 12.5 1.0 O A:HOH339 4.3 17.2 1.0 OP1 A:A5 4.3 11.7 1.0 O B:HOH312 4.3 13.3 1.0 O A:HOH367 4.3 25.9 1.0 O B:HOH377 4.4 28.2 1.0 OP2 B:U7 4.4 12.0 1.0 OP1 A:LCG4 4.4 11.6 1.0 OP1 B:C6 4.5 11.3 1.0 P A:A5 4.8 11.3 1.0

Magnesium binding site 2 out of 4 in the Magnesium Catalyzed Primer Extension Product with 14MER Primer and Mixed Phosphorothioate Activated G Monomer


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Magnesium Catalyzed Primer Extension Product with 14MER Primer and Mixed Phosphorothioate Activated G Monomer within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg202 b:27.6 occ:0.33 O2' A:G4615 2.3 23.4 1.0 O3' A:G4615 2.3 25.6 1.0 C3' A:G4615 3.3 25.4 1.0 C2' A:G4615 3.3 24.2 1.0 C4' A:G4615 3.7 25.4 1.0 C1' A:G4615 4.5 21.2 1.0 O4' A:G4615 4.5 24.0 1.0 O A:HOH301 4.6 42.5 1.0 C5' A:G4615 5.0 25.8 1.0

Magnesium binding site 3 out of 4 in the Magnesium Catalyzed Primer Extension Product with 14MER Primer and Mixed Phosphorothioate Activated G Monomer


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Magnesium Catalyzed Primer Extension Product with 14MER Primer and Mixed Phosphorothioate Activated G Monomer within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg201 b:11.7 occ:1.00 O A:HOH364 2.0 11.9 1.0 O B:HOH313 2.1 14.5 1.0 O A:HOH347 2.1 13.1 1.0 O B:HOH348 2.1 14.0 1.0 O B:HOH346 2.1 11.7 1.0 O A:HOH343 2.1 13.2 1.0 O A:HOH369 4.0 29.5 1.0 O A:HOH370 4.2 29.8 1.0 OP2 B:A5 4.2 13.8 1.0 O B:HOH380 4.3 30.1 1.0 O A:HOH319 4.3 12.9 1.0 OP1 B:A5 4.3 13.6 1.0 O B:HOH318 4.3 19.1 1.0 O B:HOH386 4.3 30.3 1.0 OP2 A:U7 4.4 10.8 1.0 OP1 B:LCG4 4.5 12.5 1.0 OP1 A:C6 4.5 10.7 1.0 P B:A5 4.8 12.5 1.0

Magnesium binding site 4 out of 4 in the Magnesium Catalyzed Primer Extension Product with 14MER Primer and Mixed Phosphorothioate Activated G Monomer


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Magnesium Catalyzed Primer Extension Product with 14MER Primer and Mixed Phosphorothioate Activated G Monomer within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg202 b:19.1 occ:0.33 O2' B:G4615 2.4 18.0 1.0 O3' B:G4615 2.4 18.9 1.0 C3' B:G4615 3.3 17.1 1.0 C2' B:G4615 3.3 16.4 1.0 C4' B:G4615 3.8 17.4 1.0 O B:HOH302 4.3 32.6 1.0 C1' B:G4615 4.5 14.7 1.0 O4' B:G4615 4.7 15.8 1.0 O B:HOH330 4.8 25.7 1.0 O B:HOH373 4.9 40.3 1.0 C5' B:G4615 5.0 19.1 1.0

Z.Fang, L.T.Pazienza, J.Zhang, C.P.Tam, J.W.Szostak. Catalytic Metal Ion-Substrate Coordination During Nonenzymatic Rna Primer Extension. J.Am.Chem.Soc. 2024.
ISSN: ESSN 1520-5126
PubMed: 38579124
DOI: 10.1021/JACS.4C00323