Magnesium in PDB 6mkk: Crystallographic Solvent Mapping Analysis of Dmso/Mg Bound to APE1

All present enzymatic activity of Crystallographic Solvent Mapping Analysis of Dmso/Mg Bound to APE1:
4.2.99.18;

The structure of Crystallographic Solvent Mapping Analysis of Dmso/Mg Bound to APE1, PDB code: 6mkk was solved by M.M.Georgiadis, H.He, Q.Chen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.20 / 1.44
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	46.697, 141.487, 45.334, 90.00, 90.00, 90.00
R / Rfree (%)	18.3 / 21.2

The binding sites of Magnesium atom in the Crystallographic Solvent Mapping Analysis of Dmso/Mg Bound to APE1 (pdb code 6mkk). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the Crystallographic Solvent Mapping Analysis of Dmso/Mg Bound to APE1, PDB code: 6mkk:

Magnesium binding site 1 out of 1 in the Crystallographic Solvent Mapping Analysis of Dmso/Mg Bound to APE1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystallographic Solvent Mapping Analysis of Dmso/Mg Bound to APE1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg401 b:14.5 occ:1.00 OE2 A:GLU96 2.1 15.3 1.0 OD1 A:ASP70 2.1 14.9 1.0 O A:HOH502 2.1 18.0 1.0 O A:HOH659 2.2 17.3 1.0 O A:HOH535 2.2 13.7 1.0 O A:HOH505 2.2 18.0 1.0 CD A:GLU96 3.0 14.2 1.0 CG A:ASP70 3.1 13.4 1.0 OE1 A:GLU96 3.2 16.4 1.0 CB A:ASP70 3.8 11.9 1.0 OD2 A:ASP70 4.0 15.0 1.0 CA A:ASP70 4.0 8.3 1.0 OD1 A:ASP308 4.0 9.7 1.0 OD2 A:ASP308 4.0 13.1 1.0 NZ A:LYS98 4.1 22.7 1.0 O A:HOH596 4.2 16.3 1.0 CE A:LYS98 4.3 16.4 1.0 CG A:GLU96 4.4 14.3 1.0 CG A:ASP308 4.5 11.9 1.0 ND2 A:ASN68 4.5 6.4 1.0 O A:HOH517 4.6 27.3 1.0 O A:HOH758 5.0 36.6 1.0 N A:ASP70 5.0 10.2 1.0

R.Trilles, D.Beglov, Q.Chen, H.He, R.Wireman, A.Reed, S.Chennamadhavuni, J.S.Panek, L.E.Brown, S.Vajda, J.A.Porco Jr., M.R.Kelley, M.M.Georgiadis. Discovery of Macrocyclic Inhibitors of Apurinic/Apyrimidinic Endonuclease 1. J. Med. Chem. V. 62 1971 2019.
ISSN: ISSN 1520-4804
PubMed: 30653918
DOI: 10.1021/ACS.JMEDCHEM.8B01529