Magnesium in PDB 6g2m: Crystal Structure of Human Mitochondrial 5'(3')-Deoxyribonucleotidase in Complex with the Inhibitor Pb-Pau

The structure of Crystal Structure of Human Mitochondrial 5'(3')-Deoxyribonucleotidase in Complex with the Inhibitor Pb-Pau, PDB code: 6g2m was solved by P.Pachl, P.Rezacova, J.Brynda, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.86 / 1.37
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	73.858, 73.858, 106.121, 90.00, 90.00, 90.00
R / Rfree (%)	12.5 / 15.1

The structure of Crystal Structure of Human Mitochondrial 5'(3')-Deoxyribonucleotidase in Complex with the Inhibitor Pb-Pau also contains other interesting chemical elements:

Potassium

(K)

1 atom

The binding sites of Magnesium atom in the Crystal Structure of Human Mitochondrial 5'(3')-Deoxyribonucleotidase in Complex with the Inhibitor Pb-Pau (pdb code 6g2m). 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 Crystal Structure of Human Mitochondrial 5'(3')-Deoxyribonucleotidase in Complex with the Inhibitor Pb-Pau, PDB code: 6g2m:

Magnesium binding site 1 out of 1 in the Crystal Structure of Human Mitochondrial 5'(3')-Deoxyribonucleotidase in Complex with the Inhibitor Pb-Pau


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Human Mitochondrial 5'(3')-Deoxyribonucleotidase in Complex with the Inhibitor Pb-Pau within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg307 b:9.5 occ:1.00 O A:HOH455 2.0 13.3 1.0 O A:HOH422 2.1 12.6 1.0 OD1 A:ASP176 2.1 12.3 1.0 O A:ASP43 2.1 12.5 1.0 OD2 A:ASP41 2.1 12.2 1.0 O11 A:O84305 2.1 14.0 1.0 CG A:ASP41 3.1 12.6 1.0 CG A:ASP176 3.1 13.0 1.0 C A:ASP43 3.2 11.5 1.0 OD1 A:ASP41 3.4 13.1 1.0 P2 A:O84305 3.5 13.2 1.0 OD2 A:ASP176 3.5 13.9 1.0 O10 A:O84305 3.7 13.4 1.0 OD1 A:ASP175 3.9 12.6 1.0 N A:GLY44 4.1 11.7 1.0 CA A:ASP43 4.1 11.1 1.0 CB A:ASP43 4.2 11.1 1.0 CA A:GLY44 4.3 11.8 1.0 N A:ASP176 4.3 12.1 1.0 C18 A:O84305 4.3 18.4 1.0 CB A:ASP176 4.4 12.0 1.0 CB A:ASP41 4.4 12.4 1.0 N A:ASP43 4.4 10.8 1.0 O9 A:O84305 4.5 13.5 1.0 CG A:ASP175 4.5 11.9 1.0 C19 A:O84305 4.5 14.9 1.0 CE1 A:PHE75 4.5 17.0 1.0 O6 A:O84305 4.6 19.8 1.0 CZ A:PHE75 4.6 16.0 1.0 CG2 A:VAL45 4.8 13.7 1.0 OD2 A:ASP175 4.8 13.4 1.0 N A:ARG177 4.8 12.5 1.0 C A:GLY44 4.8 12.9 1.0 CA A:ASP176 4.8 12.5 1.0 O A:HOH420 4.9 13.2 1.0

P.Pachl, O.Simak, M.Budesinsky, J.Brynda, I.Rosenberg, P.Rezacova. Structure-Based Optimization of Bisphosphonate Nucleoside Inhibitors of Human 5'(3')-Deoxyribonucleotidases Eur.J.Org.Chem. 2018.
ISSN: ISSN 1434-193X
DOI: 10.1002/EJOC.201800515