Magnesium in PDB 6g2n: Crystal Structure of Human Cytosolic 5'(3')-Deoxyribonucleotidase in Complex with the Inhibitor Pb-Pau

The structure of Crystal Structure of Human Cytosolic 5'(3')-Deoxyribonucleotidase in Complex with the Inhibitor Pb-Pau, PDB code: 6g2n 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)	42.41 / 1.40
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	38.877, 47.231, 61.795, 67.86, 88.69, 77.37
R / Rfree (%)	15.1 / 19.2

The binding sites of Magnesium atom in the Crystal Structure of Human Cytosolic 5'(3')-Deoxyribonucleotidase in Complex with the Inhibitor Pb-Pau (pdb code 6g2n). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of Human Cytosolic 5'(3')-Deoxyribonucleotidase in Complex with the Inhibitor Pb-Pau, PDB code: 6g2n:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Human Cytosolic 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 Cytosolic 5'(3')-Deoxyribonucleotidase in Complex with the Inhibitor Pb-Pau within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg301 b:17.2 occ:1.00 OD1 A:ASP149 2.1 17.6 1.0 O A:HOH409 2.1 18.3 1.0 OD2 A:ASP14 2.1 17.5 1.0 O A:HOH408 2.1 18.0 1.0 O A:ASP16 2.1 16.4 1.0 O11 A:O84302 2.2 18.6 1.0 CG A:ASP14 3.0 17.4 1.0 CG A:ASP149 3.1 17.2 1.0 C A:ASP16 3.2 16.9 1.0 OD1 A:ASP14 3.3 17.4 1.0 P2 A:O84302 3.5 18.6 1.0 OD2 A:ASP149 3.5 18.3 1.0 O10 A:O84302 3.8 20.0 1.0 OD1 A:ASP148 3.9 18.4 1.0 N A:GLY17 4.1 16.6 1.0 CA A:ASP16 4.1 16.5 1.0 CB A:ASP16 4.1 16.3 1.0 CA A:GLY17 4.2 17.6 1.0 N A:ASP149 4.2 19.1 1.0 C18 A:O84302 4.3 18.3 1.0 CB A:ASP14 4.4 18.3 1.0 CB A:ASP149 4.4 16.8 1.0 N A:ASP16 4.4 15.8 1.0 O9 A:O84302 4.5 16.9 1.0 O6 A:O84302 4.5 22.5 1.0 C19 A:O84302 4.5 16.7 1.0 CE1 A:PHE48 4.5 26.0 1.0 CG A:ASP148 4.6 19.2 1.0 N A:LYS150 4.7 18.2 1.0 CZ A:PHE48 4.7 22.8 1.0 CA A:ASP149 4.7 17.5 1.0 OD2 A:ASP148 4.8 19.3 1.0 C A:GLY17 4.8 19.0 1.0 O A:HOH419 4.9 21.3 1.0 CG2 A:VAL18 4.9 18.6 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Human Cytosolic 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 2 of Crystal Structure of Human Cytosolic 5'(3')-Deoxyribonucleotidase in Complex with the Inhibitor Pb-Pau within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg301 b:18.4 occ:1.00 OD2 B:ASP14 2.0 20.0 1.0 OD1 B:ASP149 2.0 19.9 1.0 O B:ASP16 2.1 18.9 1.0 O B:HOH421 2.1 20.4 1.0 O B:HOH420 2.1 19.7 1.0 O11 B:O84302 2.2 19.9 1.0 CG B:ASP14 3.0 19.5 1.0 CG B:ASP149 3.1 20.0 1.0 C B:ASP16 3.2 18.8 1.0 OD1 B:ASP14 3.3 19.6 1.0 P2 B:O84302 3.5 19.3 1.0 OD2 B:ASP149 3.5 21.9 1.0 O10 B:O84302 3.8 20.0 1.0 OD1 B:ASP148 3.9 20.4 1.0 N B:GLY17 4.1 18.4 1.0 CA B:ASP16 4.2 17.9 1.0 CB B:ASP16 4.2 16.9 1.0 CA B:GLY17 4.2 17.6 1.0 N B:ASP149 4.3 20.9 1.0 C18 B:O84302 4.3 22.1 1.0 CB B:ASP14 4.3 18.9 1.0 CB B:ASP149 4.4 18.4 1.0 C19 B:O84302 4.5 19.2 1.0 O9 B:O84302 4.5 18.7 1.0 N B:ASP16 4.5 17.1 1.0 CG B:ASP148 4.5 21.1 1.0 CE1 B:PHE48 4.5 24.6 1.0 O6 B:O84302 4.6 26.4 1.0 N B:LYS150 4.7 19.4 1.0 OD2 B:ASP148 4.8 22.2 1.0 CA B:ASP149 4.8 20.7 1.0 C B:GLY17 4.8 19.7 1.0 CZ B:PHE48 4.8 24.8 1.0 CG2 B:VAL18 4.9 19.0 1.0 O B:HOH411 4.9 21.4 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