Magnesium in PDB 4yik: Crystal Structure of Human Cytosolic 5'(3')-Deoxyribonucleotidase in Complex with the Inhibitor Pb-Pvu

The structure of Crystal Structure of Human Cytosolic 5'(3')-Deoxyribonucleotidase in Complex with the Inhibitor Pb-Pvu, PDB code: 4yik 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)	60.64 / 1.48
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	73.870, 73.870, 106.190, 90.00, 90.00, 90.00
R / Rfree (%)	15.3 / 17.6

The binding sites of Magnesium atom in the Crystal Structure of Human Cytosolic 5'(3')-Deoxyribonucleotidase in Complex with the Inhibitor Pb-Pvu (pdb code 4yik). 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 Cytosolic 5'(3')-Deoxyribonucleotidase in Complex with the Inhibitor Pb-Pvu, PDB code: 4yik:

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


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-Pvu within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg301 b:12.6 occ:1.00 OD2 A:ASP41 2.0 14.5 1.0 OBG A:2O2306 2.0 13.8 0.8 O A:ASP43 2.1 15.0 1.0 O A:HOH448 2.1 14.7 1.0 OD1 A:ASP176 2.1 12.5 1.0 O A:HOH465 2.1 17.1 1.0 CG A:ASP41 3.1 13.2 1.0 CG A:ASP176 3.1 12.5 1.0 C A:ASP43 3.3 14.0 1.0 PBD A:2O2306 3.4 17.1 0.8 OD2 A:ASP176 3.5 14.6 1.0 OD1 A:ASP41 3.6 13.7 1.0 OBE A:2O2306 3.8 18.1 0.8 OD1 A:ASP175 4.0 13.2 1.0 CA A:ASP43 4.1 12.9 1.0 CB A:ASP43 4.2 14.2 1.0 N A:ASP43 4.3 12.3 1.0 N A:GLY44 4.3 13.4 1.0 CAR A:2O2306 4.3 18.2 0.8 O A:HOH427 4.3 16.6 1.0 CAS A:2O2306 4.3 16.3 0.8 CB A:ASP41 4.4 12.9 1.0 CA A:GLY44 4.5 14.0 1.0 N A:ASP176 4.5 12.0 1.0 CB A:ASP176 4.5 12.6 1.0 OBF A:2O2306 4.6 20.8 0.8 CZ A:PHE75 4.6 21.2 1.0 C1 A:TRS307 4.7 13.9 0.2 CG A:ASP175 4.7 12.5 1.0 N A:ARG177 4.8 12.6 1.0 CE1 A:PHE75 4.8 20.9 1.0 CG2 A:VAL45 4.8 13.5 1.0 CA A:ASP176 4.9 12.3 1.0 O4 A:2O2306 4.9 20.6 0.8 C A:GLY44 4.9 15.2 1.0

P.Pachl, O.Simak, P.Rezacova, M.Fabry, M.Budesinsky, I.Rosenberg, J.Brynda. Structure-Based Design of A Bisphosphonate 5'(3')-Deoxyribonucleotidase Inhibitor Medchemcomm V. 6 1635 2015.
ISSN: ISSN 2040-2503
DOI: 10.1039/C5MD00235D