Magnesium in PDB 4yih: 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: 4yih 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)	57.44 / 1.82
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	38.818, 46.451, 61.738, 111.18, 88.16, 104.70
R / Rfree (%)	18.5 / 22.8

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 4yih). 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-Pvu, PDB code: 4yih:
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-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:Mg201 b:23.2 occ:1.00 O A:HOH358 2.0 30.8 1.0 O4 A:PO4202 2.1 15.5 0.2 OD2 A:ASP10 2.1 25.0 1.0 OD1 A:ASP145 2.4 25.8 1.0 O A:ASP12 2.6 21.7 1.0 O1 A:GOL204 2.9 39.9 1.0 C1 A:GOL204 2.9 40.6 1.0 CG A:ASP10 3.1 25.1 1.0 CG A:ASP145 3.4 24.4 1.0 OBC A:2O2203 3.5 37.8 0.8 P A:PO4202 3.6 15.1 0.2 OD1 A:ASP10 3.6 28.4 1.0 C A:ASP12 3.6 21.9 1.0 OD2 A:ASP145 3.9 25.0 1.0 OBB A:2O2203 4.0 34.7 0.8 O A:HOH377 4.0 31.0 0.8 CB A:ASP12 4.0 22.0 1.0 OD1 A:ASP144 4.0 38.9 1.0 PAA A:2O2203 4.0 38.6 0.8 CA A:ASP12 4.1 21.6 1.0 OBA A:2O2203 4.2 33.4 0.8 O3 A:PO4202 4.3 17.1 0.2 N A:ASP12 4.3 19.2 1.0 N A:ASP145 4.3 22.1 1.0 O2 A:PO4202 4.4 15.0 0.2 O1 A:PO4202 4.4 15.7 0.2 C2 A:GOL204 4.4 31.9 1.0 CB A:ASP10 4.5 22.1 1.0 O A:HOH351 4.5 23.7 0.8 CB A:ASP145 4.6 22.6 1.0 CG A:ASP144 4.7 32.9 1.0 N A:GLY13 4.7 19.8 1.0 C3 A:GOL204 4.9 39.0 1.0 CA A:ASP145 4.9 23.4 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-Pvu


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-Pvu within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg201 b:33.3 occ:1.00 O B:HOH344 1.8 43.4 1.0 OD2 B:ASP10 2.1 43.4 1.0 OD1 B:ASP145 2.3 52.9 1.0 O B:ASP12 2.5 46.8 1.0 O1 B:PO4202 2.5 30.7 0.5 CG B:ASP10 3.2 40.5 1.0 CG B:ASP145 3.3 52.3 1.0 OBB B:2O2203 3.5 39.9 0.5 C B:ASP12 3.5 40.8 1.0 OD1 B:ASP10 3.6 43.2 1.0 OBC B:2O2203 3.7 51.0 0.5 OD2 B:ASP145 3.8 52.8 1.0 O B:HOH304 3.9 33.3 0.5 OD1 B:ASP144 4.0 52.2 1.0 PAA B:2O2203 4.0 47.2 0.5 P B:PO4202 4.0 35.0 0.5 CB B:ASP12 4.1 37.4 1.0 CA B:ASP12 4.2 40.8 1.0 N B:ASP145 4.2 50.7 1.0 N B:ASP12 4.4 39.2 1.0 OBA B:2O2203 4.5 46.7 0.5 CB B:ASP10 4.5 36.5 1.0 CE1 B:PHE44 4.5 77.7 1.0 CB B:ASP145 4.5 50.1 1.0 N B:GLY13 4.6 46.2 1.0 O2 B:PO4202 4.6 31.4 0.5 CG B:ASP144 4.6 50.2 1.0 O4 B:PO4202 4.7 26.7 0.5 O3 B:PO4202 4.7 29.5 0.5 CA B:ASP145 4.8 49.5 1.0 N B:LYS146 5.0 49.0 1.0 CA B:GLY13 5.0 47.0 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