Magnesium in PDB 4nfl: Crystal Structure of Human Mitochondrial 5'(3')-Deoxyribonucleotidase in Complex with the Inhibitor Npb-T

The structure of Crystal Structure of Human Mitochondrial 5'(3')-Deoxyribonucleotidase in Complex with the Inhibitor Npb-T, PDB code: 4nfl 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)	46.73 / 1.38
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	73.650, 73.650, 105.910, 90.00, 90.00, 90.00
R / Rfree (%)	15.3 / 17.6

The binding sites of Magnesium atom in the Crystal Structure of Human Mitochondrial 5'(3')-Deoxyribonucleotidase in Complex with the Inhibitor Npb-T (pdb code 4nfl). 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 Npb-T, PDB code: 4nfl:

Magnesium binding site 1 out of 1 in the Crystal Structure of Human Mitochondrial 5'(3')-Deoxyribonucleotidase in Complex with the Inhibitor Npb-T


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 Npb-T within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg301 b:10.3 occ:1.00 O A:HOH402 2.0 15.2 1.0 O A:ASP43 2.0 12.5 1.0 OD1 A:ASP176 2.1 11.2 1.0 O2 A:PO4302 2.1 12.0 1.0 OD2 A:ASP41 2.1 12.5 1.0 O A:HOH401 2.1 11.4 1.0 CG A:ASP41 3.1 11.8 1.0 CG A:ASP176 3.1 11.2 1.0 C A:ASP43 3.2 11.9 1.0 OD1 A:ASP41 3.3 11.5 1.0 OD2 A:ASP176 3.6 13.2 1.0 P A:PO4302 3.7 11.3 1.0 OD1 A:ASP175 3.9 11.5 1.0 CA A:ASP43 4.0 10.6 1.0 CB A:ASP43 4.0 11.4 1.0 O A:HOH523 4.1 16.5 0.5 N A:ASP43 4.2 10.5 1.0 O4 A:PO4302 4.2 12.9 1.0 N A:GLY44 4.2 11.3 1.0 O A:HOH418 4.2 13.5 1.0 N A:ASP176 4.3 10.8 1.0 O3 A:GOL310 4.4 16.6 0.3 CB A:ASP41 4.4 11.1 1.0 CB A:ASP176 4.4 11.5 1.0 O1 A:PO4302 4.4 10.9 1.0 O3 A:PO4302 4.4 11.6 1.0 CA A:GLY44 4.4 11.9 1.0 C3 A:GOL310 4.4 17.7 0.3 CG A:ASP175 4.6 10.9 1.0 CAR A:2JW303 4.7 34.3 0.7 CE1 A:PHE75 4.7 20.2 1.0 CZ A:PHE75 4.7 20.3 1.0 N A:ARG177 4.8 11.1 1.0 CA A:ASP176 4.8 11.2 1.0 O4 A:2JW303 4.9 38.4 0.7 OD2 A:ASP175 4.9 11.8 1.0 C A:MET42 4.9 10.6 1.0 CG2 A:VAL45 4.9 12.5 1.0 C A:GLY44 4.9 12.4 1.0

O.Simak, P.Pachl, M.Fabry, M.Budesinsky, T.Jandusik, A.Hnizda, R.Sklenickova, M.Petrova, V.Veverka, P.Rezacova, J.Brynda, I.Rosenberg. Conformationally Constrained Nucleoside Phosphonic Acids - Potent Inhibitors of Human Mitochondrial and Cytosolic 5'(3')-Nucleotidases. Org.Biomol.Chem. V. 12 7971 2014.
ISSN: ISSN 1477-0520
PubMed: 25178098
DOI: 10.1039/C4OB01332H