Magnesium in PDB 4l6a: Structure of Human Mitochondrial 5'(3')-Deoxyribonucleotidase

The structure of Structure of Human Mitochondrial 5'(3')-Deoxyribonucleotidase, PDB code: 4l6a was solved by P.Pachl, J.Brynda, P.Rezacova, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.50 / 1.40
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	73.410, 73.410, 106.340, 90.00, 90.00, 90.00
R / Rfree (%)	14.1 / 15.4

The structure of Structure of Human Mitochondrial 5'(3')-Deoxyribonucleotidase also contains other interesting chemical elements:

Potassium

(K)

1 atom

The binding sites of Magnesium atom in the Structure of Human Mitochondrial 5'(3')-Deoxyribonucleotidase (pdb code 4l6a). 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 Structure of Human Mitochondrial 5'(3')-Deoxyribonucleotidase, PDB code: 4l6a:

Magnesium binding site 1 out of 1 in the Structure of Human Mitochondrial 5'(3')-Deoxyribonucleotidase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of Human Mitochondrial 5'(3')-Deoxyribonucleotidase within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg301 b:7.4 occ:1.00 O A:HOH448 2.0 10.1 1.0 OD1 A:ASP176 2.0 7.6 1.0 O A:HOH430 2.1 8.0 1.0 O A:ASP43 2.1 8.4 1.0 O2 A:PO4302 2.1 7.4 1.0 OD2 A:ASP41 2.1 8.1 1.0 CG A:ASP41 3.1 8.2 1.0 CG A:ASP176 3.1 8.5 1.0 C A:ASP43 3.2 7.2 1.0 OD1 A:ASP41 3.3 8.0 1.0 OD2 A:ASP176 3.6 9.7 1.0 P A:PO4302 3.7 7.6 1.0 OD1 A:ASP175 3.9 8.3 1.0 CA A:ASP43 4.0 6.7 1.0 CB A:ASP43 4.0 7.3 1.0 O A:HOH503 4.2 11.3 0.7 N A:ASP43 4.2 7.0 1.0 O1 A:PO4302 4.2 8.2 1.0 N A:GLY44 4.2 7.4 1.0 O A:HOH403 4.3 8.0 1.0 N A:ASP176 4.3 7.5 1.0 CB A:ASP176 4.4 7.8 1.0 O3 A:GOL303 4.4 16.9 1.0 CA A:GLY44 4.4 8.5 1.0 O3 A:PO4302 4.4 7.4 1.0 CB A:ASP41 4.4 7.1 1.0 O4 A:PO4302 4.5 7.8 1.0 CG A:ASP175 4.6 7.6 1.0 CE1 A:PHE75 4.6 14.2 1.0 N A:ARG177 4.8 8.4 1.0 CZ A:PHE75 4.8 15.2 1.0 CA A:ASP176 4.8 7.9 1.0 OD2 A:ASP175 4.9 8.3 1.0 C A:MET42 4.9 6.7 1.0 CG2 A:VAL45 4.9 9.3 1.0 C A:GLY44 4.9 9.0 1.0

P.Pachl, M.Fabry, I.Rosenberg, O.Simak, P.Rezacova, J.Brynda. Structures of Human Cytosolic and Mitochondrial Nucleotidases: Implications For Structure-Based Design of Selective Inhibitors Acta Crystallogr.,Sect.D V. 70 461 2014.
ISSN: ISSN 0907-4449
DOI: 10.1107/S139900471303050