Magnesium in PDB 4mum: Crystal Structure of Mitochondrial 5'(3')-Deoxy Ribonucleotidase Alternative Spliced Variant

The structure of Crystal Structure of Mitochondrial 5'(3')-Deoxy Ribonucleotidase Alternative Spliced Variant, PDB code: 4mum was solved by P.Pachl, P.Rezacova, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.66 / 1.27
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	73.372, 73.372, 106.672, 90.00, 90.00, 90.00
R / Rfree (%)	13.1 / 14.9

The structure of Crystal Structure of Mitochondrial 5'(3')-Deoxy Ribonucleotidase Alternative Spliced Variant also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Magnesium atom in the Crystal Structure of Mitochondrial 5'(3')-Deoxy Ribonucleotidase Alternative Spliced Variant (pdb code 4mum). 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 Mitochondrial 5'(3')-Deoxy Ribonucleotidase Alternative Spliced Variant, PDB code: 4mum:

Magnesium binding site 1 out of 1 in the Crystal Structure of Mitochondrial 5'(3')-Deoxy Ribonucleotidase Alternative Spliced Variant


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 Mitochondrial 5'(3')-Deoxy Ribonucleotidase Alternative Spliced Variant within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg301 b:9.3 occ:1.00 O A:HOH401 2.0 11.4 1.0 OD1 A:ASP176 2.0 9.7 1.0 O A:HOH402 2.1 10.0 1.0 O A:ASP43 2.1 9.6 1.0 OD2 A:ASP41 2.1 9.8 1.0 O2 A:PO4302 2.1 9.7 1.0 CG A:ASP41 3.1 9.5 1.0 CG A:ASP176 3.1 9.8 1.0 C A:ASP43 3.2 8.8 1.0 OD1 A:ASP41 3.4 10.2 1.0 OD2 A:ASP176 3.6 11.5 1.0 P A:PO4302 3.7 9.6 1.0 OD1 A:ASP175 4.0 10.1 1.0 CA A:ASP43 4.0 8.4 1.0 CB A:ASP43 4.0 8.7 1.0 N A:ASP43 4.2 8.5 1.0 O A:HOH457 4.2 11.1 0.5 O4 A:PO4302 4.2 11.0 1.0 N A:GLY44 4.2 8.9 1.0 O A:HOH408 4.2 12.6 1.0 N A:ASP176 4.3 9.2 1.0 O3 A:GOL303 4.4 19.1 1.0 CB A:ASP176 4.4 9.4 1.0 CB A:ASP41 4.4 9.6 1.0 O3 A:PO4302 4.4 9.6 1.0 O1 A:PO4302 4.4 10.3 1.0 CA A:GLY44 4.4 9.6 1.0 CG A:ASP175 4.6 10.0 1.0 CE1 A:PHE75 4.6 15.6 1.0 CZ A:PHE75 4.7 16.1 1.0 CA A:ASP176 4.8 9.7 1.0 OD2 A:ASP175 4.8 11.2 1.0 N A:ARG177 4.8 10.4 1.0 C A:MET42 4.9 8.6 1.0 CG2 A:VAL45 4.9 9.8 1.0 C A:GLY44 5.0 9.7 1.0

P.Pachl, M.Fabry, V.Veverka, J.Brynda, P.Rezacova. Kinetic and Structural Characterization of An Alternatively Spliced Variant of Human Mitochondrial 5'(3')-Deoxyribonucleotidase. J Enzyme Inhib Med Chem 2014.
ISSN: ESSN 1475-6374
PubMed: 24506201
DOI: 10.3109/14756366.2013.879577