Magnesium in PDB 1z4m: Structure of the D41N Variant of the Human Mitochondrial Deoxyribonucleotidase in Complex with Uridine 5'-Monophosphate

The structure of Structure of the D41N Variant of the Human Mitochondrial Deoxyribonucleotidase in Complex with Uridine 5'-Monophosphate, PDB code: 1z4m was solved by K.Wallden, B.Ruzzenente, A.Rinaldo-Matthis, V.Bianchi, P.Nordlund, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.00 / 1.70
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	73.572, 73.572, 105.748, 90.00, 90.00, 90.00
R / Rfree (%)	19.3 / 21.5

The binding sites of Magnesium atom in the Structure of the D41N Variant of the Human Mitochondrial Deoxyribonucleotidase in Complex with Uridine 5'-Monophosphate (pdb code 1z4m). 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 the D41N Variant of the Human Mitochondrial Deoxyribonucleotidase in Complex with Uridine 5'-Monophosphate, PDB code: 1z4m:

Magnesium binding site 1 out of 1 in the Structure of the D41N Variant of the Human Mitochondrial Deoxyribonucleotidase in Complex with Uridine 5'-Monophosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of the D41N Variant of the Human Mitochondrial Deoxyribonucleotidase in Complex with Uridine 5'-Monophosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg2001 b:17.5 occ:1.00 O1P A:U5P1001 2.0 19.3 0.5 OD1 A:ASN41 2.0 17.4 1.0 O3P A:U5P1001 2.1 14.8 0.5 O A:ASP43 2.1 16.3 1.0 O A:HOH3050 2.1 18.9 1.0 OD1 A:ASP176 2.2 15.7 1.0 O A:HOH3051 2.2 18.0 1.0 CG A:ASN41 3.1 15.3 1.0 CG A:ASP176 3.2 17.4 1.0 C A:ASP43 3.3 15.5 1.0 P A:U5P1001 3.3 21.5 0.5 P A:U5P1001 3.5 16.1 0.5 OD2 A:ASP176 3.6 18.9 1.0 ND2 A:ASN41 3.6 15.6 1.0 O3P A:U5P1001 3.8 21.1 0.5 O A:HOH3161 3.9 20.0 0.5 OD1 A:ASP175 4.0 19.0 1.0 CA A:ASP43 4.1 15.7 1.0 O1P A:U5P1001 4.1 16.2 0.5 CB A:ASP43 4.1 15.7 1.0 N A:ASP43 4.2 15.5 1.0 O2P A:U5P1001 4.2 20.9 0.5 N A:GLY44 4.3 15.3 1.0 O5' A:U5P1001 4.4 23.6 0.5 O A:HOH3151 4.4 21.3 0.5 CB A:ASN41 4.4 14.4 1.0 O2P A:U5P1001 4.4 15.9 0.5 N A:ASP176 4.4 16.3 1.0 CA A:GLY44 4.4 16.5 1.0 O5' A:U5P1001 4.5 18.4 0.5 CE1 A:PHE75 4.5 27.0 1.0 CB A:ASP176 4.5 16.6 1.0 C5' A:U5P1001 4.5 27.9 0.5 C5' A:U5P1001 4.6 23.8 0.5 CG A:ASP175 4.7 17.6 1.0 CG2 A:VAL45 4.8 16.6 1.0 N A:ARG177 4.9 16.0 1.0 O A:HOH3052 4.9 31.8 1.0 C A:GLY44 4.9 17.2 1.0 C A:MET42 4.9 15.3 1.0 CA A:ASP176 4.9 15.9 1.0 OD2 A:ASP175 5.0 18.5 1.0

K.Wallden, B.Ruzzenente, A.Rinaldo-Matthis, V.Bianchi, P.Nordlund. Structural Basis For Substrate Specificity of the Human Mitochondrial Deoxyribonucleotidase Structure V. 13 1081 2005.
ISSN: ISSN 0969-2126
PubMed: 16004879
DOI: 10.1016/J.STR.2005.04.023