Magnesium in PDB 1z4j: Structure of the D41N Variant of the Human Mitochondrial Deoxyribonucleotidase in Complex with Uridine 2'-Monophosphate

The structure of Structure of the D41N Variant of the Human Mitochondrial Deoxyribonucleotidase in Complex with Uridine 2'-Monophosphate, PDB code: 1z4j 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 / 1.80
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	73.453, 73.453, 106.085, 90.00, 90.00, 90.00
R / Rfree (%)	17.2 / 20.2

The binding sites of Magnesium atom in the Structure of the D41N Variant of the Human Mitochondrial Deoxyribonucleotidase in Complex with Uridine 2'-Monophosphate (pdb code 1z4j). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Structure of the D41N Variant of the Human Mitochondrial Deoxyribonucleotidase in Complex with Uridine 2'-Monophosphate, PDB code: 1z4j:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Structure of the D41N Variant of the Human Mitochondrial Deoxyribonucleotidase in Complex with Uridine 2'-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 2'-Monophosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1001 b:2.0 occ:1.00 O A:ASP43 1.9 13.3 1.0 O A:HOH4004 1.9 16.0 1.0 O2P A:U2P3001 1.9 19.7 1.0 OD1 A:ASN41 2.0 16.5 1.0 OD1 A:ASP176 2.0 13.9 1.0 O A:HOH4008 2.0 17.6 1.0 CG A:ASP176 3.1 16.2 1.0 C A:ASP43 3.1 13.4 1.0 CG A:ASN41 3.1 12.6 1.0 OD2 A:ASP176 3.4 15.0 1.0 P A:U2P3001 3.5 25.6 1.0 ND2 A:ASN41 3.7 13.2 1.0 CA A:ASP43 3.9 13.8 1.0 CB A:ASP43 4.1 14.2 1.0 N A:GLY44 4.1 14.2 1.0 OD1 A:ASP175 4.1 17.1 1.0 N A:ASP43 4.1 14.3 1.0 CA A:GLY44 4.3 15.4 1.0 O3P A:U2P3001 4.3 19.5 1.0 O1P A:U2P3001 4.3 19.3 1.0 CB A:ASP176 4.4 17.2 1.0 O2 A:U2P3001 4.4 17.7 1.0 CE1 A:PHE75 4.4 23.0 1.0 N A:ASP176 4.4 16.1 1.0 O2' A:U2P3001 4.5 26.1 1.0 CB A:ASN41 4.5 14.6 1.0 C2' A:U2P3001 4.6 20.7 1.0 O A:HOH4070 4.7 26.9 1.0 CG A:ASP175 4.8 17.3 1.0 CZ A:PHE75 4.8 22.2 1.0 C A:GLY44 4.8 15.5 1.0 C A:MET42 4.9 14.3 1.0 N A:ARG177 4.9 17.1 1.0 OD2 A:ASP175 4.9 18.5 1.0 CA A:ASP176 4.9 16.6 1.0 CG2 A:VAL45 4.9 15.7 1.0 O A:HOH4145 4.9 29.0 1.0 NZ A:LYS165 5.0 25.6 1.0

Magnesium binding site 2 out of 2 in the Structure of the D41N Variant of the Human Mitochondrial Deoxyribonucleotidase in Complex with Uridine 2'-Monophosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of the D41N Variant of the Human Mitochondrial Deoxyribonucleotidase in Complex with Uridine 2'-Monophosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg2001 b:29.0 occ:1.00 O A:ALA119 2.4 23.3 1.0 O A:THR124 2.4 21.0 1.0 O A:HOH4146 2.4 33.8 1.0 O A:LEU121 2.5 23.4 1.0 O A:HOH4149 2.5 29.6 1.0 O A:HOH4147 2.7 32.3 1.0 C A:ALA119 3.5 23.0 1.0 C A:THR124 3.5 20.6 1.0 C A:LEU121 3.6 25.0 1.0 N A:THR124 3.9 23.1 1.0 N A:LEU121 3.9 24.1 1.0 C A:SER120 4.0 26.0 1.0 CA A:THR124 4.1 21.8 1.0 CB A:THR124 4.1 21.8 1.0 O A:HOH4148 4.2 32.0 1.0 N A:SER120 4.3 24.3 1.0 CA A:SER120 4.4 25.9 1.0 CA A:LEU121 4.4 24.7 1.0 CA A:ALA119 4.4 21.9 1.0 O A:SER120 4.4 25.8 1.0 N A:ASP125 4.6 20.2 1.0 O A:MET118 4.6 18.9 1.0 N A:GLN122 4.6 26.8 1.0 OD1 A:ASP125 4.7 24.1 1.0 N A:ASN123 4.8 26.0 1.0 C A:GLN122 4.8 26.6 1.0 CA A:GLN122 4.8 28.5 1.0 CA A:ASP125 4.9 20.1 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