Magnesium in PDB 1z4l: Structure of the D41N Variant of the Human Mitochondrial Deoxyribonucleotidase in Complex with Thymidine 5'- Monophosphate

The structure of Structure of the D41N Variant of the Human Mitochondrial Deoxyribonucleotidase in Complex with Thymidine 5'- Monophosphate, PDB code: 1z4l 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 (°)	73.646, 73.646, 106.375, 90.00, 90.00, 90.00
R / Rfree (%)	17.2 / 21

The binding sites of Magnesium atom in the Structure of the D41N Variant of the Human Mitochondrial Deoxyribonucleotidase in Complex with Thymidine 5'- Monophosphate (pdb code 1z4l). 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 Thymidine 5'- Monophosphate, PDB code: 1z4l:
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 Thymidine 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 Thymidine 5'- Monophosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg2001 b:13.5 occ:1.00 O A:ASP43 2.0 12.3 1.0 O1P A:TMP1001 2.0 15.1 1.0 OD1 A:ASN41 2.0 13.6 1.0 O A:HOH2037 2.0 14.1 1.0 O A:HOH2163 2.1 16.0 1.0 OD1 A:ASP176 2.2 13.3 1.0 CG A:ASN41 3.1 12.3 1.0 CG A:ASP176 3.2 15.2 1.0 C A:ASP43 3.2 12.8 1.0 P A:TMP1001 3.3 16.4 1.0 OD2 A:ASP176 3.5 14.4 1.0 O2P A:TMP1001 3.7 14.4 1.0 ND2 A:ASN41 3.7 11.7 1.0 OD1 A:ASP175 4.1 15.9 1.0 CA A:ASP43 4.1 13.3 1.0 N A:GLY44 4.2 13.7 1.0 CB A:ASP43 4.2 13.2 1.0 O3P A:TMP1001 4.2 15.8 1.0 N A:ASP43 4.3 14.4 1.0 CA A:GLY44 4.3 13.7 1.0 CB A:ASN41 4.4 11.9 1.0 O5' A:TMP1001 4.4 18.3 1.0 N A:ASP176 4.4 13.4 1.0 CB A:ASP176 4.5 14.7 1.0 CE1 A:PHE75 4.5 21.5 1.0 CG A:ASP175 4.7 16.2 1.0 O A:HOH2165 4.7 23.5 1.0 O A:HOH2042 4.7 14.3 1.0 C A:GLY44 4.8 14.2 1.0 N A:ARG177 4.8 14.9 1.0 CG2 A:VAL45 4.9 15.1 1.0 CA A:ASP176 4.9 14.2 1.0 OD2 A:ASP175 4.9 15.0 1.0 C5' A:TMP1001 4.9 22.9 1.0 C A:MET42 5.0 12.7 1.0

Magnesium binding site 2 out of 2 in the Structure of the D41N Variant of the Human Mitochondrial Deoxyribonucleotidase in Complex with Thymidine 5'- 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 Thymidine 5'- Monophosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg2002 b:26.8 occ:1.00 O A:ALA119 2.3 21.1 1.0 O A:THR124 2.3 18.4 1.0 O A:HOH2107 2.4 32.3 1.0 O A:LEU121 2.4 21.8 1.0 O A:HOH2134 2.6 33.3 1.0 O A:HOH2116 2.6 36.7 1.0 C A:ALA119 3.4 21.0 1.0 C A:THR124 3.5 18.2 1.0 C A:LEU121 3.6 23.2 1.0 N A:LEU121 3.9 21.4 1.0 N A:THR124 3.9 21.0 1.0 C A:SER120 4.0 23.6 1.0 CA A:THR124 4.1 19.1 1.0 CB A:THR124 4.2 19.4 1.0 O A:HOH2072 4.2 24.5 1.0 N A:SER120 4.2 21.2 1.0 CA A:SER120 4.3 22.9 1.0 CA A:LEU121 4.4 22.1 1.0 CA A:ALA119 4.4 18.6 1.0 O A:SER120 4.4 23.4 1.0 O A:MET118 4.5 17.0 1.0 O A:HOH2161 4.5 36.8 1.0 N A:ASP125 4.6 17.6 1.0 N A:GLN122 4.6 24.9 1.0 OD1 A:ASP125 4.8 23.2 1.0 N A:ASN123 4.8 24.0 1.0 C A:GLN122 4.8 23.5 1.0 CA A:GLN122 4.8 26.2 1.0 CA A:ASP125 4.9 17.5 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