Magnesium in PDB 1z4q: Structure of the D41N Variant of the Human Mitochondrial Deoxyribonucleotidase in Complex with 2',3'-Dideoxy-2',3- Didehydrothymidine 5'-Monophosphate (D4T-Mp)

The structure of Structure of the D41N Variant of the Human Mitochondrial Deoxyribonucleotidase in Complex with 2',3'-Dideoxy-2',3- Didehydrothymidine 5'-Monophosphate (D4T-Mp), PDB code: 1z4q 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)	20.00 / 2.05
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	73.770, 73.770, 106.057, 90.00, 90.00, 90.00
R / Rfree (%)	17.4 / 21

The binding sites of Magnesium atom in the Structure of the D41N Variant of the Human Mitochondrial Deoxyribonucleotidase in Complex with 2',3'-Dideoxy-2',3- Didehydrothymidine 5'-Monophosphate (D4T-Mp) (pdb code 1z4q). 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 2',3'-Dideoxy-2',3- Didehydrothymidine 5'-Monophosphate (D4T-Mp), PDB code: 1z4q:
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 2',3'-Dideoxy-2',3- Didehydrothymidine 5'-Monophosphate (D4T-Mp)


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 2',3'-Dideoxy-2',3- Didehydrothymidine 5'-Monophosphate (D4T-Mp) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg2229 b:35.1 occ:1.00 O A:ALA119 2.4 26.9 1.0 O A:THR124 2.4 27.1 1.0 O A:HOH2376 2.5 35.4 1.0 O A:HOH2349 2.5 34.5 1.0 O A:LEU121 2.5 28.5 1.0 O A:HOH2330 2.7 36.8 1.0 C A:ALA119 3.4 26.7 1.0 C A:THR124 3.5 25.7 1.0 C A:LEU121 3.7 30.6 1.0 N A:THR124 4.0 26.8 1.0 N A:LEU121 4.0 30.2 1.0 C A:SER120 4.0 30.3 1.0 CA A:THR124 4.1 27.1 1.0 O A:HOH2306 4.2 34.8 1.0 CB A:THR124 4.3 26.9 1.0 N A:SER120 4.3 28.9 1.0 CA A:ALA119 4.3 26.6 1.0 CA A:SER120 4.3 29.7 1.0 O A:SER120 4.4 30.3 1.0 CA A:LEU121 4.5 30.0 1.0 O A:MET118 4.6 24.6 1.0 N A:ASP125 4.6 25.3 1.0 N A:GLN122 4.7 31.9 1.0 OD1 A:ASP125 4.8 26.6 1.0 N A:ASN123 4.9 29.3 1.0 C A:GLN122 4.9 31.2 1.0 CA A:GLN122 4.9 33.2 1.0

Magnesium binding site 2 out of 2 in the Structure of the D41N Variant of the Human Mitochondrial Deoxyribonucleotidase in Complex with 2',3'-Dideoxy-2',3- Didehydrothymidine 5'-Monophosphate (D4T-Mp)


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 2',3'-Dideoxy-2',3- Didehydrothymidine 5'-Monophosphate (D4T-Mp) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg2001 b:18.4 occ:1.00 OP3 A:D4M1489 2.0 24.4 1.0 O A:ASP43 2.0 17.4 1.0 OD1 A:ASN41 2.0 20.3 1.0 O A:HOH2264 2.1 16.7 1.0 O A:HOH2309 2.1 17.8 1.0 OD1 A:ASP176 2.2 17.2 1.0 CG A:ASN41 3.1 18.5 1.0 C A:ASP43 3.2 18.5 1.0 CG A:ASP176 3.2 17.6 1.0 P A:D4M1489 3.2 29.6 1.0 OD2 A:ASP176 3.5 17.5 1.0 OP2 A:D4M1489 3.6 19.1 1.0 ND2 A:ASN41 3.7 16.6 1.0 OD1 A:ASP175 4.0 19.2 1.0 CA A:ASP43 4.1 17.3 1.0 CB A:ASP43 4.1 18.0 1.0 OP1 A:D4M1489 4.2 21.7 1.0 N A:GLY44 4.2 18.2 1.0 N A:ASP43 4.3 18.0 1.0 O5' A:D4M1489 4.4 29.5 1.0 CA A:GLY44 4.4 20.0 1.0 CB A:ASN41 4.4 17.6 1.0 CE1 A:PHE75 4.4 25.9 1.0 N A:ASP176 4.4 18.2 1.0 O A:HOH2378 4.5 39.5 1.0 CB A:ASP176 4.6 18.2 1.0 O A:HOH2310 4.6 30.7 1.0 C5' A:D4M1489 4.7 29.5 1.0 CG A:ASP175 4.7 19.8 1.0 C A:GLY44 4.9 19.7 1.0 N A:ARG177 4.9 20.0 1.0 CA A:ASP176 5.0 18.3 1.0 CG2 A:VAL45 5.0 21.0 1.0 OD2 A:ASP175 5.0 21.4 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