Magnesium in PDB 2jau: Crystal Structure of D41N Variant of Human Mitochondrial 5'(3')- Deoxyribonucleotidase (Mdn) in Complex with 3'-Azidothymidine 5'- Monophosphate

The structure of Crystal Structure of D41N Variant of Human Mitochondrial 5'(3')- Deoxyribonucleotidase (Mdn) in Complex with 3'-Azidothymidine 5'- Monophosphate, PDB code: 2jau was solved by K.Wallden, B.Ruzzenente, 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 (°)	73.590, 73.590, 105.740, 90.00, 90.00, 90.00
R / Rfree (%)	18.2 / 21.4

The binding sites of Magnesium atom in the Crystal Structure of D41N Variant of Human Mitochondrial 5'(3')- Deoxyribonucleotidase (Mdn) in Complex with 3'-Azidothymidine 5'- Monophosphate (pdb code 2jau). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of D41N Variant of Human Mitochondrial 5'(3')- Deoxyribonucleotidase (Mdn) in Complex with 3'-Azidothymidine 5'- Monophosphate, PDB code: 2jau:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of D41N Variant of Human Mitochondrial 5'(3')- Deoxyribonucleotidase (Mdn) in Complex with 3'-Azidothymidine 5'- Monophosphate


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 D41N Variant of Human Mitochondrial 5'(3')- Deoxyribonucleotidase (Mdn) in Complex with 3'-Azidothymidine 5'- Monophosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1228 b:23.8 occ:1.00 O A:THR124 2.3 15.9 1.0 O A:ALA119 2.4 18.2 1.0 O A:LEU121 2.5 19.7 1.0 O A:HOH2085 2.5 34.4 1.0 O A:HOH2092 2.6 22.5 1.0 O A:HOH2091 2.7 31.9 1.0 C A:THR124 3.4 16.1 1.0 C A:ALA119 3.5 18.1 1.0 C A:LEU121 3.6 20.7 1.0 N A:THR124 3.9 19.0 1.0 N A:LEU121 4.0 19.1 1.0 CA A:THR124 4.0 17.0 1.0 C A:SER120 4.0 20.5 1.0 CB A:THR124 4.1 17.6 1.0 O A:SER120 4.3 20.2 1.0 CA A:LEU121 4.3 19.7 1.0 N A:SER120 4.3 18.2 1.0 CA A:SER120 4.4 20.0 1.0 CA A:ALA119 4.4 16.9 1.0 O A:HOH2093 4.5 35.5 1.0 O A:HOH2096 4.5 33.1 1.0 O A:MET118 4.5 13.5 1.0 N A:ASP125 4.5 15.7 1.0 N A:GLN122 4.6 22.2 1.0 N A:ASN123 4.8 22.2 1.0 OD1 A:ASP125 4.8 19.8 1.0 C A:GLN122 4.8 22.8 1.0 CA A:GLN122 4.8 24.1 1.0 CA A:ASP125 4.9 15.6 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of D41N Variant of Human Mitochondrial 5'(3')- Deoxyribonucleotidase (Mdn) in Complex with 3'-Azidothymidine 5'- Monophosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of D41N Variant of Human Mitochondrial 5'(3')- Deoxyribonucleotidase (Mdn) in Complex with 3'-Azidothymidine 5'- Monophosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1231 b:14.6 occ:1.00 OP1 A:ATM1230 2.0 15.3 0.5 OD1 A:ASN41 2.0 13.0 1.0 O A:ASP43 2.1 11.1 1.0 O A:HOH2140 2.1 16.7 1.0 OD1 A:ASP176 2.2 11.1 1.0 O A:HOH2141 2.2 13.5 1.0 O4 A:PO41229 2.2 13.3 0.5 CG A:ASN41 3.1 11.9 1.0 CG A:ASP176 3.2 13.1 1.0 C A:ASP43 3.3 12.0 1.0 P A:ATM1230 3.4 15.6 0.5 OD2 A:ASP176 3.6 13.6 1.0 ND2 A:ASN41 3.6 9.9 1.0 P A:PO41229 3.6 16.7 0.5 OP3 A:ATM1230 3.8 16.4 0.5 OD1 A:ASP175 4.0 14.3 1.0 O A:HOH2202 4.1 19.1 0.5 CA A:ASP43 4.1 11.8 1.0 CB A:ASP43 4.2 12.0 1.0 O1 A:PO41229 4.2 16.4 0.5 O2 A:PO41229 4.2 16.2 0.5 N A:ASP43 4.2 12.1 1.0 OP2 A:ATM1230 4.2 16.9 0.5 O5' A:ATM1230 4.3 18.9 0.5 N A:GLY44 4.3 11.8 1.0 CB A:ASN41 4.4 10.7 1.0 O A:HOH2199 4.4 12.1 0.5 N A:ASP176 4.5 10.9 1.0 CB A:ASP176 4.5 11.8 1.0 CA A:GLY44 4.6 12.7 1.0 CE1 A:PHE75 4.6 20.8 1.0 O3 A:PO41229 4.6 17.5 0.5 CZ A:PHE75 4.7 21.3 1.0 CG A:ASP175 4.7 14.1 1.0 CG2 A:VAL45 4.8 11.8 1.0 N A:ARG177 4.9 13.0 1.0 C A:MET42 4.9 10.4 1.0 C A:GLY44 4.9 12.2 1.0 OD2 A:ASP175 4.9 15.2 1.0 CA A:ASP176 5.0 12.2 1.0

K.Wallden, A.Rinaldo-Matthis, B.Ruzzenente, C.Rampazzo, V.Bianchi, P.Nordlund. Crystal Structures of Human and Murine Deoxyribonucleotidases: Insights Into Recognition of Substrates and Nucleotide Analogues. Biochemistry V. 46 13809 2007.
ISSN: ISSN 0006-2960
PubMed: 17985935
DOI: 10.1021/BI7014794