Magnesium in PDB 2jar: Crystal Structure of D12N Variant of Mouse Cytosolic 5'(3')- Deoxyribonucleotidase (Cdn) in Complex with Deoxyuridine 5'- Monophosphate

The structure of Crystal Structure of D12N Variant of Mouse Cytosolic 5'(3')- Deoxyribonucleotidase (Cdn) in Complex with Deoxyuridine 5'- Monophosphate, PDB code: 2jar 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 / 1.94
Space group	P 62
Cell size a, b, c (Å), α, β, γ (°)	75.309, 75.309, 85.174, 90.00, 90.00, 120.00
R / Rfree (%)	15.6 / 20.1

The binding sites of Magnesium atom in the Crystal Structure of D12N Variant of Mouse Cytosolic 5'(3')- Deoxyribonucleotidase (Cdn) in Complex with Deoxyuridine 5'- Monophosphate (pdb code 2jar). 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 Crystal Structure of D12N Variant of Mouse Cytosolic 5'(3')- Deoxyribonucleotidase (Cdn) in Complex with Deoxyuridine 5'- Monophosphate, PDB code: 2jar:

Magnesium binding site 1 out of 1 in the Crystal Structure of D12N Variant of Mouse Cytosolic 5'(3')- Deoxyribonucleotidase (Cdn) in Complex with Deoxyuridine 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 D12N Variant of Mouse Cytosolic 5'(3')- Deoxyribonucleotidase (Cdn) in Complex with Deoxyuridine 5'- Monophosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1201 b:17.0 occ:1.00 OP3 A:UMP1200 2.0 16.2 0.5 OP2 A:UMP1200 2.0 12.1 0.5 OD1 A:ASN12 2.1 13.8 1.0 O A:ASP14 2.1 16.5 1.0 OD1 A:ASP147 2.1 15.3 1.0 O A:HOH2123 2.1 16.2 1.0 O A:HOH2177 2.2 18.4 1.0 CG A:ASN12 3.2 13.0 1.0 CG A:ASP147 3.2 17.0 1.0 C A:ASP14 3.2 16.6 1.0 P A:UMP1200 3.3 20.1 0.5 OD2 A:ASP147 3.5 15.1 1.0 P A:UMP1200 3.6 17.3 0.5 ND2 A:ASN12 3.7 9.5 1.0 OP1 A:UMP1200 3.8 16.6 0.5 CA A:ASP14 3.9 16.4 1.0 CB A:ASP14 4.0 17.5 1.0 OD1 A:ASP146 4.0 14.5 1.0 N A:ASP14 4.1 15.3 1.0 O A:HOH2176 4.1 8.7 0.5 OP3 A:UMP1200 4.1 14.0 0.5 OP2 A:UMP1200 4.2 16.1 0.5 N A:GLY15 4.2 16.6 1.0 CE1 A:PHE46 4.3 22.3 1.0 OP1 A:UMP1200 4.3 14.2 0.5 N A:ASP147 4.4 15.9 1.0 CB A:ASN12 4.4 12.7 1.0 O5' A:UMP1200 4.4 18.7 0.5 CB A:ASP147 4.5 15.8 1.0 CA A:GLY15 4.5 16.0 1.0 O5' A:UMP1200 4.5 18.4 0.5 O A:HOH2175 4.5 14.0 0.5 O A:HOH2004 4.6 22.2 1.0 C5' A:UMP1200 4.7 21.3 1.0 CG A:ASP146 4.7 15.3 1.0 CZ A:PHE46 4.8 22.9 1.0 C A:MET13 4.8 15.2 1.0 N A:LYS148 4.8 18.4 0.5 N A:LYS148 4.9 18.2 0.5 CG2 A:VAL16 4.9 14.4 1.0 CA A:ASP147 4.9 16.7 1.0 O A:HOH2124 5.0 23.0 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