Magnesium in PDB 2g09: X-Ray Structure of Mouse Pyrimidine 5'-Nucleotidase Type 1, Product Complex

All present enzymatic activity of X-Ray Structure of Mouse Pyrimidine 5'-Nucleotidase Type 1, Product Complex:
3.1.1.5;

The structure of X-Ray Structure of Mouse Pyrimidine 5'-Nucleotidase Type 1, Product Complex, PDB code: 2g09 was solved by E.Bitto, C.A.Bingman, G.E.Wesenberg, G.N.Phillips Jr., Center Foreukaryotic Structural Genomics (Cesg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	32.19 / 2.10
Space group	P 32
Cell size a, b, c (Å), α, β, γ (°)	134.006, 134.006, 39.087, 90.00, 90.00, 120.00
R / Rfree (%)	15 / 19.8

The binding sites of Magnesium atom in the X-Ray Structure of Mouse Pyrimidine 5'-Nucleotidase Type 1, Product Complex (pdb code 2g09). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the X-Ray Structure of Mouse Pyrimidine 5'-Nucleotidase Type 1, Product Complex, PDB code: 2g09:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the X-Ray Structure of Mouse Pyrimidine 5'-Nucleotidase Type 1, Product Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of X-Ray Structure of Mouse Pyrimidine 5'-Nucleotidase Type 1, Product Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg901 b:24.8 occ:1.00 O2 A:PO4903 2.1 21.5 1.0 O A:HOH1254 2.1 25.5 1.0 OD1 A:ASP238 2.2 32.0 1.0 O A:ASP51 2.2 30.0 1.0 OD1 A:ASP49 2.2 34.7 1.0 O A:HOH1119 2.2 18.9 1.0 CG A:ASP238 3.1 32.8 1.0 CG A:ASP49 3.3 38.0 1.0 C A:ASP51 3.3 30.4 1.0 OD2 A:ASP238 3.4 31.4 1.0 P A:PO4903 3.5 22.3 1.0 CA A:ASP51 4.0 30.2 1.0 O1 A:PO4903 4.0 22.5 1.0 N A:ASP51 4.0 29.3 1.0 O4 A:PO4903 4.0 22.9 1.0 OG1 A:THR53 4.0 32.8 1.0 CB A:ASP51 4.1 31.3 1.0 OD2 A:ASP242 4.1 29.6 1.0 OD2 A:ASP49 4.1 35.4 1.0 CB A:ASP49 4.1 35.6 1.0 O A:HOH958 4.1 23.4 1.0 O A:HOH930 4.2 24.6 1.0 O A:HOH994 4.2 28.6 1.0 CB A:MSE52 4.4 28.7 1.0 N A:MSE52 4.4 28.9 1.0 O3 A:PO4903 4.4 25.3 1.0 CB A:ASP238 4.5 30.4 1.0 C A:PHE50 4.5 31.3 1.0 CG A:MSE52 4.6 30.2 1.0 N A:THR53 4.6 30.7 1.0 CA A:MSE52 4.7 29.7 1.0 CB A:THR53 4.8 32.0 1.0 N A:PHE50 4.8 34.8 1.0 C A:MSE52 4.8 29.2 1.0 O A:PHE50 4.9 31.4 1.0 N A:ASP238 4.9 29.3 1.0 CG A:ASP242 5.0 31.0 1.0 OD1 A:ASP242 5.0 32.1 1.0

Magnesium binding site 2 out of 2 in the X-Ray Structure of Mouse Pyrimidine 5'-Nucleotidase Type 1, Product Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of X-Ray Structure of Mouse Pyrimidine 5'-Nucleotidase Type 1, Product Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg902 b:25.0 occ:1.00 O B:HOH1309 2.1 28.5 1.0 O1 B:PO4904 2.1 21.9 1.0 O B:ASP51 2.2 30.1 1.0 OD1 B:ASP238 2.2 33.2 1.0 OD1 B:ASP49 2.2 34.8 1.0 O B:HOH1265 2.2 19.2 1.0 CG B:ASP238 3.1 32.0 1.0 CG B:ASP49 3.3 37.5 1.0 C B:ASP51 3.3 30.5 1.0 OD2 B:ASP238 3.4 29.9 1.0 P B:PO4904 3.5 22.4 1.0 CA B:ASP51 4.0 30.2 1.0 O3 B:PO4904 4.0 23.3 1.0 OG1 B:THR53 4.0 30.8 1.0 N B:ASP51 4.0 29.2 1.0 CB B:ASP51 4.0 31.0 1.0 O4 B:PO4904 4.1 22.2 1.0 OD2 B:ASP49 4.1 36.0 1.0 CB B:ASP49 4.1 35.7 1.0 OD2 B:ASP242 4.1 29.1 1.0 O B:HOH974 4.2 25.9 1.0 O B:HOH948 4.2 26.2 1.0 O B:HOH1000 4.3 27.4 1.0 CB B:MSE52 4.3 29.2 1.0 N B:MSE52 4.4 28.7 1.0 O2 B:PO4904 4.4 23.5 1.0 CB B:ASP238 4.5 28.9 1.0 C B:PHE50 4.5 31.6 1.0 N B:THR53 4.6 30.4 1.0 CG B:MSE52 4.6 30.8 1.0 CA B:MSE52 4.7 29.6 1.0 N B:PHE50 4.8 34.9 1.0 CB B:THR53 4.8 30.8 1.0 C B:MSE52 4.8 29.4 1.0 O B:PHE50 4.8 31.4 1.0 N B:ASP238 4.9 29.2 1.0 O B:HOH1037 5.0 34.5 1.0

E.Bitto, C.A.Bingman, G.E.Wesenberg, J.G.Mccoy, G.N.Phillips. Structure of Pyrimidine 5'-Nucleotidase Type 1. Insight Into Mechanism of Action and Inhibition During Lead Poisoning. J.Biol.Chem. V. 281 20521 2006.
ISSN: ISSN 0021-9258
PubMed: 16672222
DOI: 10.1074/JBC.M602000200