Magnesium in PDB 2g06: X-Ray Structure of Mouse Pyrimidine 5'-Nucleotidase Type 1, with Bound Magnesium(II)

All present enzymatic activity of X-Ray Structure of Mouse Pyrimidine 5'-Nucleotidase Type 1, with Bound Magnesium(II):
3.1.3.5;

The structure of X-Ray Structure of Mouse Pyrimidine 5'-Nucleotidase Type 1, with Bound Magnesium(II), PDB code: 2g06 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)	67.17 / 2.25
Space group	P 32
Cell size a, b, c (Å), α, β, γ (°)	134.343, 134.343, 39.152, 90.00, 90.00, 120.00
R / Rfree (%)	15.5 / 21.9

The binding sites of Magnesium atom in the X-Ray Structure of Mouse Pyrimidine 5'-Nucleotidase Type 1, with Bound Magnesium(II) (pdb code 2g06). 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, with Bound Magnesium(II), PDB code: 2g06:
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, with Bound Magnesium(II)


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, with Bound Magnesium(II) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg900 b:36.1 occ:1.00 OD2 A:ASP49 2.2 45.0 1.0 OD1 A:ASP238 2.2 42.8 1.0 O A:ASP51 2.2 33.4 1.0 O A:HOH1353 2.3 22.6 1.0 O A:HOH1217 2.5 37.6 1.0 O A:HOH1405 2.5 29.8 1.0 CG A:ASP49 3.0 41.4 1.0 CG A:ASP238 3.2 34.1 1.0 C A:ASP51 3.3 29.6 1.0 OD1 A:ASP49 3.3 39.8 1.0 OD2 A:ASP238 3.5 34.6 1.0 CA A:ASP51 3.8 29.3 1.0 O A:HOH1407 3.8 27.1 1.0 CB A:ASP51 3.8 29.4 1.0 N A:ASP51 3.8 26.7 1.0 O A:HOH1092 4.0 41.0 1.0 O A:HOH1406 4.0 23.4 1.0 O A:HOH1026 4.1 22.1 1.0 O A:HOH1056 4.2 39.4 1.0 OG1 A:THR53 4.2 36.2 1.0 CB A:ASP49 4.4 31.4 1.0 OD2 A:ASP242 4.4 28.4 1.0 N A:MSE52 4.4 28.1 1.0 CB A:MSE52 4.5 30.0 1.0 C A:PHE50 4.5 27.4 1.0 CB A:ASP238 4.6 31.6 1.0 CG A:MSE52 4.6 34.4 1.0 N A:THR53 4.8 28.1 1.0 N A:PHE50 4.8 29.8 1.0 CA A:MSE52 4.9 30.1 1.0 O A:HOH1144 4.9 45.7 1.0 O A:PHE50 5.0 28.8 1.0

Magnesium binding site 2 out of 2 in the X-Ray Structure of Mouse Pyrimidine 5'-Nucleotidase Type 1, with Bound Magnesium(II)


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, with Bound Magnesium(II) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg901 b:35.2 occ:1.00 OD2 B:ASP49 2.2 43.3 1.0 O B:ASP51 2.2 33.6 1.0 OD1 B:ASP238 2.2 41.7 1.0 O B:HOH1408 2.4 29.5 1.0 O B:HOH1407 2.4 25.0 1.0 O B:HOH1360 2.7 36.6 1.0 CG B:ASP49 3.0 39.3 1.0 CG B:ASP238 3.1 34.2 1.0 C B:ASP51 3.3 29.7 1.0 OD1 B:ASP49 3.3 38.1 1.0 OD2 B:ASP238 3.4 32.2 1.0 O B:HOH1410 3.8 29.7 1.0 N B:ASP51 3.8 26.5 1.0 CA B:ASP51 3.8 29.1 1.0 CB B:ASP51 3.9 29.4 1.0 O B:HOH1409 4.0 19.8 1.0 OG1 B:THR53 4.0 33.6 1.0 O B:HOH1043 4.2 24.1 1.0 O B:HOH1094 4.2 46.0 1.0 CB B:ASP49 4.3 31.9 1.0 N B:MSE52 4.4 27.9 1.0 O B:HOH1068 4.4 41.7 1.0 OD2 B:ASP242 4.4 26.3 1.0 C B:PHE50 4.4 27.8 1.0 CB B:ASP238 4.5 31.5 1.0 CB B:MSE52 4.6 29.4 1.0 N B:PHE50 4.7 29.5 1.0 CG B:MSE52 4.7 33.1 1.0 N B:THR53 4.7 28.0 1.0 CA B:MSE52 4.8 29.9 1.0 CB B:THR53 4.9 26.7 1.0 O B:PHE50 4.9 29.4 1.0 C B:MSE52 4.9 26.9 1.0 N B:ASP238 4.9 30.4 1.0 O B:HOH1131 5.0 37.7 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