Magnesium in PDB 4l57: High Resolutin Structure of Human Cytosolic 5'(3')- Deoxyribonucleotidase

The structure of High Resolutin Structure of Human Cytosolic 5'(3')- Deoxyribonucleotidase, PDB code: 4l57 was solved by P.Pachl, J.Brynda, P.Rezacova, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	22.48 / 1.08
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	39.128, 46.493, 61.409, 68.16, 81.47, 75.28
R / Rfree (%)	14.4 / 18.3

The structure of High Resolutin Structure of Human Cytosolic 5'(3')- Deoxyribonucleotidase also contains other interesting chemical elements:

Sodium

(Na)

1 atom

The binding sites of Magnesium atom in the High Resolutin Structure of Human Cytosolic 5'(3')- Deoxyribonucleotidase (pdb code 4l57). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the High Resolutin Structure of Human Cytosolic 5'(3')- Deoxyribonucleotidase, PDB code: 4l57:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the High Resolutin Structure of Human Cytosolic 5'(3')- Deoxyribonucleotidase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of High Resolutin Structure of Human Cytosolic 5'(3')- Deoxyribonucleotidase within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg201 b:6.7 occ:1.00 OD1 A:ASP145 2.0 7.2 1.0 O A:HOH320 2.1 9.0 1.0 O A:ASP12 2.1 7.7 1.0 O A:HOH311 2.1 7.0 1.0 O2 A:PO4202 2.1 8.0 1.0 OD2 A:ASP10 2.1 7.9 1.0 CG A:ASP10 3.1 7.8 1.0 CG A:ASP145 3.1 7.5 1.0 C A:ASP12 3.2 6.7 1.0 OD1 A:ASP10 3.4 8.4 1.0 OD2 A:ASP145 3.6 10.2 1.0 P A:PO4202 3.7 7.9 1.0 OD1 A:ASP144 3.9 7.9 1.0 CA A:ASP12 4.0 7.0 1.0 CB A:ASP12 4.0 7.5 1.0 N A:ASP12 4.2 6.9 1.0 O A:HOH326 4.2 13.7 1.0 O1 A:PO4202 4.2 9.3 1.0 N A:GLY13 4.2 7.0 1.0 O A:HOH301 4.3 9.3 1.0 N A:ASP145 4.3 6.6 1.0 CB A:ASP145 4.4 7.3 1.0 O3 A:PO4202 4.4 9.2 1.0 CB A:ASP10 4.4 7.7 1.0 O4 A:PO4202 4.4 8.6 1.0 CE1 A:PHE44 4.4 11.3 1.0 O3 A:GOL204 4.5 20.7 1.0 CA A:GLY13 4.5 7.7 1.0 CG A:ASP144 4.6 7.1 1.0 CZ A:PHE44 4.7 12.4 1.0 N A:LYS146 4.7 6.4 1.0 CA A:ASP145 4.8 6.8 1.0 C A:MET11 4.9 6.8 1.0 OD2 A:ASP144 4.9 9.2 1.0

Magnesium binding site 2 out of 2 in the High Resolutin Structure of Human Cytosolic 5'(3')- Deoxyribonucleotidase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of High Resolutin Structure of Human Cytosolic 5'(3')- Deoxyribonucleotidase within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg201 b:8.6 occ:1.00 OD1 B:ASP145 2.0 9.2 1.0 O B:HOH315 2.0 10.0 1.0 O B:HOH314 2.1 9.0 1.0 O B:ASP12 2.1 8.9 1.0 O2 B:PO4202 2.1 9.6 1.0 OD2 B:ASP10 2.1 9.5 1.0 CG B:ASP10 3.1 9.6 1.0 CG B:ASP145 3.1 8.5 1.0 C B:ASP12 3.2 8.2 1.0 OD1 B:ASP10 3.4 9.9 1.0 OD2 B:ASP145 3.6 12.0 1.0 P B:PO4202 3.7 9.0 1.0 OD1 B:ASP144 3.9 9.7 1.0 CA B:ASP12 4.0 8.3 1.0 CB B:ASP12 4.0 8.4 1.0 O B:HOH335 4.1 15.4 1.0 N B:ASP12 4.2 8.0 1.0 O B:HOH371 4.2 24.3 1.0 O1 B:PO4202 4.2 10.6 1.0 N B:GLY13 4.2 8.8 1.0 O B:HOH301 4.2 10.4 1.0 N B:ASP145 4.3 8.7 1.0 CB B:ASP145 4.4 9.1 1.0 CB B:ASP10 4.4 9.4 1.0 O4 B:PO4202 4.4 8.9 1.0 O3 B:PO4202 4.5 10.6 1.0 CA B:GLY13 4.5 9.5 1.0 CE1 B:PHE44 4.5 12.8 1.0 CG B:ASP144 4.6 8.8 1.0 CZ B:PHE44 4.7 12.3 1.0 N B:LYS146 4.8 9.1 1.0 CA B:ASP145 4.8 8.6 1.0 C B:MET11 4.9 7.5 1.0 CG2 B:VAL14 4.9 10.0 1.0 OD2 B:ASP144 4.9 10.7 1.0

P.Pachl, M.Fabry, I.Rosenberg, O.Simak, P.Rezacova, J.Brynda. Structures of Human Cytosolic and Mitochondrial Nucleotidases: Implications For Structure-Based Design of Selective Inhibitors Acta Crystallogr.,Sect.D V. 70 461 2014.
ISSN: ISSN 0907-4449
DOI: 10.1107/S139900471303050