Sodium 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:

Magnesium

(Mg)

2 atoms

The binding sites of Sodium 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 Sodium atom.
In total only one binding site of Sodium was determined in the High Resolutin Structure of Human Cytosolic 5'(3')- Deoxyribonucleotidase, PDB code: 4l57:

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


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na 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:Na208 b:43.0 occ:1.00 O A:HOH423 2.6 31.3 1.0 O A:LEU90 2.6 14.8 1.0 O A:ASN88 2.6 17.0 1.0 O A:HOH429 2.7 31.8 1.0 O A:THR93 3.0 16.2 1.0 C A:ASN88 3.6 14.4 1.0 C A:LEU90 3.6 13.7 1.0 C A:ASP89 3.9 17.6 1.0 N A:LEU90 4.0 13.3 1.0 C A:THR93 4.1 11.8 1.0 CA A:ASP89 4.2 17.9 1.0 O A:ASP89 4.3 22.6 1.0 N A:ASP89 4.3 15.0 1.0 N A:THR93 4.3 12.0 1.0 CA A:LEU90 4.4 13.7 1.0 CB A:THR93 4.5 10.8 1.0 CA A:THR93 4.6 10.3 1.0 N A:PRO91 4.6 15.9 1.0 CA A:ASN88 4.7 13.1 1.0 CA A:PRO91 4.7 17.0 1.0 O A:MET87 4.7 10.7 1.0 O A:HOH508 4.7 35.2 1.0 N A:ASP92 4.8 13.6 1.0 C A:PRO91 4.8 14.7 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