Sodium in PDB 3lrk: Structure of Alfa-Galactosidase (MEL1) From Saccharomyces Cerevisiae

All present enzymatic activity of Structure of Alfa-Galactosidase (MEL1) From Saccharomyces Cerevisiae:
3.2.1.22;

The structure of Structure of Alfa-Galactosidase (MEL1) From Saccharomyces Cerevisiae, PDB code: 3lrk was solved by R.Fernandez-Leiro, A.Pereira-Rodriguez, M.E.Cerdan, M.Becerra, J.Sanz-Aparicio, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	111.52 / 1.95
Space group	P 4 21 2
Cell size a, b, c (Å), α, β, γ (°)	101.243, 101.243, 111.521, 90.00, 90.00, 90.00
R / Rfree (%)	20.4 / 23.4

The binding sites of Sodium atom in the Structure of Alfa-Galactosidase (MEL1) From Saccharomyces Cerevisiae (pdb code 3lrk). 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 Structure of Alfa-Galactosidase (MEL1) From Saccharomyces Cerevisiae, PDB code: 3lrk:

Sodium binding site 1 out of 1 in the Structure of Alfa-Galactosidase (MEL1) From Saccharomyces Cerevisiae


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of Alfa-Galactosidase (MEL1) From Saccharomyces Cerevisiae within 5.0Å range: probe atom residue distance (Å) B Occ A:Na8001 b:18.1 occ:1.00 O8 A:BTB9001 2.2 33.1 1.0 O3 A:BTB9001 2.2 30.2 1.0 O6 A:BTB9001 2.2 27.4 1.0 O1 A:BTB9001 2.2 32.2 1.0 NE2 A:HIS102 2.3 23.9 1.0 NE2 A:HIS98 2.3 24.7 1.0 N A:BTB9001 2.3 29.0 1.0 C2 A:BTB9001 2.9 30.7 1.0 C5 A:BTB9001 3.0 29.7 1.0 C3 A:BTB9001 3.1 30.6 1.0 C6 A:BTB9001 3.1 30.1 1.0 C1 A:BTB9001 3.1 31.5 1.0 CD2 A:HIS98 3.2 23.9 1.0 CD2 A:HIS102 3.2 22.8 1.0 CE1 A:HIS102 3.3 24.3 1.0 CE1 A:HIS98 3.3 23.4 1.0 C8 A:BTB9001 3.4 31.1 1.0 C7 A:BTB9001 3.4 30.5 1.0 OE2 A:GLU46 4.1 37.2 1.0 CG A:HIS98 4.3 23.4 1.0 ND1 A:HIS98 4.4 24.1 1.0 CG A:HIS102 4.4 23.1 1.0 ND1 A:HIS102 4.4 24.1 1.0 C4 A:BTB9001 4.4 32.1 1.0 C8 A:NAG1001 4.7 26.8 1.0 ND2 A:ASN94 4.9 26.5 1.0

R.Fernandez-Leiro, A.Pereira-Rodriguez, M.E.Cerdan, M.Becerra, J.Sanz-Aparicio. Structural Analysis of Saccharomyces Cerevisiae Alpha-Galactosidase and Its Complexes with Natural Substrates Reveals New Insights Into Substrate Specificity of GH27 Glycosidases. J.Biol.Chem. V. 285 28020 2010.
ISSN: ISSN 0021-9258
PubMed: 20592022
DOI: 10.1074/JBC.M110.144584