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

Enzymatic activity of Structure of Alfa-Galactosidase (MEL1) From Saccharomyces Cerevisiae with Melibiose

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

Protein crystallography data

The structure of Structure of Alfa-Galactosidase (MEL1) From Saccharomyces Cerevisiae with Melibiose, PDB code: 3lrl 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) 59.99 / 2.40
Space group P 4 21 2
Cell size a, b, c (Å), α, β, γ (°) 100.729, 100.729, 111.280, 90.00, 90.00, 90.00
R / Rfree (%) 19.8 / 25.3

Sodium Binding Sites:

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

Sodium binding site 1 out of 1 in 3lrl

Go back to Sodium Binding Sites List in 3lrl
Sodium binding site 1 out of 1 in the Structure of Alfa-Galactosidase (MEL1) From Saccharomyces Cerevisiae with Melibiose


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 with Melibiose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na8001

b:11.3
occ:1.00
NE2 A:HIS98 2.3 22.6 1.0
NE2 A:HIS102 2.3 23.8 1.0
CE1 A:HIS98 3.1 23.3 1.0
CD2 A:HIS102 3.2 25.2 1.0
CE1 A:HIS102 3.3 27.3 1.0
CD2 A:HIS98 3.3 25.3 1.0
ND1 A:HIS98 4.2 24.3 1.0
OE2 A:GLU46 4.3 48.8 1.0
CG A:HIS98 4.4 25.6 1.0
CG A:HIS102 4.4 23.3 1.0
ND1 A:HIS102 4.4 23.9 1.0
C8 A:NAG1001 4.7 29.4 1.0

Reference:

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
Page generated: Tue Dec 15 06:16:58 2020

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