Sodium in PDB 4iic: Crystal Structure of Beta-Glucosidase 1 From Aspergillus Aculeatus in Complex with Isofagomine

All present enzymatic activity of Crystal Structure of Beta-Glucosidase 1 From Aspergillus Aculeatus in Complex with Isofagomine:
3.2.1.21;

The structure of Crystal Structure of Beta-Glucosidase 1 From Aspergillus Aculeatus in Complex with Isofagomine, PDB code: 4iic was solved by K.Suzuki, J.Sumitani, T.Kawaguchi, S.Fushinobu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.23 / 1.90
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	82.142, 122.478, 222.107, 90.00, 90.00, 90.00
R / Rfree (%)	14.5 / 18.4

The binding sites of Sodium atom in the Crystal Structure of Beta-Glucosidase 1 From Aspergillus Aculeatus in Complex with Isofagomine (pdb code 4iic). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of Beta-Glucosidase 1 From Aspergillus Aculeatus in Complex with Isofagomine, PDB code: 4iic:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Beta-Glucosidase 1 From Aspergillus Aculeatus in Complex with Isofagomine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Beta-Glucosidase 1 From Aspergillus Aculeatus in Complex with Isofagomine within 5.0Å range: probe atom residue distance (Å) B Occ A:Na943 b:26.4 occ:1.00 OD1 A:ASN539 2.3 31.0 1.0 O7 A:NAG932 2.3 24.2 1.0 O A:HOH1326 2.4 26.9 1.0 O3 A:NAG932 2.4 19.5 1.0 O A:ASN539 2.5 15.6 1.0 O A:HOH1631 2.5 36.6 1.0 CG A:ASN539 3.1 27.8 1.0 C7 A:NAG932 3.3 21.5 1.0 C3 A:NAG932 3.4 19.8 1.0 C A:ASN539 3.4 18.6 1.0 C2 A:NAG932 3.5 17.9 1.0 CA A:ASN539 3.7 18.4 1.0 N2 A:NAG932 3.8 19.2 1.0 ND2 A:ASN539 3.9 29.8 1.0 O5 A:NAG933 3.9 24.9 1.0 CB A:ASN539 4.0 22.1 1.0 C4 A:NAG932 4.0 20.6 1.0 O A:HOH1630 4.0 41.3 1.0 C6 A:NAG933 4.3 32.0 1.0 C5 A:NAG933 4.3 28.6 1.0 C8 A:NAG932 4.5 24.0 1.0 C1 A:NAG933 4.5 22.9 1.0 N A:ASN540 4.7 14.7 1.0 O4 A:NAG932 4.8 22.0 1.0 C1 A:NAG932 4.9 18.9 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Beta-Glucosidase 1 From Aspergillus Aculeatus in Complex with Isofagomine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Beta-Glucosidase 1 From Aspergillus Aculeatus in Complex with Isofagomine within 5.0Å range: probe atom residue distance (Å) B Occ B:Na949 b:29.7 occ:1.00 OD1 B:ASN539 2.3 29.7 1.0 O7 B:NAG936 2.4 20.7 1.0 O B:HOH1721 2.4 30.5 1.0 O B:HOH1686 2.4 35.2 1.0 O3 B:NAG936 2.4 21.2 1.0 O B:ASN539 2.5 16.4 1.0 CG B:ASN539 3.2 26.6 1.0 C7 B:NAG936 3.3 16.1 1.0 C B:ASN539 3.4 17.1 1.0 C3 B:NAG936 3.4 19.4 1.0 C2 B:NAG936 3.5 15.6 1.0 CA B:ASN539 3.7 17.4 1.0 N2 B:NAG936 3.7 16.7 1.0 ND2 B:ASN539 4.0 28.3 1.0 CB B:ASN539 4.0 19.4 1.0 C4 B:NAG936 4.1 20.1 1.0 O5 B:NAG937 4.1 28.2 1.0 O B:HOH1536 4.2 30.7 1.0 C8 B:NAG936 4.5 18.6 1.0 C5 B:NAG937 4.5 35.9 1.0 C6 B:NAG937 4.5 36.1 1.0 C1 B:NAG937 4.7 25.0 1.0 N B:ASN540 4.7 15.8 1.0 C1 B:NAG936 4.9 16.8 1.0 O4 B:NAG936 4.9 21.2 1.0

K.Suzuki, J.Sumitani, Y.W.Nam, T.Nishimaki, S.Tani, T.Wakagi, T.Kawaguchi, S.Fushinobu. Crystal Structures of Glycoside Hydrolase Family 3 Beta-Glucosidase 1 From Aspergillus Aculeatus Biochem.J. V. 452 211 2013.
ISSN: ISSN 0264-6021
PubMed: 23537284
DOI: 10.1042/BJ20130054