Sodium in PDB 4iie: Crystal Structure of Beta-Glucosidase 1 From Aspergillus Aculeatus in Complex with Calystegine B(2)

All present enzymatic activity of Crystal Structure of Beta-Glucosidase 1 From Aspergillus Aculeatus in Complex with Calystegine B(2):
3.2.1.21;

The structure of Crystal Structure of Beta-Glucosidase 1 From Aspergillus Aculeatus in Complex with Calystegine B(2), PDB code: 4iie 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)	39.07 / 2.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	82.130, 122.147, 222.091, 90.00, 90.00, 90.00
R / Rfree (%)	14.9 / 19.3

The binding sites of Sodium atom in the Crystal Structure of Beta-Glucosidase 1 From Aspergillus Aculeatus in Complex with Calystegine B(2) (pdb code 4iie). 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 Calystegine B(2), PDB code: 4iie:
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 Calystegine B(2)


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 Calystegine B(2) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na942 b:29.9 occ:1.00 O A:HOH1577 2.3 35.5 1.0 OD1 A:ASN539 2.3 33.8 1.0 O A:HOH1578 2.3 33.3 1.0 O7 A:NAG931 2.3 26.1 1.0 O3 A:NAG931 2.4 22.2 1.0 O A:ASN539 2.6 22.0 1.0 CG A:ASN539 3.2 34.4 1.0 C7 A:NAG931 3.3 24.5 1.0 C3 A:NAG931 3.4 25.5 1.0 C A:ASN539 3.5 22.1 1.0 C2 A:NAG931 3.5 23.0 1.0 CA A:ASN539 3.7 22.5 1.0 N2 A:NAG931 3.9 21.8 1.0 ND2 A:ASN539 4.0 34.2 1.0 CB A:ASN539 4.0 22.8 1.0 O5 A:NAG932 4.0 26.8 1.0 C4 A:NAG931 4.1 22.7 1.0 O A:HOH1576 4.1 36.5 1.0 C6 A:NAG932 4.2 36.2 1.0 C5 A:NAG932 4.3 32.2 1.0 C8 A:NAG931 4.5 22.0 1.0 C1 A:NAG932 4.6 23.7 1.0 N A:ASN540 4.7 19.7 1.0 O4 A:NAG931 4.8 23.5 1.0 C1 A:NAG931 4.9 22.5 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Beta-Glucosidase 1 From Aspergillus Aculeatus in Complex with Calystegine B(2)


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 Calystegine B(2) within 5.0Å range: probe atom residue distance (Å) B Occ B:Na951 b:32.9 occ:1.00 OD1 B:ASN539 2.2 36.0 1.0 O7 B:NAG938 2.3 21.8 1.0 O3 B:NAG938 2.4 23.9 1.0 O B:HOH1695 2.4 34.8 1.0 O B:ASN539 2.5 18.1 1.0 O B:HOH1712 2.6 43.6 1.0 CG B:ASN539 3.2 29.1 1.0 C7 B:NAG938 3.3 19.5 1.0 C2 B:NAG938 3.4 19.7 1.0 C3 B:NAG938 3.4 23.3 1.0 C B:ASN539 3.4 19.2 1.0 CA B:ASN539 3.6 18.3 1.0 N2 B:NAG938 3.7 20.6 1.0 CB B:ASN539 4.0 21.9 1.0 ND2 B:ASN539 4.1 35.6 1.0 C4 B:NAG938 4.1 22.3 1.0 O5 B:NAG939 4.2 31.7 1.0 O B:HOH1687 4.3 34.7 1.0 C8 B:NAG938 4.5 21.1 1.0 C6 B:NAG939 4.6 35.0 1.0 C5 B:NAG939 4.6 40.0 1.0 N B:ASN540 4.7 16.7 1.0 C1 B:NAG939 4.8 26.7 1.0 C1 B:NAG938 4.8 19.2 1.0 O4 B:NAG938 5.0 24.4 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