Sodium in PDB 5ayi: Crystal Structure of GH1 Beta-Glucosidase TD2F2 N223Q Mutant

All present enzymatic activity of Crystal Structure of GH1 Beta-Glucosidase TD2F2 N223Q Mutant:
3.2.1.21;

The structure of Crystal Structure of GH1 Beta-Glucosidase TD2F2 N223Q Mutant, PDB code: 5ayi was solved by T.Jo, J.A.Manninen, T.Matsuzawa, T.Uchiyama, K.Yaoi, T.Arakawa, S.Fushinobu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.97 / 1.85
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	69.060, 69.803, 96.335, 90.00, 90.00, 90.00
R / Rfree (%)	14 / 17.5

The binding sites of Sodium atom in the Crystal Structure of GH1 Beta-Glucosidase TD2F2 N223Q Mutant (pdb code 5ayi). 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 Crystal Structure of GH1 Beta-Glucosidase TD2F2 N223Q Mutant, PDB code: 5ayi:

Sodium binding site 1 out of 1 in the Crystal Structure of GH1 Beta-Glucosidase TD2F2 N223Q Mutant


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 GH1 Beta-Glucosidase TD2F2 N223Q Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Na502 b:25.2 occ:1.00 O A:HOH667 2.3 13.3 1.0 O A:HOH820 2.4 21.5 1.0 O A:HIS321 2.4 11.7 1.0 O A:HOH796 2.6 28.8 1.0 C A:HIS321 3.5 13.1 1.0 N A:HIS321 4.0 14.2 1.0 O A:HOH919 4.1 23.7 1.0 CA A:HIS321 4.1 13.9 1.0 OE1 A:GLN371 4.2 11.6 1.0 NE2 A:GLN371 4.2 15.8 1.0 O A:HOH904 4.4 24.9 1.0 CB A:HIS321 4.4 17.6 1.0 O A:THR322 4.5 13.5 1.0 N A:THR322 4.5 11.5 1.0 CD A:GLN371 4.6 13.5 1.0 CA A:THR322 4.8 11.9 1.0 C A:THR322 4.9 12.2 1.0

T.Matsuzawa, T.Jo, T.Uchiyama, J.A.Manninen, T.Arakawa, K.Miyazaki, S.Fushinobu, K.Yaoi. Crystal Structure and Identification of A Key Amino Acid For Glucose Tolerance, Substrate Specificity, and Transglycosylation Activity of Metagenomic Beta-Glucosidase TD2F2 Febs J. V. 283 2340 2016.
ISSN: ISSN 1742-464X
PubMed: 27092463
DOI: 10.1111/FEBS.13743