Sodium in PDB 7e5j: Crystal Structure of Beta-Glucosidase From Thermoanaerobacterium Saccharolyticum

All present enzymatic activity of Crystal Structure of Beta-Glucosidase From Thermoanaerobacterium Saccharolyticum:
3.2.1.21;

The structure of Crystal Structure of Beta-Glucosidase From Thermoanaerobacterium Saccharolyticum, PDB code: 7e5j was solved by K.H.Nam, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.67 / 1.71
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	65.139, 71.293, 99.24, 90, 90, 90
R / Rfree (%)	14.1 / 18.2

The binding sites of Sodium atom in the Crystal Structure of Beta-Glucosidase From Thermoanaerobacterium Saccharolyticum (pdb code 7e5j). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Crystal Structure of Beta-Glucosidase From Thermoanaerobacterium Saccharolyticum, PDB code: 7e5j:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Crystal Structure of Beta-Glucosidase From Thermoanaerobacterium Saccharolyticum


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 From Thermoanaerobacterium Saccharolyticum within 5.0Å range: probe atom residue distance (Å) B Occ A:Na502 b:21.4 occ:1.00 O A:GLY49 2.7 13.3 1.0 O A:TYR17 2.8 11.4 1.0 O A:HOH867 2.8 14.0 1.0 N A:GLY21 2.9 11.0 1.0 CA A:GLY21 3.4 11.2 1.0 C A:TYR17 3.5 11.5 1.0 C A:GLY49 3.6 12.9 1.0 CA A:TYR17 3.7 11.7 1.0 CA A:GLY49 3.8 13.3 1.0 CD1 A:TYR17 3.8 14.0 1.0 N A:GLU20 3.9 10.5 1.0 O A:SER16 3.9 11.7 1.0 CB A:ALA52 4.0 12.8 1.0 C A:GLU20 4.0 11.3 1.0 O A:GLY21 4.1 10.1 1.0 CE1 A:TYR17 4.2 13.5 1.0 C A:GLY21 4.3 10.6 1.0 CG A:TYR17 4.3 12.1 1.0 CA A:GLU20 4.3 10.9 1.0 CB A:GLU20 4.5 11.2 1.0 C A:VAL19 4.6 10.6 1.0 CB A:TYR17 4.6 11.4 1.0 N A:GLN18 4.6 11.2 1.0 N A:VAL19 4.7 11.1 1.0 N A:TYR17 4.7 11.7 1.0 O A:HOH685 4.7 14.8 1.0 C A:SER16 4.7 11.6 1.0 CZ A:TYR17 4.9 12.8 1.0 N A:ASP50 4.9 13.7 1.0 CD2 A:TYR17 4.9 12.1 1.0 C A:GLN18 4.9 11.9 1.0

Sodium binding site 2 out of 3 in the Crystal Structure of Beta-Glucosidase From Thermoanaerobacterium Saccharolyticum


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 From Thermoanaerobacterium Saccharolyticum within 5.0Å range: probe atom residue distance (Å) B Occ A:Na503 b:25.3 occ:1.00 O A:HOH1136 2.6 31.6 1.0 O A:SER46 2.6 14.1 1.0 O A:SER37 2.8 15.0 0.6 O A:SER37 2.9 14.8 0.4 ND2 A:ASN48 3.0 15.1 1.0 C A:SER37 3.5 14.6 0.6 C A:SER37 3.5 14.5 0.4 C A:SER46 3.5 15.9 1.0 CB A:ASN48 3.8 13.6 1.0 CG A:ASN48 3.8 14.3 1.0 O A:HIS47 3.9 13.3 1.0 CB A:SER46 3.9 19.0 1.0 CA A:ARG38 3.9 15.6 1.0 N A:ARG38 4.0 15.4 1.0 CG A:ARG38 4.0 16.1 1.0 CA A:SER46 4.0 15.6 1.0 O A:HOH757 4.1 39.1 1.0 OG A:SER37 4.1 17.4 0.6 O A:HOH1123 4.1 53.9 1.0 C A:HIS47 4.1 12.7 1.0 CB A:SER37 4.3 14.3 0.4 CB A:SER37 4.4 15.2 0.6 N A:ASN48 4.4 12.4 1.0 CA A:SER37 4.5 14.4 0.4 CB A:ARG38 4.5 16.4 1.0 CA A:SER37 4.5 14.9 0.6 N A:HIS47 4.6 13.8 1.0 CA A:ASN48 4.7 12.9 1.0 CA A:HIS47 4.8 13.4 1.0 OG A:SER46 5.0 20.1 1.0 OD1 A:ASN48 5.0 12.9 1.0

Sodium binding site 3 out of 3 in the Crystal Structure of Beta-Glucosidase From Thermoanaerobacterium Saccharolyticum


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of Beta-Glucosidase From Thermoanaerobacterium Saccharolyticum within 5.0Å range: probe atom residue distance (Å) B Occ A:Na504 b:26.0 occ:1.00 O A:HOH810 2.7 34.8 1.0 O A:HOH837 2.7 27.1 1.0 N A:LEU286 3.0 13.5 1.0 O A:HOH944 3.1 48.1 1.0 CE A:MET345 3.3 28.3 1.0 CE1 A:PHE253 3.6 14.5 1.0 CA A:LYS285 3.6 15.2 1.0 CB A:LEU286 3.7 12.3 1.0 CD1 A:PHE253 3.7 13.7 1.0 C A:LYS285 3.8 15.0 1.0 CG A:LEU286 3.8 12.7 1.0 CD A:LYS285 3.9 20.3 1.0 CA A:LEU286 3.9 13.1 1.0 O A:GLN284 3.9 14.3 1.0 O A:LEU286 4.3 14.0 1.0 O A:HOH824 4.4 37.5 1.0 CD1 A:LEU286 4.5 12.4 1.0 CE A:LYS285 4.5 24.4 1.0 N A:LYS285 4.5 14.7 1.0 O A:HOH719 4.6 41.8 1.0 C A:LEU286 4.6 13.0 1.0 SD A:MET345 4.6 23.7 1.0 C A:GLN284 4.6 15.3 1.0 CG A:LYS285 4.6 18.4 1.0 CB A:LYS285 4.6 17.4 1.0 NZ A:LYS285 4.7 27.0 1.0 O A:LEU252 4.7 13.0 1.0 CZ A:PHE253 4.8 14.3 1.0 O A:HOH778 4.9 12.8 1.0 O A:LYS285 5.0 15.7 1.0 O A:SER283 5.0 14.2 1.0

I.J.Kim, U.T.Bornscheuer, K.H.Nam. Biochemical and Structural Analysis of A Glucose-Tolerant Beta-Glucosidase From the Hemicellulose-Degrading Thermoanaerobacterium Saccharolyticum. Molecules V. 27 2022.
ISSN: ESSN 1420-3049
PubMed: 35011521
DOI: 10.3390/MOLECULES27010290