Sodium in PDB 8wfv: Crystal Structure of Beta-Glucosidase From Thermoanaerobacterium Saccharolyticum (Data 3)

The structure of Crystal Structure of Beta-Glucosidase From Thermoanaerobacterium Saccharolyticum (Data 3), PDB code: 8wfv 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)	49.44 / 1.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	64.97, 70.948, 98.876, 90, 90, 90
R / Rfree (%)	15.5 / 17.1

The binding sites of Sodium atom in the Crystal Structure of Beta-Glucosidase From Thermoanaerobacterium Saccharolyticum (Data 3) (pdb code 8wfv). 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 (Data 3), PDB code: 8wfv:
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 (Data 3)


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 (Data 3) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na502 b:13.9 occ:1.00 O A:GLY49 2.7 7.4 1.0 O A:HOH817 2.8 7.9 1.0 O A:TYR17 2.8 6.8 1.0 N A:GLY21 2.9 7.3 1.0 CA A:GLY21 3.4 6.6 1.0 C A:TYR17 3.5 7.0 1.0 C A:GLY49 3.6 7.0 1.0 CA A:TYR17 3.7 6.6 1.0 CD1 A:TYR17 3.8 9.9 1.0 N A:GLU20 3.8 6.2 1.0 CA A:GLY49 3.8 8.1 1.0 CB A:ALA52 3.9 8.0 1.0 O A:SER16 3.9 6.7 1.0 C A:GLU20 4.0 8.2 1.0 O A:GLY21 4.1 7.7 1.0 CE1 A:TYR17 4.2 9.2 1.0 C A:GLY21 4.2 8.6 1.0 CA A:GLU20 4.2 5.7 1.0 CG A:TYR17 4.2 8.7 1.0 CB A:GLU20 4.4 6.9 1.0 C A:VAL19 4.5 6.5 1.0 CB A:TYR17 4.6 7.8 1.0 N A:GLN18 4.6 4.8 1.0 N A:VAL19 4.7 7.3 1.0 C A:SER16 4.8 6.2 1.0 N A:TYR17 4.8 7.3 1.0 O A:HOH763 4.8 10.8 1.0 N A:ASP50 4.9 8.3 1.0 CZ A:TYR17 4.9 8.6 1.0 C A:GLN18 4.9 7.4 1.0 CD2 A:TYR17 4.9 9.7 1.0

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


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 (Data 3) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na503 b:19.1 occ:1.00 O A:HOH1205 2.7 25.1 1.0 O A:SER46 2.8 11.2 1.0 O A:SER37 2.8 11.5 0.5 O A:SER37 2.8 11.5 0.5 ND2 A:ASN48 3.0 12.5 1.0 C A:SER37 3.5 11.1 0.5 C A:SER37 3.5 11.1 0.5 C A:SER46 3.6 12.1 1.0 CB A:ASN48 3.7 9.8 1.0 CA A:ARG38 3.8 10.7 1.0 CG A:ASN48 3.8 11.1 1.0 CG A:ARG38 3.8 11.9 1.0 N A:ARG38 3.9 10.5 1.0 O A:HIS47 3.9 10.3 1.0 CB A:SER46 4.0 16.6 1.0 CA A:SER46 4.1 11.6 1.0 C A:HIS47 4.2 7.4 1.0 OG A:SER37 4.2 10.6 0.5 O A:HOH827 4.3 29.2 1.0 CB A:SER37 4.3 9.5 0.5 CB A:SER37 4.3 9.6 0.5 CB A:ARG38 4.4 10.6 1.0 CA A:SER37 4.5 9.2 0.5 N A:ASN48 4.5 8.0 1.0 CA A:SER37 4.5 9.2 0.5 O A:HOH1081 4.6 37.0 1.0 N A:HIS47 4.6 9.6 1.0 CA A:ASN48 4.7 7.3 1.0 CA A:HIS47 4.9 7.6 1.0 C A:ARG38 5.0 16.0 1.0 OD1 A:ASN48 5.0 9.9 1.0

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


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 (Data 3) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na504 b:19.8 occ:1.00 N A:LEU286 2.9 8.5 1.0 O A:HOH926 2.9 25.9 1.0 O A:HOH862 2.9 17.6 1.0 O A:HOH951 3.1 27.8 1.0 CE A:MET345 3.2 19.8 1.0 CA A:LYS285 3.5 6.7 1.0 CE1 A:PHE253 3.6 13.2 1.0 C A:LYS285 3.6 8.4 1.0 CB A:LEU286 3.7 7.0 1.0 CD A:LYS285 3.7 10.0 1.0 CD1 A:PHE253 3.8 13.0 1.0 CA A:LEU286 3.8 7.1 1.0 CG A:LEU286 3.8 8.0 1.0 O A:GLN284 3.8 10.7 1.0 O A:LEU286 4.2 10.3 1.0 CE A:LYS285 4.4 12.8 1.0 CG A:LYS285 4.4 9.6 1.0 C A:LEU286 4.4 10.2 1.0 N A:LYS285 4.4 8.5 1.0 CB A:LYS285 4.5 13.2 1.0 CD1 A:LEU286 4.5 8.8 1.0 C A:GLN284 4.5 7.7 1.0 O A:HOH783 4.6 26.4 1.0 O A:HOH689 4.6 29.1 1.0 NZ A:LYS285 4.6 14.5 1.0 SD A:MET345 4.6 15.5 1.0 O A:LEU252 4.8 8.8 1.0 O A:LYS285 4.8 9.6 1.0 CZ A:PHE253 4.9 14.2 1.0 O A:HOH710 5.0 9.3 1.0

K.H.Nam, K.H.Nam. N/A N/A.