Sodium in PDB 9k73: Crystal Structure of Tsabgl

All present enzymatic activity of Crystal Structure of Tsabgl:
3.2.1.21;

The structure of Crystal Structure of Tsabgl, PDB code: 9k73 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)	49.34 / 1.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	64.686, 71.545, 98.674, 90, 90, 90
R / Rfree (%)	14.4 / 17.8

The binding sites of Sodium atom in the Crystal Structure of Tsabgl (pdb code 9k73). 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 Tsabgl, PDB code: 9k73:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Crystal Structure of Tsabgl


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 Tsabgl within 5.0Å range: probe atom residue distance (Å) B Occ A:Na502 b:17.9 occ:1.00 O A:GLY49 2.6 11.0 1.0 O A:TYR17 2.7 8.4 1.0 N A:GLY21 2.8 9.4 1.0 O A:HOH766 3.0 12.2 1.0 CA A:GLY21 3.4 8.7 1.0 C A:TYR17 3.5 8.3 1.0 C A:GLY49 3.6 10.5 1.0 CA A:TYR17 3.7 7.0 1.0 CA A:GLY49 3.8 10.7 1.0 CB A:ALA52 3.8 11.2 1.0 CD1 A:TYR17 3.9 10.8 1.0 N A:GLU20 3.9 8.1 1.0 O A:SER16 3.9 10.2 1.0 C A:GLU20 3.9 11.6 1.0 O A:GLY21 4.1 9.9 1.0 C A:GLY21 4.2 11.7 1.0 CE1 A:TYR17 4.2 12.7 1.0 CG A:TYR17 4.2 7.6 1.0 CA A:GLU20 4.3 8.0 1.0 CB A:GLU20 4.5 8.1 1.0 C A:VAL19 4.6 8.4 1.0 CB A:TYR17 4.6 5.8 1.0 N A:GLN18 4.6 6.8 1.0 N A:VAL19 4.7 7.4 1.0 C A:SER16 4.8 11.2 1.0 N A:TYR17 4.8 8.5 1.0 N A:ASP50 4.8 9.5 1.0 CZ A:TYR17 4.9 13.0 1.0 CD2 A:TYR17 4.9 9.7 1.0 O A:HOH752 4.9 12.4 1.0 C A:GLN18 4.9 8.7 1.0

Sodium binding site 2 out of 3 in the Crystal Structure of Tsabgl


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 Tsabgl within 5.0Å range: probe atom residue distance (Å) B Occ A:Na503 b:22.6 occ:1.00 O A:HOH1045 2.6 30.2 1.0 O A:SER37 2.8 14.5 0.5 O A:SER46 2.8 12.6 1.0 O A:SER37 2.8 14.5 0.5 ND2 A:ASN48 2.9 15.2 1.0 C A:SER37 3.5 12.4 0.5 C A:SER37 3.5 12.4 0.5 CB A:ASN48 3.7 11.8 1.0 C A:SER46 3.7 18.6 1.0 CG A:ASN48 3.8 14.4 1.0 CA A:ARG38 3.9 15.5 1.0 CG A:ARG38 3.9 11.6 1.0 N A:ARG38 4.0 14.2 1.0 O A:HIS47 4.0 8.7 1.0 CB A:SER46 4.1 23.3 1.0 CA A:SER46 4.2 13.8 1.0 OG A:SER37 4.2 10.8 0.5 C A:HIS47 4.3 9.3 1.0 CB A:SER37 4.3 12.3 0.5 CB A:SER37 4.3 12.3 0.5 CB A:ARG38 4.5 12.0 1.0 O A:HOH839 4.5 42.9 1.0 N A:ASN48 4.5 8.7 1.0 CA A:SER37 4.6 11.8 0.5 CA A:SER37 4.6 11.8 0.5 CA A:ASN48 4.7 10.3 1.0 N A:HIS47 4.7 12.3 1.0 OD1 A:ASN48 4.9 14.2 1.0 CA A:HIS47 5.0 11.9 1.0

Sodium binding site 3 out of 3 in the Crystal Structure of Tsabgl


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 Tsabgl within 5.0Å range: probe atom residue distance (Å) B Occ A:Na504 b:27.3 occ:1.00 O A:HOH712 2.7 41.2 1.0 O A:HOH829 2.8 33.6 1.0 N A:LEU286 2.9 11.3 1.0 CE1 A:PHE253 3.5 16.1 1.0 CA A:LYS285 3.6 15.2 1.0 CB A:LEU286 3.7 11.7 1.0 CD A:LYS285 3.7 25.9 1.0 C A:LYS285 3.7 14.0 1.0 CD1 A:PHE253 3.7 17.1 1.0 CA A:LEU286 3.8 11.6 1.0 CG A:LEU286 3.9 11.1 1.0 O A:GLN284 4.1 13.8 1.0 CE A:LYS285 4.1 30.8 1.0 O A:HOH902 4.1 41.0 1.0 SD A:MET345 4.1 26.0 1.0 O A:LEU286 4.1 11.2 1.0 C A:LEU286 4.4 13.9 1.0 CG A:LYS285 4.4 20.6 1.0 CB A:LYS285 4.5 17.1 1.0 NZ A:LYS285 4.5 41.7 1.0 CD1 A:LEU286 4.5 8.5 1.0 N A:LYS285 4.6 13.7 1.0 C A:GLN284 4.7 15.6 1.0 CZ A:PHE253 4.8 14.4 1.0 O A:LYS285 4.9 12.3 1.0 CE A:MET345 4.9 20.6 1.0 O A:LEU252 5.0 11.2 1.0

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