Sodium in PDB 9k72: Crystal Structure of Tsabgl Using Merged Datasets

All present enzymatic activity of Crystal Structure of Tsabgl Using Merged Datasets:
3.2.1.21;

The structure of Crystal Structure of Tsabgl Using Merged Datasets, PDB code: 9k72 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)	57.86 / 1.55
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	65.21, 71.12, 99.49, 90, 90, 90
R / Rfree (%)	20.1 / 23.3

The binding sites of Sodium atom in the Crystal Structure of Tsabgl Using Merged Datasets (pdb code 9k72). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 5 binding sites of Sodium where determined in the Crystal Structure of Tsabgl Using Merged Datasets, PDB code: 9k72:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in the Crystal Structure of Tsabgl Using Merged Datasets


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 Using Merged Datasets within 5.0Å range: probe atom residue distance (Å) B Occ A:Na502 b:22.8 occ:1.00 O A:GLY49 2.7 15.2 1.0 O A:HOH715 2.7 16.8 1.0 N A:GLY21 2.8 15.7 1.0 O A:TYR17 2.9 13.4 1.0 CA A:GLY21 3.5 13.9 1.0 C A:TYR17 3.6 14.0 1.0 C A:GLY49 3.7 13.9 1.0 CA A:TYR17 3.7 14.0 1.0 N A:GLU20 3.8 17.9 1.0 O A:SER16 3.9 13.8 1.0 CD1 A:TYR17 3.9 15.4 1.0 C A:GLU20 3.9 14.8 1.0 CA A:GLY49 3.9 14.2 1.0 O A:GLY21 4.0 13.9 1.0 CB A:ALA52 4.0 13.8 1.0 CA A:GLU20 4.2 13.9 1.0 C A:GLY21 4.2 16.1 1.0 CE1 A:TYR17 4.2 16.1 1.0 CB A:GLU20 4.3 13.8 1.0 CG A:TYR17 4.3 15.5 1.0 C A:VAL19 4.5 13.2 1.0 CB A:TYR17 4.6 12.8 1.0 N A:GLN18 4.7 14.3 1.0 N A:VAL19 4.7 13.5 1.0 C A:SER16 4.7 15.2 1.0 N A:TYR17 4.8 12.3 1.0 O A:HOH646 4.8 20.1 1.0 N A:ASP50 4.9 15.3 1.0 CZ A:TYR17 5.0 16.0 1.0 C A:GLN18 5.0 13.5 1.0 CD2 A:TYR17 5.0 15.8 1.0

Sodium binding site 2 out of 5 in the Crystal Structure of Tsabgl Using Merged Datasets


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 Using Merged Datasets within 5.0Å range: probe atom residue distance (Å) B Occ A:Na503 b:27.3 occ:1.00 O A:HOH1030 2.7 31.2 1.0 O A:SER46 2.7 18.0 1.0 ND2 A:ASN48 2.9 17.0 1.0 O A:SER37 3.0 17.9 0.4 O A:SER37 3.0 17.9 0.6 C A:SER37 3.6 17.7 0.4 C A:SER37 3.6 17.7 0.6 C A:SER46 3.7 19.2 1.0 CB A:ASN48 3.8 17.7 1.0 CG A:ASN48 3.8 17.2 1.0 CG A:ARG38 3.9 19.4 1.0 CA A:ARG38 3.9 21.4 1.0 O A:HIS47 4.0 13.8 1.0 N A:ARG38 4.0 15.7 1.0 CB A:SER46 4.0 22.8 1.0 CA A:SER46 4.2 17.8 1.0 C A:HIS47 4.2 15.1 1.0 OG A:SER37 4.2 16.4 0.6 CB A:SER37 4.3 17.7 0.6 CB A:SER37 4.4 17.7 0.4 CB A:ARG38 4.5 19.1 1.0 N A:ASN48 4.5 13.4 1.0 O A:HOH941 4.6 39.0 1.0 CA A:SER37 4.6 16.0 0.4 CA A:SER37 4.6 16.0 0.6 N A:HIS47 4.7 17.9 1.0 CA A:ASN48 4.7 12.9 1.0 CA A:HIS47 4.9 15.3 1.0 OD1 A:ASN48 4.9 16.6 1.0

Sodium binding site 3 out of 5 in the Crystal Structure of Tsabgl Using Merged Datasets


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 Using Merged Datasets within 5.0Å range: probe atom residue distance (Å) B Occ A:Na504 b:27.2 occ:1.00 O A:HOH618 2.7 31.9 1.0 N A:LEU286 2.9 15.2 1.0 O A:HOH852 3.0 27.7 1.0 CE A:MET345 3.3 27.6 1.0 CD A:LYS285 3.5 21.4 1.0 CA A:LYS285 3.6 16.2 1.0 CE1 A:PHE253 3.6 24.3 1.0 C A:LYS285 3.7 17.6 1.0 O A:HOH883 3.7 36.9 1.0 CB A:LEU286 3.7 15.2 1.0 CD1 A:PHE253 3.8 20.2 1.0 CA A:LEU286 3.8 13.9 1.0 CG A:LEU286 3.9 17.5 1.0 O A:GLN284 4.0 16.7 1.0 O A:LEU286 4.2 16.3 1.0 CE A:LYS285 4.3 30.2 1.0 CG A:LYS285 4.4 18.9 1.0 NZ A:LYS285 4.4 24.1 1.0 C A:LEU286 4.5 15.2 1.0 N A:LYS285 4.5 17.6 1.0 CB A:LYS285 4.5 18.7 1.0 SD A:MET345 4.5 25.1 1.0 CD1 A:LEU286 4.6 14.7 1.0 C A:GLN284 4.6 16.0 1.0 O A:LEU252 4.9 16.0 1.0 CZ A:PHE253 4.9 20.8 1.0 O A:LYS285 4.9 17.0 1.0

Sodium binding site 4 out of 5 in the Crystal Structure of Tsabgl Using Merged Datasets


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of Tsabgl Using Merged Datasets within 5.0Å range: probe atom residue distance (Å) B Occ A:Na505 b:33.5 occ:1.00 O A:ASP287 3.0 16.2 1.0 O A:HOH637 3.3 32.0 1.0 C A:ASP287 3.7 18.7 1.0 CG A:PRO346 3.8 18.8 1.0 CB A:ASP287 3.9 15.0 1.0 CB A:PRO346 3.9 21.2 1.0 CG A:LYS214 4.0 25.7 1.0 CB A:PHE288 4.1 13.9 1.0 CD A:LYS214 4.1 34.3 1.0 O A:HOH815 4.1 23.3 1.0 CD2 A:PHE288 4.3 12.6 1.0 CA A:ASP287 4.3 15.2 1.0 CB A:LYS214 4.4 14.7 1.0 N A:PHE288 4.5 15.0 1.0 CE A:LYS214 4.6 36.6 1.0 CD A:PRO346 4.6 18.7 1.0 CG A:PHE288 4.7 15.0 1.0 CA A:PHE288 4.7 12.7 1.0 O A:HOH788 4.8 25.5 1.0 OH A:TYR348 4.9 23.3 1.0 NZ A:LYS214 4.9 29.7 1.0 CE1 A:TYR348 5.0 22.1 1.0

Sodium binding site 5 out of 5 in the Crystal Structure of Tsabgl Using Merged Datasets


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Crystal Structure of Tsabgl Using Merged Datasets within 5.0Å range: probe atom residue distance (Å) B Occ A:Na506 b:27.2 occ:1.00 N A:GLU328 2.9 23.6 1.0 CG A:GLU328 3.0 27.6 1.0 CB A:GLU328 3.1 23.7 1.0 N A:PRO327 3.4 16.8 1.0 CD A:PRO327 3.5 19.7 1.0 CD1 A:TYR326 3.5 19.1 1.0 C A:TYR326 3.6 16.4 1.0 CA A:GLU328 3.6 18.7 1.0 CE1 A:TYR326 3.6 25.8 1.0 CG A:TYR326 3.7 18.0 1.0 CA A:TYR326 3.9 17.0 1.0 CZ A:TYR326 3.9 28.9 1.0 CG A:PRO327 4.0 19.8 1.0 C A:PRO327 4.0 19.0 1.0 CD2 A:TYR326 4.0 15.9 1.0 CE2 A:TYR326 4.1 19.6 1.0 CA A:PRO327 4.1 15.2 1.0 CD A:GLU328 4.2 51.3 1.0 O A:TYR326 4.2 14.1 1.0 CB A:TYR326 4.4 18.7 1.0 CB A:PRO327 4.6 20.2 1.0 O A:HOH1005 4.6 31.5 1.0 OE1 A:GLU328 4.6 51.8 1.0 OH A:TYR326 4.7 27.5 1.0 C A:GLU328 4.8 17.9 1.0 N A:SER329 4.9 17.9 1.0 OE2 A:GLU328 5.0 65.0 1.0

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