Sodium in PDB 8xpe: Crystal Structure of Tris-Bound Tsabgl (Data III)

All present enzymatic activity of Crystal Structure of Tris-Bound Tsabgl (Data III):
3.2.1.21;

The structure of Crystal Structure of Tris-Bound Tsabgl (Data III), PDB code: 8xpe 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)	49.50 / 1.95
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	64.939, 70.815, 98.993, 90, 90, 90
R / Rfree (%)	14 / 17.8

The binding sites of Sodium atom in the Crystal Structure of Tris-Bound Tsabgl (Data III) (pdb code 8xpe). 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 Tris-Bound Tsabgl (Data III), PDB code: 8xpe:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in the Crystal Structure of Tris-Bound Tsabgl (Data III)


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 Tris-Bound Tsabgl (Data III) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na502 b:22.4 occ:1.00 O A:GLY49 2.7 13.1 1.0 N A:GLY21 2.7 11.4 1.0 O A:HOH738 2.8 13.1 1.0 O A:TYR17 2.9 14.0 1.0 CA A:GLY21 3.3 10.8 1.0 C A:TYR17 3.6 15.4 1.0 C A:GLY49 3.7 10.0 1.0 N A:GLU20 3.8 9.8 1.0 CA A:TYR17 3.8 9.0 1.0 CB A:ALA52 3.8 10.4 1.0 C A:GLU20 3.8 12.0 1.0 O A:GLY21 3.9 12.8 1.0 O A:SER16 3.9 14.4 1.0 CA A:GLY49 3.9 14.6 1.0 CD1 A:TYR17 3.9 16.6 1.0 C A:GLY21 4.0 13.9 1.0 CA A:GLU20 4.1 13.1 1.0 CE1 A:TYR17 4.3 11.9 1.0 CB A:GLU20 4.3 8.8 1.0 CG A:TYR17 4.4 16.6 1.0 C A:VAL19 4.5 9.5 1.0 N A:VAL19 4.7 12.2 1.0 N A:GLN18 4.7 12.5 1.0 O A:HOH708 4.8 15.0 1.0 CB A:TYR17 4.8 10.9 1.0 C A:SER16 4.8 12.4 1.0 N A:TYR17 4.8 9.1 1.0 N A:ASP50 4.9 11.6 1.0 C A:GLN18 4.9 10.7 1.0 O A:GLU20 4.9 10.8 1.0 CZ A:TYR17 5.0 14.6 1.0

Sodium binding site 2 out of 5 in the Crystal Structure of Tris-Bound Tsabgl (Data III)


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 Tris-Bound Tsabgl (Data III) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na503 b:30.7 occ:1.00 O A:HOH1083 2.6 29.6 1.0 O A:SER46 2.8 16.1 1.0 O A:SER37 2.9 15.5 0.6 O A:SER37 3.0 15.5 0.4 ND2 A:ASN48 3.0 17.6 1.0 C A:SER37 3.6 15.5 0.6 C A:SER37 3.6 15.5 0.4 C A:SER46 3.7 19.7 1.0 CG A:ARG38 3.8 12.8 1.0 CB A:ASN48 3.8 17.1 1.0 CA A:ARG38 3.8 16.0 1.0 CG A:ASN48 3.8 15.9 1.0 O A:HOH966 3.9 35.1 1.0 N A:ARG38 4.0 16.4 1.0 CB A:SER46 4.0 23.9 1.0 O A:HIS47 4.0 11.7 1.0 CA A:SER46 4.1 24.2 1.0 C A:HIS47 4.3 14.8 1.0 OG A:SER37 4.3 16.5 0.6 CB A:SER37 4.4 15.7 0.4 CB A:ARG38 4.4 17.1 1.0 CB A:SER37 4.5 15.6 0.6 N A:ASN48 4.6 12.5 1.0 O A:HOH939 4.6 41.4 1.0 CA A:SER37 4.6 13.4 0.4 CA A:SER37 4.7 13.4 0.6 N A:HIS47 4.7 13.3 1.0 CA A:ASN48 4.8 12.3 1.0 OD1 A:ASN48 5.0 13.1 1.0 CA A:HIS47 5.0 12.7 1.0

Sodium binding site 3 out of 5 in the Crystal Structure of Tris-Bound Tsabgl (Data III)


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 Tris-Bound Tsabgl (Data III) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na504 b:19.4 occ:1.00 O A:HOH821 2.4 24.6 1.0 N A:LEU286 2.9 14.4 1.0 O A:HOH933 3.4 30.9 1.0 CE A:MET345 3.5 32.0 1.0 CE1 A:PHE253 3.5 18.0 1.0 CA A:LYS285 3.6 14.5 1.0 CD1 A:PHE253 3.7 11.4 1.0 CB A:LEU286 3.7 8.6 1.0 C A:LYS285 3.7 19.3 1.0 O A:GLN284 3.8 14.4 1.0 CG A:LEU286 3.8 10.2 1.0 CA A:LEU286 3.8 11.9 1.0 CD A:LYS285 3.9 18.7 1.0 O A:LEU286 4.3 9.3 1.0 N A:LYS285 4.5 15.7 1.0 CE A:LYS285 4.5 26.6 1.0 CD1 A:LEU286 4.5 11.8 1.0 C A:GLN284 4.5 15.7 1.0 CG A:LYS285 4.5 18.8 1.0 SD A:MET345 4.5 25.4 1.0 C A:LEU286 4.6 12.2 1.0 CB A:LYS285 4.6 17.0 1.0 NZ A:LYS285 4.6 27.9 1.0 O A:LEU252 4.6 14.8 1.0 CZ A:PHE253 4.7 14.3 1.0 O A:HOH717 4.8 14.8 1.0 O A:LYS285 4.9 12.8 1.0 O A:SER283 4.9 15.6 1.0 CG A:PHE253 5.0 12.0 1.0 CD2 A:LEU286 5.0 11.5 1.0

Sodium binding site 4 out of 5 in the Crystal Structure of Tris-Bound Tsabgl (Data III)


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 Tris-Bound Tsabgl (Data III) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na505 b:32.6 occ:1.00 O A:HOH868 2.4 34.8 1.0 O A:ASP287 3.0 11.3 1.0 CD A:LYS214 3.1 37.6 1.0 C A:ASP287 3.6 17.0 1.0 CG A:PRO346 3.8 17.3 1.0 CE A:LYS214 3.8 53.6 1.0 CB A:ASP287 3.9 18.1 1.0 CG A:LYS214 3.9 20.8 1.0 CB A:PRO346 3.9 15.0 1.0 CB A:PHE288 4.0 9.5 1.0 CD2 A:PHE288 4.2 13.5 1.0 CB A:LYS214 4.2 12.6 1.0 CA A:ASP287 4.3 15.2 1.0 O A:HOH830 4.4 18.7 1.0 N A:PHE288 4.4 14.2 1.0 NZ A:LYS214 4.4 47.6 1.0 O A:HOH882 4.5 29.1 1.0 CG A:PHE288 4.6 8.7 1.0 CD A:PRO346 4.7 17.8 1.0 CA A:PHE288 4.7 14.6 1.0 O A:HOH953 4.8 46.1 1.0 OH A:TYR348 4.9 15.9 1.0 CE1 A:TYR348 5.0 20.0 1.0 CG A:ASP287 5.0 18.5 1.0

Sodium binding site 5 out of 5 in the Crystal Structure of Tris-Bound Tsabgl (Data III)


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 Tris-Bound Tsabgl (Data III) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na506 b:30.1 occ:1.00 N A:GLU328 2.9 9.6 1.0 CB A:GLU328 3.2 18.6 1.0 N A:PRO327 3.4 11.1 1.0 CD A:PRO327 3.4 18.6 1.0 CD1 A:TYR326 3.5 19.8 1.0 C A:TYR326 3.6 14.9 1.0 CE1 A:TYR326 3.6 22.4 1.0 CA A:GLU328 3.7 13.3 1.0 CG A:TYR326 3.7 17.8 1.0 CA A:TYR326 3.8 14.9 1.0 CG A:PRO327 3.9 18.3 1.0 C A:PRO327 4.0 14.7 1.0 CZ A:TYR326 4.0 21.0 1.0 CG A:GLU328 4.0 38.1 1.0 CD2 A:TYR326 4.0 12.8 1.0 CA A:PRO327 4.1 14.0 1.0 CE2 A:TYR326 4.2 15.5 1.0 OE1 A:GLU328 4.2 51.2 1.0 O A:TYR326 4.2 13.0 1.0 CB A:TYR326 4.3 20.6 1.0 CD A:GLU328 4.3 51.5 1.0 CB A:PRO327 4.5 8.4 1.0 O A:HOH886 4.5 45.3 1.0 O A:HOH1026 4.6 30.2 1.0 OH A:TYR326 4.7 27.7 1.0 C A:GLU328 4.8 17.8 1.0 O A:HOH759 4.9 37.7 1.0 N A:SER329 4.9 14.0 1.0

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