Sodium in PDB 8xpc: Crystal Structure of Tris-Bound Tsabgl (Data I)

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

The structure of Crystal Structure of Tris-Bound Tsabgl (Data I), PDB code: 8xpc 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 / 1.55
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	64.752, 71.023, 98.873, 90, 90, 90
R / Rfree (%)	14.9 / 16.9

The binding sites of Sodium atom in the Crystal Structure of Tris-Bound Tsabgl (Data I) (pdb code 8xpc). 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 I), PDB code: 8xpc:
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 I)


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 I) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na502 b:14.8 occ:1.00 O A:GLY49 2.6 8.3 1.0 O A:HOH761 2.7 8.5 1.0 O A:TYR17 2.8 7.4 1.0 N A:GLY21 2.9 8.6 1.0 CA A:GLY21 3.5 9.2 1.0 C A:TYR17 3.5 9.8 1.0 C A:GLY49 3.6 8.9 1.0 CA A:TYR17 3.7 9.6 1.0 CD1 A:TYR17 3.8 9.5 1.0 N A:GLU20 3.8 7.5 1.0 O A:SER16 3.8 7.3 1.0 CA A:GLY49 3.9 6.9 1.0 CB A:ALA52 3.9 11.3 1.0 C A:GLU20 4.0 7.8 1.0 O A:GLY21 4.1 8.1 1.0 CE1 A:TYR17 4.2 12.8 1.0 C A:GLY21 4.2 7.1 1.0 CG A:TYR17 4.3 8.7 1.0 CA A:GLU20 4.3 6.9 1.0 CB A:GLU20 4.4 6.7 1.0 C A:VAL19 4.6 7.6 1.0 CB A:TYR17 4.6 6.5 1.0 N A:GLN18 4.6 7.4 1.0 N A:VAL19 4.7 7.7 1.0 C A:SER16 4.7 8.9 1.0 O A:HOH733 4.7 10.7 1.0 N A:TYR17 4.7 6.2 1.0 N A:ASP50 4.9 8.6 1.0 CZ A:TYR17 4.9 8.9 1.0 C A:GLN18 4.9 10.3 1.0 CD2 A:TYR17 4.9 9.1 1.0

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


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 I) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na503 b:20.4 occ:1.00 O A:HOH1150 2.7 27.4 1.0 O A:SER46 2.8 11.8 1.0 O A:SER37 2.8 11.9 0.6 O A:SER37 2.9 11.9 0.4 ND2 A:ASN48 3.0 14.9 1.0 C A:SER37 3.5 9.5 0.6 C A:SER37 3.5 9.6 0.4 C A:SER46 3.6 12.9 1.0 CB A:ASN48 3.7 8.9 1.0 CG A:ASN48 3.8 11.0 1.0 CA A:ARG38 3.8 10.9 1.0 CG A:ARG38 3.9 13.4 1.0 O A:HIS47 4.0 10.8 1.0 N A:ARG38 4.0 10.7 1.0 CB A:SER46 4.0 20.1 1.0 CA A:SER46 4.1 12.2 1.0 C A:HIS47 4.2 10.5 1.0 OG A:SER37 4.3 11.0 0.6 CB A:SER37 4.3 10.5 0.4 CB A:SER37 4.4 10.6 0.6 CB A:ARG38 4.5 12.2 1.0 N A:ASN48 4.5 8.1 1.0 CA A:SER37 4.6 9.5 0.4 CA A:SER37 4.6 9.5 0.6 N A:HIS47 4.6 10.2 1.0 CA A:ASN48 4.7 7.8 1.0 O A:HOH969 4.7 36.6 1.0 CA A:HIS47 4.9 8.8 1.0 OD1 A:ASN48 5.0 10.5 1.0

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


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 I) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na504 b:23.1 occ:1.00 O A:HOH672 2.9 22.8 1.0 O A:HOH867 2.9 38.5 1.0 N A:LEU286 2.9 10.5 1.0 CE A:MET345 3.2 22.2 1.0 O A:HOH919 3.5 32.1 1.0 CE1 A:PHE253 3.5 10.2 1.0 CB A:LEU286 3.6 8.7 1.0 CA A:LYS285 3.7 8.1 1.0 CD1 A:PHE253 3.7 13.1 1.0 C A:LYS285 3.8 11.0 1.0 CG A:LEU286 3.8 9.5 1.0 CA A:LEU286 3.8 8.6 1.0 CD A:LYS285 3.9 13.3 1.0 O A:GLN284 3.9 12.0 1.0 O A:LEU286 4.2 11.5 1.0 O A:HOH789 4.4 34.2 1.0 CD1 A:LEU286 4.4 9.0 1.0 SD A:MET345 4.4 17.4 1.0 C A:LEU286 4.5 10.1 1.0 CE A:LYS285 4.5 18.4 1.0 CG A:LYS285 4.5 12.7 1.0 N A:LYS285 4.6 10.7 1.0 C A:GLN284 4.6 10.6 1.0 NZ A:LYS285 4.6 24.1 1.0 CB A:LYS285 4.6 12.2 1.0 O A:HOH842 4.7 36.1 1.0 CZ A:PHE253 4.7 11.5 1.0 O A:LEU252 4.8 10.3 1.0 O A:LYS285 4.9 10.9 1.0 O A:HOH734 5.0 11.8 1.0

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


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 I) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na505 b:30.4 occ:1.00 O A:HOH977 2.2 35.5 1.0 O A:ASP287 2.9 10.7 1.0 O A:HOH649 3.2 25.3 1.0 C A:ASP287 3.6 9.5 1.0 CG A:PRO346 3.8 12.8 1.0 CB A:PHE288 3.8 8.2 1.0 CB A:ASP287 3.8 10.7 1.0 CB A:PRO346 3.9 11.4 1.0 CG A:LYS214 4.1 18.4 1.0 CD2 A:PHE288 4.1 9.8 1.0 CD A:LYS214 4.1 27.6 1.0 O A:HOH787 4.2 21.0 1.0 CB A:LYS214 4.2 9.7 1.0 CA A:ASP287 4.2 9.2 1.0 N A:PHE288 4.3 8.5 1.0 CG A:PHE288 4.4 8.7 1.0 CA A:PHE288 4.5 7.1 1.0 CD A:PRO346 4.6 10.8 1.0 O A:HOH792 4.8 28.4 1.0 CE A:LYS214 4.8 31.5 1.0 CE1 A:TYR348 4.8 12.2 1.0 OH A:TYR348 4.9 14.6 1.0

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


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 I) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na506 b:26.1 occ:1.00 N A:GLU328 3.0 9.2 1.0 CB A:GLU328 3.3 17.6 1.0 N A:PRO327 3.4 9.1 1.0 CD A:PRO327 3.4 10.0 1.0 CG A:GLU328 3.5 27.6 1.0 CD1 A:TYR326 3.5 12.7 1.0 CE1 A:TYR326 3.6 16.5 1.0 C A:TYR326 3.6 10.7 1.0 CG A:TYR326 3.7 10.2 1.0 CA A:GLU328 3.7 11.1 1.0 CA A:TYR326 3.8 9.8 1.0 CZ A:TYR326 3.9 19.6 1.0 CG A:PRO327 3.9 13.5 1.0 C A:PRO327 4.0 9.1 1.0 CD2 A:TYR326 4.0 11.8 1.0 OE2 A:GLU328 4.1 51.3 1.0 CE2 A:TYR326 4.1 12.8 1.0 CA A:PRO327 4.1 9.0 1.0 CD A:GLU328 4.2 44.5 1.0 O A:TYR326 4.2 10.9 1.0 CB A:TYR326 4.4 11.1 1.0 O A:HOH1102 4.5 30.6 1.0 CB A:PRO327 4.5 9.4 1.0 OH A:TYR326 4.7 18.5 1.0 C A:GLU328 4.8 10.7 1.0 N A:SER329 4.9 8.9 1.0

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