Sodium in PDB 8xpd: Crystal Structure of Tris-Bound Tsabgl (Data II)

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

The structure of Crystal Structure of Tris-Bound Tsabgl (Data II), PDB code: 8xpd 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)	49.52 / 1.70
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	65.044, 70.95, 99.032, 90, 90, 90
R / Rfree (%)	15.1 / 17.9

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


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 II) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na502 b:18.9 occ:1.00 O A:GLY49 2.7 10.6 1.0 O A:HOH804 2.7 11.0 1.0 N A:GLY21 2.8 9.0 1.0 O A:TYR17 2.9 7.9 1.0 CA A:GLY21 3.4 9.9 1.0 C A:TYR17 3.5 10.1 1.0 C A:GLY49 3.6 9.0 1.0 CA A:TYR17 3.7 10.5 1.0 N A:GLU20 3.8 9.8 1.0 CD1 A:TYR17 3.8 11.8 1.0 O A:SER16 3.9 8.8 1.0 CB A:ALA52 3.9 10.4 1.0 CA A:GLY49 3.9 7.2 1.0 C A:GLU20 3.9 9.6 1.0 O A:GLY21 4.1 10.2 1.0 C A:GLY21 4.2 8.7 1.0 CA A:GLU20 4.2 8.0 1.0 CE1 A:TYR17 4.2 12.2 1.0 CG A:TYR17 4.3 10.9 1.0 CB A:GLU20 4.3 7.9 1.0 C A:VAL19 4.5 8.8 1.0 CB A:TYR17 4.6 11.3 1.0 N A:GLN18 4.7 8.7 1.0 N A:VAL19 4.7 8.8 1.0 C A:SER16 4.7 11.1 1.0 O A:HOH774 4.8 13.2 1.0 N A:TYR17 4.8 8.2 1.0 N A:ASP50 4.9 11.9 1.0 C A:GLN18 4.9 9.8 1.0 CZ A:TYR17 4.9 10.6 1.0

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


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 II) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na503 b:21.1 occ:1.00 O A:SER46 2.7 13.0 1.0 O A:HOH1197 2.7 25.3 1.0 O A:SER37 2.9 12.5 0.5 O A:SER37 2.9 12.5 0.5 ND2 A:ASN48 3.0 15.8 1.0 C A:SER46 3.6 16.3 1.0 C A:SER37 3.6 11.2 0.5 C A:SER37 3.6 11.2 0.5 CB A:ASN48 3.7 11.4 1.0 CG A:ASN48 3.8 14.9 1.0 O A:HIS47 3.9 11.9 1.0 CA A:ARG38 3.9 12.0 1.0 CG A:ARG38 4.0 12.4 1.0 CB A:SER46 4.0 20.1 1.0 N A:ARG38 4.0 11.9 1.0 C A:HIS47 4.1 11.9 1.0 O A:HOH923 4.1 35.8 1.0 CA A:SER46 4.1 12.6 1.0 OG A:SER37 4.2 16.1 0.5 CB A:SER37 4.3 11.6 0.5 CB A:SER37 4.4 11.6 0.5 N A:ASN48 4.4 11.1 1.0 O A:HOH1107 4.4 34.0 1.0 CB A:ARG38 4.6 12.4 1.0 N A:HIS47 4.6 14.6 1.0 CA A:ASN48 4.6 10.8 1.0 CA A:SER37 4.6 10.5 0.5 CA A:SER37 4.6 10.5 0.5 O A:HOH868 4.8 38.7 1.0 CA A:HIS47 4.8 9.6 1.0 OD1 A:ASN48 4.9 13.8 1.0 O A:HOH677 4.9 26.0 1.0

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


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 II) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na504 b:22.7 occ:1.00 O A:HOH855 2.7 21.8 1.0 O A:HOH787 2.8 30.8 1.0 N A:LEU286 2.9 9.9 1.0 CE A:MET345 3.3 25.5 1.0 CE1 A:PHE253 3.6 13.2 1.0 CA A:LYS285 3.6 10.6 1.0 CB A:LEU286 3.6 9.2 1.0 O A:HOH739 3.6 30.5 1.0 C A:LYS285 3.7 12.6 1.0 CG A:LEU286 3.7 11.0 1.0 CD1 A:PHE253 3.7 14.4 1.0 CA A:LEU286 3.8 8.2 1.0 CD A:LYS285 3.8 13.8 1.0 O A:GLN284 3.8 13.6 1.0 O A:LEU286 4.2 11.9 1.0 CE A:LYS285 4.3 22.4 1.0 CD1 A:LEU286 4.4 8.8 1.0 C A:LEU286 4.4 9.8 1.0 CG A:LYS285 4.5 14.1 1.0 N A:LYS285 4.5 12.1 1.0 C A:GLN284 4.5 13.8 1.0 O A:HOH693 4.5 34.0 1.0 CB A:LYS285 4.6 17.3 1.0 SD A:MET345 4.6 20.3 1.0 NZ A:LYS285 4.6 18.5 1.0 O A:LEU252 4.8 12.3 1.0 CZ A:PHE253 4.8 18.2 1.0 O A:LYS285 4.9 12.5 1.0 O A:HOH814 4.9 36.3 1.0 CD2 A:LEU286 4.9 11.6 1.0 O A:SER283 5.0 13.9 1.0 O A:HOH649 5.0 10.1 1.0

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


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 II) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na505 b:30.1 occ:1.00 O A:HOH987 2.8 31.3 1.0 O A:ASP287 2.9 10.3 1.0 C A:ASP287 3.6 12.3 1.0 O A:HOH609 3.6 29.1 1.0 CB A:ASP287 3.8 11.1 1.0 CG A:PRO346 3.8 12.6 1.0 CD A:LYS214 3.8 37.5 1.0 CB A:PRO346 4.0 14.2 1.0 O A:HOH859 4.0 17.1 1.0 CG A:LYS214 4.0 21.9 1.0 CB A:PHE288 4.2 10.2 1.0 CA A:ASP287 4.2 10.3 1.0 CB A:LYS214 4.3 13.4 1.0 O A:HOH731 4.3 25.7 1.0 CD2 A:PHE288 4.4 11.4 1.0 N A:PHE288 4.4 8.3 1.0 CD A:PRO346 4.6 12.2 1.0 CA A:PHE288 4.7 7.4 1.0 CG A:PHE288 4.8 10.5 1.0 CG A:ASP287 4.9 15.6 1.0

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


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 II) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na506 b:24.6 occ:1.00 N A:GLU328 2.9 12.2 1.0 CB A:GLU328 3.2 13.2 1.0 N A:PRO327 3.3 10.5 1.0 CG A:GLU328 3.3 26.0 1.0 CD A:PRO327 3.4 12.2 1.0 CD1 A:TYR326 3.4 13.8 1.0 C A:TYR326 3.5 12.3 1.0 CE1 A:TYR326 3.5 18.5 1.0 CG A:TYR326 3.6 13.6 1.0 CA A:GLU328 3.6 9.1 1.0 CA A:TYR326 3.7 13.0 1.0 CZ A:TYR326 3.8 21.3 1.0 CD2 A:TYR326 3.8 10.0 1.0 C A:PRO327 3.9 12.4 1.0 CG A:PRO327 3.9 16.9 1.0 CE2 A:TYR326 3.9 13.4 1.0 CA A:PRO327 4.0 8.2 1.0 O A:TYR326 4.1 10.3 1.0 CB A:TYR326 4.2 10.9 1.0 O A:HOH611 4.3 36.9 1.0 CD A:GLU328 4.4 43.6 1.0 CB A:PRO327 4.5 10.8 1.0 OH A:TYR326 4.6 17.7 1.0 O A:HOH1156 4.6 31.6 1.0 C A:GLU328 4.7 12.1 1.0 N A:SER329 4.8 12.6 1.0 OE2 A:GLU328 5.0 47.3 1.0 N A:TYR326 5.0 11.7 1.0

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