Sodium in PDB 6toz: Crystal Structure of Bacillus Paralicheniformis Alpha-Amylase in Complex with Acarbose

All present enzymatic activity of Crystal Structure of Bacillus Paralicheniformis Alpha-Amylase in Complex with Acarbose:
3.2.1.1;

The structure of Crystal Structure of Bacillus Paralicheniformis Alpha-Amylase in Complex with Acarbose, PDB code: 6toz was solved by H.J.Rozeboom, D.B.Janssen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.01 / 1.94
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	83.060, 83.060, 188.050, 90.00, 90.00, 90.00
R / Rfree (%)	15.6 / 18.1

The structure of Crystal Structure of Bacillus Paralicheniformis Alpha-Amylase in Complex with Acarbose also contains other interesting chemical elements:

Calcium

(Ca)

2 atoms

The binding sites of Sodium atom in the Crystal Structure of Bacillus Paralicheniformis Alpha-Amylase in Complex with Acarbose (pdb code 6toz). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of Bacillus Paralicheniformis Alpha-Amylase in Complex with Acarbose, PDB code: 6toz:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Bacillus Paralicheniformis Alpha-Amylase in Complex with Acarbose


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 Bacillus Paralicheniformis Alpha-Amylase in Complex with Acarbose within 5.0Å range: probe atom residue distance (Å) B Occ A:Na503 b:15.1 occ:1.00 OD2 A:ASP200 2.3 15.2 1.0 OD2 A:ASP194 2.3 15.2 1.0 OD2 A:ASP161 2.4 15.0 1.0 O A:ILE201 2.5 13.9 1.0 OD2 A:ASP183 2.6 15.6 1.0 OD1 A:ASP194 2.9 15.3 1.0 CG A:ASP194 2.9 15.2 1.0 CG A:ASP183 3.2 16.3 1.0 CG A:ASP161 3.4 15.3 1.0 CG A:ASP200 3.5 15.0 1.0 C A:ILE201 3.5 14.3 1.0 O A:HOH778 3.5 12.2 1.0 OD1 A:ASP183 3.7 16.6 1.0 CB A:ASP161 3.8 15.2 1.0 O A:HOH797 3.9 13.9 1.0 CA A:CA501 3.9 14.5 1.0 CA A:ASP202 4.0 15.0 1.0 CB A:ASP183 4.1 16.5 1.0 N A:ASP202 4.1 14.5 1.0 OD1 A:ASP200 4.1 14.8 1.0 N A:TYR203 4.3 15.3 1.0 CB A:ASP194 4.4 15.4 1.0 N A:ASP183 4.4 16.5 1.0 O A:ASP200 4.4 14.9 1.0 OD1 A:ASP161 4.5 15.6 1.0 CA A:CA502 4.5 16.2 1.0 C A:ASP200 4.5 14.6 1.0 CB A:ASP200 4.5 14.8 1.0 N A:ILE201 4.5 14.2 1.0 CA A:ILE201 4.7 14.3 1.0 C A:ASP202 4.7 15.3 1.0 CE3 A:TRP182 4.9 15.0 1.0 CA A:ASP183 4.9 17.2 1.0 N A:ASP161 4.9 15.0 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Bacillus Paralicheniformis Alpha-Amylase in Complex with Acarbose


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 Bacillus Paralicheniformis Alpha-Amylase in Complex with Acarbose within 5.0Å range: probe atom residue distance (Å) B Occ A:Na504 b:22.2 occ:1.00 O A:TYR302 2.2 20.9 1.0 OD1 A:ASN407 2.4 22.1 1.0 OD1 A:ASP430 2.4 19.6 1.0 O A:GLY300 2.5 21.5 1.0 OD2 A:ASP430 2.5 19.8 1.0 O A:HIS406 2.7 23.3 1.0 CG A:ASP430 2.8 19.5 1.0 ND1 A:HIS406 3.2 29.4 1.0 C A:TYR302 3.4 20.8 1.0 C A:GLY300 3.4 21.5 1.0 CG A:ASN407 3.5 22.2 1.0 CE1 A:HIS406 3.5 29.5 1.0 C A:HIS406 3.6 23.9 1.0 CA A:ASN407 3.7 21.7 1.0 N A:TYR302 3.8 20.7 1.0 CA A:GLY300 3.9 21.1 1.0 N A:ASN407 4.0 22.6 1.0 CB A:ASN407 4.0 21.8 1.0 CG A:MET304 4.1 20.1 1.0 CG A:HIS406 4.1 29.0 1.0 CA A:TYR302 4.1 20.6 1.0 C A:GLY301 4.2 21.5 1.0 N A:GLY301 4.3 21.5 1.0 CB A:ASP430 4.3 18.9 1.0 N A:ASP303 4.4 21.2 1.0 N A:MET304 4.5 20.8 1.0 NE2 A:HIS406 4.5 29.8 1.0 ND2 A:ASN407 4.5 22.7 1.0 O A:HOH693 4.6 21.3 1.0 CA A:ASP303 4.6 21.5 1.0 CA A:GLY301 4.6 21.9 1.0 CB A:TYR302 4.6 19.9 1.0 CA A:HIS406 4.7 25.7 1.0 CB A:HIS406 4.7 27.5 1.0 O A:GLY301 4.8 21.9 1.0 CD2 A:HIS406 4.8 29.9 1.0 C A:ASP430 5.0 19.8 1.0

N.Bozic, H.J.Rozeboom, N.Loncar, M.S.Slavic, D.B.Janssen, Z.Vujcic. Characterization of the Starch Surface Binding Site on Bacillus Paralicheniformis Alpha-Amylase. Int.J.Biol.Macromol. V. 165 1529 2020.
ISSN: ISSN 0141-8130
PubMed: 33058974
DOI: 10.1016/J.IJBIOMAC.2020.10.025