Sodium in PDB 6tp2: Crystal Structure of Bacillus Paralicheniformis Alpha-Amylase in Complex with Beta-Cyclodextrin

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

The structure of Crystal Structure of Bacillus Paralicheniformis Alpha-Amylase in Complex with Beta-Cyclodextrin, PDB code: 6tp2 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)	46.80 / 1.94
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	82.940, 82.940, 187.200, 90.00, 90.00, 90.00
R / Rfree (%)	17.1 / 20

The structure of Crystal Structure of Bacillus Paralicheniformis Alpha-Amylase in Complex with Beta-Cyclodextrin 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 Beta-Cyclodextrin (pdb code 6tp2). 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 Beta-Cyclodextrin, PDB code: 6tp2:
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 Beta-Cyclodextrin


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 Beta-Cyclodextrin within 5.0Å range: probe atom residue distance (Å) B Occ A:Na503 b:15.1 occ:1.00 OD2 A:ASP200 2.3 16.5 1.0 OD2 A:ASP194 2.4 17.1 1.0 OD2 A:ASP161 2.4 15.5 1.0 O A:ILE201 2.4 15.6 1.0 OD2 A:ASP183 2.5 16.8 1.0 OD1 A:ASP194 3.0 16.5 1.0 CG A:ASP194 3.0 17.0 1.0 CG A:ASP183 3.2 17.2 1.0 CG A:ASP161 3.4 16.2 1.0 C A:ILE201 3.5 15.7 1.0 CG A:ASP200 3.5 16.5 1.0 O A:HOH733 3.6 15.8 1.0 OD1 A:ASP183 3.7 17.3 1.0 O A:HOH673 3.7 15.4 1.0 CB A:ASP161 3.8 16.0 1.0 CA A:ASP202 4.0 16.3 1.0 CA A:CA501 4.0 16.2 1.0 CB A:ASP183 4.1 17.4 1.0 N A:ASP202 4.1 16.0 1.0 OD1 A:ASP200 4.2 16.2 1.0 N A:ASP183 4.3 17.7 1.0 N A:TYR203 4.3 16.5 1.0 O A:ASP200 4.4 16.2 1.0 CA A:CA502 4.4 18.7 1.0 CB A:ASP194 4.5 17.3 1.0 C A:ASP200 4.5 16.0 1.0 CB A:ASP200 4.5 16.4 1.0 N A:ILE201 4.5 15.4 1.0 OD1 A:ASP161 4.5 16.2 1.0 CA A:ILE201 4.6 15.5 1.0 C A:ASP202 4.7 16.4 1.0 CA A:ASP183 4.9 18.1 1.0 N A:ASP161 4.9 16.4 1.0 CE3 A:TRP182 4.9 17.1 1.0

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


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 Beta-Cyclodextrin within 5.0Å range: probe atom residue distance (Å) B Occ A:Na504 b:22.5 occ:1.00 O A:TYR302 2.1 22.5 1.0 OD1 A:ASN407 2.4 22.3 1.0 OD2 A:ASP430 2.5 21.5 1.0 OD1 A:ASP430 2.5 21.6 1.0 O A:GLY300 2.5 22.9 1.0 O A:HIS406 2.7 23.5 1.0 CG A:ASP430 2.8 21.3 1.0 ND1 A:HIS406 3.2 31.9 1.0 C A:TYR302 3.3 22.7 1.0 C A:GLY300 3.4 22.8 1.0 CG A:ASN407 3.5 22.9 1.0 C A:HIS406 3.5 24.7 1.0 CE1 A:HIS406 3.6 32.1 1.0 CA A:ASN407 3.7 22.4 1.0 N A:TYR302 3.8 22.5 1.0 CG A:MET304 4.0 21.2 1.0 N A:ASN407 4.0 23.4 1.0 CA A:GLY300 4.0 22.5 1.0 CB A:ASN407 4.0 22.5 1.0 CG A:HIS406 4.1 31.1 1.0 CA A:TYR302 4.1 22.4 1.0 C A:GLY301 4.2 23.2 1.0 N A:ASP303 4.3 23.3 1.0 N A:GLY301 4.3 22.7 1.0 CB A:ASP430 4.3 21.0 1.0 N A:MET304 4.4 21.9 1.0 CA A:ASP303 4.5 23.4 1.0 NE2 A:HIS406 4.5 32.2 1.0 CB A:TYR302 4.6 21.7 1.0 ND2 A:ASN407 4.6 23.6 1.0 CA A:HIS406 4.6 27.1 1.0 CA A:GLY301 4.7 23.4 1.0 CB A:HIS406 4.7 29.2 1.0 O A:HOH810 4.7 25.0 1.0 CD2 A:HIS406 4.8 31.9 1.0 O A:GLY301 4.8 23.6 1.0 CB A:MET304 4.9 21.3 1.0 C A:ASP303 5.0 22.4 1.0 C A:ASN407 5.0 21.6 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