Sodium in PDB 6toy: Crystal Structure of Bacillus Paralicheniformis Wild-Type Alpha- Amylase

All present enzymatic activity of Crystal Structure of Bacillus Paralicheniformis Wild-Type Alpha- Amylase:
3.2.1.1;

The structure of Crystal Structure of Bacillus Paralicheniformis Wild-Type Alpha- Amylase, PDB code: 6toy 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)	47.13 / 1.95
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	83.500, 83.500, 188.510, 90.00, 90.00, 90.00
R / Rfree (%)	17 / 20.4

The structure of Crystal Structure of Bacillus Paralicheniformis Wild-Type Alpha- Amylase also contains other interesting chemical elements:

Calcium

(Ca)

2 atoms

The binding sites of Sodium atom in the Crystal Structure of Bacillus Paralicheniformis Wild-Type Alpha- Amylase (pdb code 6toy). 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 Wild-Type Alpha- Amylase, PDB code: 6toy:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Bacillus Paralicheniformis Wild-Type Alpha- Amylase


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 Wild-Type Alpha- Amylase within 5.0Å range: probe atom residue distance (Å) B Occ A:Na503 b:23.1 occ:1.00 OD2 A:ASP200 2.3 21.7 1.0 OD2 A:ASP161 2.4 21.1 1.0 OD2 A:ASP194 2.4 22.5 1.0 O A:ILE201 2.4 21.7 1.0 OD2 A:ASP183 2.5 22.3 1.0 OD1 A:ASP194 2.9 22.1 1.0 CG A:ASP194 3.0 22.7 1.0 CG A:ASP183 3.2 22.8 1.0 CG A:ASP161 3.4 22.1 1.0 C A:ILE201 3.5 21.6 1.0 O A:HOH805 3.5 22.1 1.0 CG A:ASP200 3.5 21.8 1.0 OD1 A:ASP183 3.7 22.3 1.0 O A:HOH681 3.8 19.3 1.0 CB A:ASP161 3.8 21.8 1.0 CA A:ASP202 4.0 22.2 1.0 CA A:CA501 4.0 22.3 1.0 CB A:ASP183 4.1 22.8 1.0 N A:ASP202 4.1 21.4 1.0 OD1 A:ASP200 4.3 22.2 1.0 N A:TYR203 4.3 21.8 1.0 O A:ASP200 4.4 21.4 1.0 N A:ASP183 4.4 23.5 1.0 C A:ASP200 4.5 21.6 1.0 CB A:ASP200 4.5 21.6 1.0 CB A:ASP194 4.5 22.9 1.0 N A:ILE201 4.5 21.1 1.0 CA A:CA502 4.5 22.2 1.0 OD1 A:ASP161 4.5 22.1 1.0 CA A:ILE201 4.6 20.9 1.0 C A:ASP202 4.7 22.1 1.0 CE3 A:TRP182 4.9 22.6 1.0 N A:ASP161 4.9 22.0 1.0 CA A:ASP183 4.9 24.1 1.0 CA A:ASP161 5.0 22.4 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Bacillus Paralicheniformis Wild-Type Alpha- Amylase


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 Wild-Type Alpha- Amylase within 5.0Å range: probe atom residue distance (Å) B Occ A:Na504 b:30.6 occ:1.00 O A:TYR302 2.1 29.8 1.0 OD1 A:ASN407 2.4 29.4 1.0 O A:GLY300 2.5 29.6 1.0 OD1 A:ASP430 2.5 24.8 1.0 OD2 A:ASP430 2.5 24.6 1.0 O A:HIS406 2.6 30.8 1.0 CG A:ASP430 2.9 24.9 1.0 ND1 A:HIS406 3.3 42.2 1.0 C A:TYR302 3.3 29.6 1.0 C A:GLY300 3.4 30.1 1.0 C A:HIS406 3.4 32.0 1.0 CG A:ASN407 3.5 29.8 1.0 CE1 A:HIS406 3.6 42.8 1.0 CA A:ASN407 3.7 29.1 1.0 N A:TYR302 3.8 29.8 1.0 N A:ASN407 3.9 30.3 1.0 CG A:HIS406 4.0 41.1 1.0 CA A:GLY300 4.0 29.6 1.0 CG A:MET304 4.1 27.0 1.0 CB A:ASN407 4.1 29.2 1.0 CA A:TYR302 4.1 29.2 1.0 C A:GLY301 4.2 30.5 1.0 N A:ASP303 4.3 29.7 1.0 N A:MET304 4.4 28.1 1.0 N A:GLY301 4.4 30.4 1.0 CB A:ASP430 4.4 24.7 1.0 NE2 A:HIS406 4.5 43.1 1.0 CA A:HIS406 4.5 34.8 1.0 CA A:ASP303 4.5 29.9 1.0 CB A:HIS406 4.6 37.9 1.0 ND2 A:ASN407 4.6 30.9 1.0 CB A:TYR302 4.6 28.4 1.0 CA A:GLY301 4.6 31.2 1.0 O A:GLY301 4.7 30.6 1.0 CD2 A:HIS406 4.7 42.8 1.0 O A:HOH699 4.8 26.5 1.0 C A:ASP303 4.9 28.6 1.0 C A:ASN407 5.0 28.0 1.0 CB A:MET304 5.0 27.3 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