Calcium 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:

Sodium

(Na)

2 atoms

The binding sites of Calcium 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 Calcium atom.
In total 2 binding sites of Calcium where determined in the Crystal Structure of Bacillus Paralicheniformis Wild-Type Alpha- Amylase, PDB code: 6toy:
Jump to Calcium binding site number: 1; 2;

Calcium 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 Calcium with other atoms in the Ca 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:Ca501 b:22.3 occ:1.00 O A:HIS235 2.3 22.0 1.0 OD1 A:ASP200 2.3 22.2 1.0 OD1 A:ASP194 2.4 22.1 1.0 O A:ASP194 2.4 21.0 1.0 OD1 A:ASN104 2.4 19.5 1.0 O A:HOH805 2.5 22.1 1.0 OD2 A:ASP200 3.0 21.7 1.0 CG A:ASP200 3.0 21.8 1.0 C A:ASP194 3.3 21.7 1.0 CG A:ASP194 3.4 22.7 1.0 C A:HIS235 3.4 21.9 1.0 CG A:ASN104 3.5 19.6 1.0 CA A:ASP194 3.8 22.2 1.0 O A:HOH681 3.8 19.3 1.0 NA A:NA503 4.0 23.1 1.0 O A:ASN104 4.0 19.0 1.0 CB A:HIS235 4.1 21.7 1.0 CB A:ASP194 4.2 22.9 1.0 ND2 A:ASN104 4.2 19.6 1.0 CA A:HIS235 4.2 22.0 1.0 OD2 A:ASP194 4.3 22.5 1.0 O A:HOH619 4.4 19.8 1.0 N A:TYR195 4.4 22.1 1.0 N A:ILE236 4.4 21.6 1.0 CB A:ASP200 4.5 21.6 1.0 CA A:ILE236 4.6 22.0 1.0 O A:ILE201 4.7 21.7 1.0 CB A:ASN104 4.7 19.4 1.0 C A:ASN104 4.8 19.6 1.0 CA A:TYR195 4.8 22.3 1.0 CG1 A:ILE236 4.8 21.3 1.0 CA A:ASN104 4.8 19.5 1.0

Calcium 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 Calcium with other atoms in the Ca 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:Ca502 b:22.2 occ:1.00 OD1 A:ASP202 2.3 22.6 1.0 OD1 A:ASP183 2.3 22.3 1.0 O A:ALA181 2.3 23.5 1.0 OD1 A:ASP161 2.4 22.1 1.0 OD2 A:ASP204 2.4 26.9 1.0 O A:HOH878 2.5 17.2 1.0 OD2 A:ASP161 2.6 21.1 1.0 CG A:ASP161 2.8 22.1 1.0 CG A:ASP202 3.2 22.6 1.0 CG A:ASP204 3.4 26.5 1.0 CG A:ASP183 3.5 22.8 1.0 C A:ALA181 3.6 24.2 1.0 CB A:ASP204 3.9 26.1 1.0 OD2 A:ASP202 3.9 23.2 1.0 N A:ASP183 4.0 23.5 1.0 OD2 A:ASP183 4.1 22.3 1.0 CB A:ASP202 4.1 22.0 1.0 N A:ALA181 4.2 24.4 1.0 C A:TRP182 4.2 23.6 1.0 N A:ASP204 4.2 24.2 1.0 CA A:ASP202 4.2 22.2 1.0 CB A:ASP161 4.3 21.8 1.0 OD1 A:ASP204 4.3 26.9 1.0 CA A:ASP183 4.4 24.1 1.0 CA A:ALA181 4.5 24.8 1.0 O A:HOH773 4.5 27.5 1.0 N A:TRP182 4.5 24.1 1.0 CA A:TRP182 4.5 23.6 1.0 NA A:NA503 4.5 23.1 1.0 CB A:ASP183 4.5 22.8 1.0 O A:HOH969 4.6 33.6 1.0 N A:TYR203 4.6 21.8 1.0 O A:TRP182 4.6 24.1 1.0 C A:ASP202 4.7 22.1 1.0 CA A:ASP204 4.7 25.5 1.0 OD2 A:ASP194 4.9 22.5 1.0 CB A:ALA181 4.9 25.4 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