Calcium 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:

Sodium

(Na)

2 atoms

The binding sites of Calcium 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 Calcium atom.
In total 2 binding sites of Calcium where determined in the Crystal Structure of Bacillus Paralicheniformis Alpha-Amylase in Complex with Beta-Cyclodextrin, PDB code: 6tp2:
Jump to Calcium binding site number: 1; 2;

Calcium 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 Calcium with other atoms in the Ca 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:Ca501 b:16.2 occ:1.00 O A:HIS235 2.3 16.5 1.0 OD1 A:ASP194 2.3 16.5 1.0 OD1 A:ASN104 2.3 13.8 1.0 OD1 A:ASP200 2.4 16.2 1.0 O A:ASP194 2.4 16.0 1.0 O A:HOH733 2.5 15.8 1.0 OD2 A:ASP200 3.0 16.5 1.0 CG A:ASP200 3.1 16.5 1.0 C A:ASP194 3.3 16.8 1.0 CG A:ASP194 3.4 17.0 1.0 CG A:ASN104 3.5 14.6 1.0 C A:HIS235 3.5 16.2 1.0 O A:HOH673 3.8 15.4 1.0 CA A:ASP194 3.8 16.9 1.0 NA A:NA503 4.0 15.1 1.0 O A:ASN104 4.0 15.9 1.0 ND2 A:ASN104 4.1 14.2 1.0 CB A:HIS235 4.1 16.0 1.0 CB A:ASP194 4.2 17.3 1.0 OD2 A:ASP194 4.2 17.1 1.0 CA A:HIS235 4.3 16.2 1.0 O A:HOH636 4.4 13.4 1.0 N A:ILE236 4.4 16.1 1.0 N A:TYR195 4.5 16.9 1.0 CA A:ILE236 4.6 16.0 1.0 CB A:ASP200 4.6 16.4 1.0 O A:ILE201 4.7 15.6 1.0 CB A:ASN104 4.7 14.6 1.0 C A:ASN104 4.8 15.4 1.0 CA A:ASN104 4.8 14.9 1.0 CG1 A:ILE236 4.8 15.5 1.0 CA A:TYR195 4.9 17.1 1.0

Calcium 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 Calcium with other atoms in the Ca 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:Ca502 b:18.7 occ:1.00 O A:ALA181 2.3 17.8 1.0 OD1 A:ASP183 2.4 17.3 1.0 OD1 A:ASP202 2.4 17.2 1.0 OD1 A:ASP161 2.4 16.2 1.0 OD2 A:ASP204 2.4 20.7 1.0 OD2 A:ASP161 2.5 15.5 1.0 O A:HOH922 2.6 12.0 1.0 CG A:ASP161 2.8 16.2 1.0 CG A:ASP202 3.3 17.0 1.0 CG A:ASP204 3.4 20.4 1.0 CG A:ASP183 3.5 17.2 1.0 C A:ALA181 3.5 18.1 1.0 N A:ASP183 4.0 17.7 1.0 CB A:ASP204 4.0 19.9 1.0 OD2 A:ASP202 4.0 17.3 1.0 OD2 A:ASP183 4.1 16.8 1.0 CB A:ASP202 4.1 16.6 1.0 N A:ALA181 4.1 18.6 1.0 C A:TRP182 4.2 17.5 1.0 CA A:ASP202 4.2 16.3 1.0 CB A:ASP161 4.2 16.0 1.0 N A:ASP204 4.3 18.2 1.0 O A:HOH746 4.3 21.1 1.0 OD1 A:ASP204 4.4 20.7 1.0 CA A:ASP183 4.4 18.1 1.0 CA A:ALA181 4.4 18.6 1.0 N A:TRP182 4.4 18.0 1.0 NA A:NA503 4.4 15.1 1.0 CA A:TRP182 4.5 17.4 1.0 N A:TYR203 4.5 16.5 1.0 CB A:ASP183 4.6 17.4 1.0 C A:ASP202 4.6 16.4 1.0 O A:HOH961 4.6 34.8 1.0 O A:TRP182 4.6 17.1 1.0 CA A:ASP204 4.8 19.3 1.0 OD2 A:ASP194 4.9 17.1 1.0 CB A:ALA181 4.9 19.0 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