Calcium in PDB 1bli: Bacillus Licheniformis Alpha-Amylase

All present enzymatic activity of Bacillus Licheniformis Alpha-Amylase:
3.2.1.1;

The structure of Bacillus Licheniformis Alpha-Amylase, PDB code: 1bli was solved by M.Machius, N.Declerck, R.Huber, G.Wiegand, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 1.90
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	91.300, 91.300, 137.700, 90.00, 90.00, 120.00
R / Rfree (%)	15.4 / 18.5

The structure of Bacillus Licheniformis Alpha-Amylase also contains other interesting chemical elements:

Sodium

(Na)

1 atom

The binding sites of Calcium atom in the Bacillus Licheniformis Alpha-Amylase (pdb code 1bli). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Bacillus Licheniformis Alpha-Amylase, PDB code: 1bli:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Bacillus Licheniformis Alpha-Amylase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Bacillus Licheniformis Alpha-Amylase within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca500 b:18.5 occ:1.00 OD1 A:ASP183 2.4 19.1 1.0 O A:ALA181 2.4 18.3 1.0 OD1 A:ASP202 2.4 19.7 1.0 O A:HOH2079 2.5 14.1 1.0 OD2 A:ASP204 2.5 24.4 1.0 OD2 A:ASP161 2.6 18.7 1.0 OD1 A:ASP161 2.6 20.2 1.0 CG A:ASP161 2.9 18.9 1.0 CG A:ASP202 3.3 19.7 1.0 CG A:ASP204 3.4 23.5 1.0 CG A:ASP183 3.5 15.4 1.0 C A:ALA181 3.6 17.2 1.0 CB A:ASP204 3.8 20.2 1.0 OD2 A:ASP202 3.9 18.2 1.0 N A:ASP183 4.0 16.3 1.0 N A:ALA181 4.1 19.0 1.0 OD2 A:ASP183 4.1 17.7 1.0 C A:TRP182 4.2 17.4 1.0 CB A:ASP202 4.2 17.4 1.0 CA A:ASP202 4.3 16.9 1.0 N A:ASP204 4.3 21.0 1.0 CA A:ASP183 4.3 17.6 1.0 CB A:ASP161 4.4 16.2 1.0 OD1 A:ASP204 4.4 21.6 1.0 CA A:ALA181 4.4 17.9 1.0 NA A:NA800 4.5 17.8 1.0 CA A:TRP182 4.5 17.5 1.0 N A:TRP182 4.5 16.3 1.0 CB A:ASP183 4.5 15.3 1.0 O A:TRP182 4.6 16.1 1.0 N A:TYR203 4.7 17.7 1.0 C A:ASP202 4.7 18.1 1.0 CA A:ASP204 4.7 22.1 1.0 OD2 A:ASP194 4.9 17.2 1.0 CB A:ALA181 5.0 16.9 1.0

Calcium binding site 2 out of 3 in the Bacillus Licheniformis Alpha-Amylase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Bacillus Licheniformis Alpha-Amylase within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca600 b:16.0 occ:1.00 OD1 A:ASN104 2.4 15.6 1.0 O A:ASP194 2.4 13.9 1.0 O A:HIS235 2.4 15.3 1.0 OD1 A:ASP194 2.4 16.5 1.0 OD1 A:ASP200 2.4 19.0 1.0 O A:HOH2080 2.5 14.9 1.0 OD2 A:ASP200 3.1 17.0 1.0 CG A:ASP200 3.1 16.4 1.0 C A:ASP194 3.3 14.2 1.0 CG A:ASP194 3.5 17.4 1.0 CG A:ASN104 3.5 14.0 1.0 C A:HIS235 3.5 14.8 1.0 CA A:ASP194 3.8 15.4 1.0 O A:HOH1036 3.9 12.6 1.0 CB A:HIS235 4.0 13.2 1.0 O A:ASN104 4.0 15.5 1.0 NA A:NA800 4.1 17.8 1.0 ND2 A:ASN104 4.1 12.8 1.0 CB A:ASP194 4.2 16.8 1.0 CA A:HIS235 4.3 14.2 1.0 OD2 A:ASP194 4.3 17.2 1.0 N A:TYR195 4.4 15.6 1.0 O A:HOH1037 4.5 11.3 1.0 N A:ILE236 4.5 14.6 1.0 CB A:ASP200 4.5 13.6 1.0 CA A:ILE236 4.6 15.0 1.0 CB A:ASN104 4.6 14.5 1.0 O A:ILE201 4.7 15.0 1.0 C A:ASN104 4.8 15.4 1.0 CA A:TYR195 4.8 15.6 1.0 CA A:ASN104 4.8 13.5 1.0 CG1 A:ILE236 4.8 15.8 1.0

Calcium binding site 3 out of 3 in the Bacillus Licheniformis Alpha-Amylase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Bacillus Licheniformis Alpha-Amylase within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca700 b:25.4 occ:1.00 O A:TYR302 2.3 20.6 1.0 OD1 A:ASP407 2.3 20.8 1.0 O A:GLY300 2.5 23.4 1.0 O A:HIS406 2.5 21.3 1.0 OD1 A:ASP430 2.6 19.0 1.0 OD2 A:ASP430 2.6 22.4 1.0 O A:HOH2069 2.8 30.8 1.0 CG A:ASP430 2.9 19.7 1.0 C A:GLY300 3.4 23.4 1.0 C A:TYR302 3.4 21.8 1.0 CG A:ASP407 3.4 21.9 1.0 C A:HIS406 3.5 19.4 1.0 CA A:ASP407 3.7 19.0 1.0 N A:TYR302 3.8 22.1 1.0 N A:ASP407 4.0 19.8 1.0 CB A:ASP407 4.1 19.8 1.0 C A:GLY301 4.1 22.5 1.0 CA A:GLY300 4.2 21.1 1.0 CG A:MET304 4.2 16.0 1.0 CA A:TYR302 4.2 21.9 1.0 N A:GLY301 4.3 21.7 1.0 OD2 A:ASP407 4.4 25.9 1.0 N A:ASP303 4.4 20.8 1.0 CA A:GLY301 4.4 19.8 1.0 ND1 A:HIS406 4.4 37.5 1.0 O A:HOH2057 4.5 46.9 1.0 CB A:ASP430 4.5 19.1 1.0 N A:MET304 4.5 15.5 1.0 CB A:HIS406 4.6 25.4 1.0 CA A:ASP303 4.6 20.1 1.0 O A:GLY301 4.6 22.7 1.0 CA A:HIS406 4.6 21.5 1.0 CB A:TYR302 4.8 20.7 1.0 O A:HOH1074 4.8 18.6 1.0 C A:ASP407 5.0 18.7 1.0 CG A:HIS406 5.0 32.9 1.0

M.Machius, N.Declerck, R.Huber, G.Wiegand. Activation of Bacillus Licheniformis Alpha-Amylase Through A Disorder-->Order Transition of the Substrate-Binding Site Mediated By A Calcium-Sodium-Calcium Metal Triad. Structure V. 6 281 1998.
ISSN: ISSN 0969-2126
PubMed: 9551551
DOI: 10.1016/S0969-2126(98)00032-X