Calcium in PDB 1w9x: Bacillus Halmapalus Alpha Amylase

All present enzymatic activity of Bacillus Halmapalus Alpha Amylase:
3.2.1.1;

The structure of Bacillus Halmapalus Alpha Amylase, PDB code: 1w9x was solved by G.J.Davies, A.M.Brzozowski, Z.Dauter, M.D.Rasmussen, T.V.Borchert, K.S.Wilson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	15.00 / 2.1
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	48.180, 75.847, 155.230, 90.00, 90.00, 90.00
R / Rfree (%)	15.1 / 19.8

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

Sodium

(Na)

1 atom

The binding sites of Calcium atom in the Bacillus Halmapalus Alpha Amylase (pdb code 1w9x). 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 Halmapalus Alpha Amylase, PDB code: 1w9x:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Bacillus Halmapalus 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 Halmapalus Alpha Amylase within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1486 b:8.4 occ:1.00 OD1 A:ASP199 2.3 5.0 1.0 O A:HIS240 2.3 6.7 1.0 OD1 A:ASN106 2.3 9.7 1.0 O A:ASP199 2.4 8.2 1.0 OD1 A:ASP205 2.4 8.9 1.0 O A:HOH2126 2.5 7.5 1.0 OD2 A:ASP205 3.1 10.3 1.0 CG A:ASP205 3.1 10.4 1.0 C A:ASP199 3.3 8.4 1.0 CG A:ASP199 3.4 9.1 1.0 CG A:ASN106 3.5 8.9 1.0 C A:HIS240 3.5 7.4 1.0 CA A:ASP199 3.8 8.2 1.0 O A:HOH2109 3.9 11.6 1.0 NA A:NA1489 4.0 8.8 1.0 CB A:HIS240 4.0 6.7 1.0 ND2 A:ASN106 4.1 9.0 1.0 O A:ASN106 4.2 10.7 1.0 CB A:ASP199 4.2 8.2 1.0 CA A:HIS240 4.3 7.3 1.0 OD2 A:ASP199 4.3 7.9 1.0 N A:TYR200 4.4 9.2 1.0 O A:HOH2125 4.4 5.1 1.0 N A:ILE241 4.5 7.9 1.0 CB A:ASN106 4.6 8.6 1.0 CB A:ASP205 4.6 9.6 1.0 O A:VAL206 4.6 8.9 1.0 CA A:ILE241 4.7 8.2 1.0 CA A:TYR200 4.8 9.0 1.0 CA A:ASN106 4.9 9.5 1.0 C A:ASN106 4.9 10.4 1.0 CG1 A:ILE241 4.9 8.4 1.0

Calcium binding site 2 out of 3 in the Bacillus Halmapalus 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 Halmapalus Alpha Amylase within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1487 b:9.4 occ:1.00 OD1 A:ASP207 2.3 11.1 1.0 OD1 A:ASP188 2.3 11.6 1.0 O A:ALA186 2.3 11.1 1.0 OD1 A:ASP163 2.5 9.8 1.0 OD2 A:ASP163 2.6 6.9 1.0 O A:HOH2105 2.6 13.4 1.0 OD2 A:ASP209 2.8 27.4 1.0 CG A:ASP163 2.9 10.6 1.0 CG A:ASP207 3.2 12.6 1.0 CG A:ASP188 3.4 10.8 1.0 C A:ALA186 3.5 10.9 1.0 CG A:ASP209 3.6 23.2 1.0 OD2 A:ASP207 3.8 10.9 1.0 N A:ASP188 3.9 9.4 1.0 CB A:ASP209 4.0 19.2 1.0 OD2 A:ASP188 4.0 10.3 1.0 C A:TRP187 4.1 9.7 1.0 N A:ALA186 4.2 14.3 1.0 CB A:ASP207 4.2 9.9 1.0 CA A:ASP207 4.3 10.5 1.0 CA A:ASP188 4.3 10.5 1.0 CB A:ASP163 4.4 8.7 1.0 NA A:NA1489 4.4 8.8 1.0 N A:TRP187 4.4 9.0 1.0 CA A:TRP187 4.4 9.1 1.0 N A:ASP209 4.4 16.9 1.0 CB A:ASP188 4.5 9.1 1.0 CA A:ALA186 4.5 12.1 1.0 O A:TRP187 4.6 9.6 1.0 N A:MET208 4.6 12.1 1.0 OD1 A:ASP209 4.7 22.6 1.0 C A:ASP207 4.7 11.3 1.0 CA A:ASP209 4.9 18.9 1.0 OD2 A:ASP199 4.9 7.9 1.0 O A:HOH2088 5.0 26.9 1.0

Calcium binding site 3 out of 3 in the Bacillus Halmapalus 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 Halmapalus Alpha Amylase within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1488 b:13.4 occ:1.00 O A:TYR307 2.3 12.2 1.0 O A:GLY305 2.3 14.5 1.0 O A:HOH2180 2.4 10.6 1.0 OD1 A:ASP432 2.4 14.0 1.0 O A:HIS408 2.4 13.4 1.0 OD1 A:ASN409 2.5 14.9 1.0 OD2 A:ASP432 2.6 14.8 1.0 CG A:ASP432 2.9 11.6 1.0 C A:GLY305 3.4 14.0 1.0 C A:HIS408 3.4 14.4 1.0 C A:TYR307 3.5 12.3 1.0 CG A:ASN409 3.6 15.1 1.0 CA A:ASN409 3.8 11.9 1.0 N A:TYR307 3.8 12.4 1.0 N A:ASN409 4.0 13.7 1.0 C A:ASN306 4.0 14.5 1.0 CG A:MET309 4.2 13.8 1.0 N A:ASN306 4.2 14.0 1.0 CB A:ASN409 4.3 12.1 1.0 CA A:TYR307 4.3 12.2 1.0 CA A:ASN306 4.3 15.0 1.0 CA A:GLY305 4.3 13.1 1.0 CB A:ASP432 4.4 10.8 1.0 N A:MET309 4.5 11.8 1.0 N A:ASP308 4.5 11.6 1.0 CA A:HIS408 4.6 15.9 1.0 CB A:HIS408 4.6 16.6 1.0 O A:ASN306 4.6 14.8 1.0 CA A:ASP308 4.6 12.2 1.0 O A:HOH2178 4.7 21.2 1.0 ND2 A:ASN409 4.7 15.8 1.0 ND1 A:HIS408 4.7 23.0 1.0 O A:HOH2238 4.9 10.9 1.0 O A:HOH2176 4.9 35.2 1.0 CB A:TYR307 4.9 12.0 1.0

G.J.Davies, A.M.Brzozowski, Z.Dauter, M.D.Rasmussen, T.V.Borchert, K.S.Wilson. Structure of A Bacillus Halmapalus Family 13 Alpha-Amylase, Bha, in Complex with An Acarbose-Derived Nonasaccharide at 2.1 A Resolution Acta Crystallogr.,Sect.D V. 61 190 2005.
ISSN: ISSN 0907-4449
PubMed: 15681870
DOI: 10.1107/S0907444904027118