Calcium in PDB 1hvx: Bacillus Stearothermophilus Alpha-Amylase

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

The structure of Bacillus Stearothermophilus Alpha-Amylase, PDB code: 1hvx was solved by D.Suvd, Z.Fujimoto, K.Takase, M.Matsumura, H.Mizuno, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	8.00 / 2.00
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	53.550, 93.119, 53.275, 90.00, 109.31, 90.00
R / Rfree (%)	15.4 / 19.7

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

Sodium

(Na)

1 atom

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

Calcium binding site 1 out of 3 in the Bacillus Stearothermophilus 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 Stearothermophilus Alpha-Amylase within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca516 b:4.2 occ:1.00 O A:ALA184 2.3 8.9 1.0 O A:HOH727 2.4 12.7 1.0 OD1 A:ASP205 2.5 4.2 1.0 O A:HOH655 2.5 6.1 1.0 OD1 A:ASP186 2.5 7.8 1.0 OD1 A:ASP162 2.6 7.9 1.0 OD2 A:ASP162 2.7 4.4 1.0 CG A:ASP162 3.0 7.7 1.0 CG A:ASP205 3.3 6.9 1.0 CG A:ASP186 3.4 6.3 1.0 C A:ALA184 3.5 8.1 1.0 OD2 A:ASP205 3.9 6.5 1.0 N A:ASP186 3.9 6.0 1.0 OD2 A:ASP186 4.0 5.3 1.0 C A:TRP185 4.0 6.7 1.0 N A:ALA184 4.1 9.3 1.0 OD2 A:ASP207 4.2 17.6 1.0 CB A:ASP207 4.2 13.5 1.0 CB A:ASP205 4.2 6.1 1.0 CA A:ASP186 4.2 6.8 1.0 O A:TRP185 4.4 5.2 1.0 CA A:ASP205 4.4 6.8 1.0 CA A:TRP185 4.4 5.7 1.0 N A:TRP185 4.4 6.3 1.0 CB A:ASP186 4.4 4.2 1.0 CB A:ASP162 4.4 4.2 1.0 CA A:ALA184 4.4 9.2 1.0 CG A:ASP207 4.6 17.1 1.0 NA A:NA519 4.7 2.0 1.0 N A:ASP207 4.7 8.8 1.0 O A:HOH661 4.9 14.7 1.0 C A:ASP205 4.9 6.0 1.0 O A:GLY182 4.9 15.5 1.0 N A:MET206 5.0 6.9 1.0

Calcium binding site 2 out of 3 in the Bacillus Stearothermophilus 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 Stearothermophilus Alpha-Amylase within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca517 b:7.4 occ:1.00 O A:HIS238 2.3 4.7 1.0 O A:ASP197 2.4 2.5 1.0 O A:HOH609 2.4 7.1 1.0 OD1 A:ASP105 2.4 2.0 1.0 OD1 A:ASP203 2.5 3.4 1.0 OD1 A:ASP197 2.5 3.9 1.0 C A:ASP197 3.4 4.1 1.0 CG A:ASP203 3.5 5.1 1.0 C A:HIS238 3.5 5.3 1.0 CG A:ASP105 3.5 3.5 1.0 CG A:ASP197 3.6 6.0 1.0 OD2 A:ASP203 3.8 5.6 1.0 CA A:ASP197 3.9 5.5 1.0 O A:HOH746 3.9 3.7 1.0 O A:ASP105 3.9 3.2 1.0 CB A:HIS238 4.0 5.0 1.0 O A:HOH719 4.1 2.7 1.0 NA A:NA519 4.1 2.0 1.0 OD2 A:ASP105 4.2 2.0 1.0 CA A:HIS238 4.3 4.6 1.0 CB A:ASP197 4.4 5.0 1.0 N A:TYR198 4.4 3.9 1.0 OD2 A:ASP197 4.5 3.1 1.0 N A:ILE239 4.5 5.1 1.0 CB A:ASP105 4.5 2.0 1.0 CA A:ILE239 4.6 4.3 1.0 CA A:ASP105 4.6 3.5 1.0 C A:ASP105 4.7 4.0 1.0 O A:LEU204 4.7 4.7 1.0 CA A:TYR198 4.7 3.8 1.0 CG1 A:ILE239 4.7 2.7 1.0 CB A:ASP203 4.8 3.6 1.0

Calcium binding site 3 out of 3 in the Bacillus Stearothermophilus 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 Stearothermophilus Alpha-Amylase within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca518 b:6.6 occ:1.00 O A:PHE305 2.3 7.5 1.0 O A:GLY303 2.3 9.3 1.0 O A:HOH941 2.4 8.8 1.0 O A:SER406 2.5 7.2 1.0 OD1 A:ASP407 2.6 10.6 1.0 OD1 A:ASP430 2.6 13.1 1.0 OD2 A:ASP430 2.6 8.8 1.0 CG A:ASP430 3.0 11.3 1.0 C A:GLY303 3.4 10.8 1.0 C A:PHE305 3.4 7.7 1.0 C A:SER406 3.5 8.1 1.0 CG A:ASP407 3.7 12.1 1.0 N A:PHE305 3.8 11.5 1.0 C A:THR304 3.9 13.6 1.0 CA A:ASP407 3.9 7.1 1.0 N A:ASP407 4.1 8.1 1.0 CA A:PHE305 4.2 8.5 1.0 N A:THR304 4.2 10.4 1.0 O A:THR304 4.2 14.8 1.0 CA A:GLY303 4.3 11.4 1.0 O A:HOH1000 4.3 25.1 1.0 CA A:THR304 4.3 12.7 1.0 CB A:ASP407 4.4 6.7 1.0 N A:ASP306 4.4 4.8 1.0 CG A:MET307 4.5 6.8 1.0 CB A:ASP430 4.5 7.4 1.0 CB A:SER406 4.5 11.4 1.0 N A:MET307 4.5 5.4 1.0 CA A:SER406 4.6 9.5 1.0 CA A:ASP306 4.6 5.2 1.0 OG A:SER406 4.6 13.1 1.0 O A:HOH636 4.6 27.3 1.0 OD2 A:ASP407 4.7 15.9 1.0 O A:HOH617 4.8 8.4 1.0 CB A:PHE305 4.8 9.8 1.0

D.Suvd, Z.Fujimoto, K.Takase, M.Matsumura, H.Mizuno. Crystal Structure of Bacillus Stearothermophilus Alpha-Amylase: Possible Factors Determining the Thermostability. J.Biochem. V. 129 461 2001.
ISSN: ISSN 0021-924X
PubMed: 11226887
DOI: 10.1093/OXFORDJOURNALS.JBCHEM.A002878