Calcium in PDB 2gjr: Structure of Bacillus Halmapalus Alpha-Amylase Without Any Substrate Analogues

All present enzymatic activity of Structure of Bacillus Halmapalus Alpha-Amylase Without Any Substrate Analogues:
3.2.1.1;

The structure of Structure of Bacillus Halmapalus Alpha-Amylase Without Any Substrate Analogues, PDB code: 2gjr was solved by L.Lyhne-Iversen, T.J.Hobley, S.G.Kaasgaard, P.Harris, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.95 / 2.10
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	38.550, 59.040, 209.800, 90.00, 90.00, 90.00
R / Rfree (%)	20 / 24.2

The structure of Structure of Bacillus Halmapalus Alpha-Amylase Without Any Substrate Analogues also contains other interesting chemical elements:

Sodium

(Na)

1 atom

The binding sites of Calcium atom in the Structure of Bacillus Halmapalus Alpha-Amylase Without Any Substrate Analogues (pdb code 2gjr). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Structure of Bacillus Halmapalus Alpha-Amylase Without Any Substrate Analogues, PDB code: 2gjr:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Structure of Bacillus Halmapalus Alpha-Amylase Without Any Substrate Analogues


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of Bacillus Halmapalus Alpha-Amylase Without Any Substrate Analogues within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1486 b:7.2 occ:1.00 OD1 A:ASN106 2.3 7.5 1.0 O A:HIS240 2.3 9.2 1.0 OD1 A:ASP205 2.3 8.8 1.0 OD1 A:ASP199 2.3 11.1 1.0 O A:HOH1524 2.3 8.4 1.0 O A:ASP199 2.5 10.1 1.0 CG A:ASP205 3.1 9.6 1.0 OD2 A:ASP205 3.2 9.4 1.0 C A:ASP199 3.3 10.9 1.0 CG A:ASP199 3.4 11.2 1.0 CG A:ASN106 3.4 8.0 1.0 C A:HIS240 3.4 9.9 1.0 CA A:ASP199 3.8 10.6 1.0 O A:ASN106 3.9 8.8 1.0 NA A:NA1489 3.9 10.8 1.0 CB A:HIS240 4.0 9.7 1.0 O A:HOH1512 4.0 18.2 1.0 ND2 A:ASN106 4.1 7.7 1.0 O A:HOH1515 4.2 4.7 1.0 CB A:ASP199 4.2 10.6 1.0 CA A:HIS240 4.3 9.5 1.0 OD2 A:ASP199 4.3 11.4 1.0 N A:ILE241 4.4 8.4 1.0 N A:TYR200 4.4 12.0 1.0 O A:VAL206 4.5 9.9 1.0 CB A:ASP205 4.5 9.6 1.0 CA A:ILE241 4.5 9.1 1.0 CB A:ASN106 4.6 8.8 1.0 C A:ASN106 4.7 9.4 1.0 CA A:ASN106 4.7 9.7 1.0 CG1 A:ILE241 4.8 7.7 1.0 CA A:TYR200 4.8 12.2 1.0 N A:VAL206 5.0 10.7 1.0

Calcium binding site 2 out of 3 in the Structure of Bacillus Halmapalus Alpha-Amylase Without Any Substrate Analogues


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of Bacillus Halmapalus Alpha-Amylase Without Any Substrate Analogues within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1487 b:15.4 occ:1.00 OD1 A:ASP188 2.3 9.6 1.0 OD2 A:ASP163 2.3 10.0 1.0 OD1 A:ASP163 2.3 9.6 1.0 OD1 A:ASP207 2.4 12.6 1.0 O A:ALA186 2.4 17.8 1.0 CG A:ASP163 2.6 10.4 1.0 OD2 A:ASP209 2.8 16.3 1.0 O A:HOH1574 2.8 11.3 1.0 CG A:ASP207 3.1 11.9 1.0 CG A:ASP188 3.3 10.3 1.0 CG A:ASP209 3.6 15.9 1.0 C A:ALA186 3.6 16.8 1.0 OD2 A:ASP207 3.7 12.0 1.0 OD2 A:ASP188 3.8 10.1 1.0 N A:ASP188 3.9 12.3 1.0 CB A:ASP209 4.0 14.6 1.0 C A:TRP187 4.1 13.3 1.0 CB A:ASP207 4.1 12.1 1.0 CB A:ASP163 4.2 10.0 1.0 CA A:ASP188 4.2 11.4 1.0 CA A:ASP207 4.2 11.3 1.0 N A:ALA186 4.3 18.3 1.0 CB A:ASP188 4.3 10.5 1.0 NA A:NA1489 4.3 10.8 1.0 CA A:TRP187 4.4 14.6 1.0 N A:ASP209 4.5 13.1 1.0 O A:TRP187 4.5 13.0 1.0 O A:HOH1573 4.5 20.2 1.0 N A:TRP187 4.5 15.5 1.0 OD1 A:ASP209 4.6 15.7 1.0 CA A:ALA186 4.6 17.4 1.0 N A:MET208 4.6 10.7 1.0 C A:ASP207 4.7 11.5 1.0 OD2 A:ASP199 4.8 11.4 1.0 CA A:ASP209 4.9 13.4 1.0

Calcium binding site 3 out of 3 in the Structure of Bacillus Halmapalus Alpha-Amylase Without Any Substrate Analogues


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure of Bacillus Halmapalus Alpha-Amylase Without Any Substrate Analogues within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1488 b:15.5 occ:1.00 OD1 A:ASP432 2.2 8.5 1.0 O A:TYR307 2.3 15.1 1.0 OD2 A:ASP432 2.3 7.5 1.0 OD1 A:ASN409 2.3 12.1 1.0 O A:HIS408 2.3 11.1 1.0 O A:GLY305 2.5 18.6 1.0 CG A:ASP432 2.6 7.7 1.0 C A:HIS408 3.4 12.0 1.0 CG A:ASN409 3.4 11.8 1.0 C A:GLY305 3.5 18.1 1.0 C A:TYR307 3.5 15.1 1.0 CA A:ASN409 3.6 11.1 1.0 N A:TYR307 3.8 16.2 1.0 N A:ASN409 3.9 11.7 1.0 CG A:MET309 3.9 11.9 1.0 CB A:ASN409 4.0 11.1 1.0 C A:ASN306 4.1 17.3 1.0 CB A:ASP432 4.1 9.0 1.0 CA A:TYR307 4.2 14.9 1.0 N A:ASN306 4.2 18.4 1.0 CA A:GLY305 4.3 18.4 1.0 N A:MET309 4.4 13.2 1.0 CA A:ASN306 4.4 17.8 1.0 N A:ASP308 4.5 15.1 1.0 ND2 A:ASN409 4.6 12.0 1.0 CA A:HIS408 4.6 12.9 1.0 O A:ASN306 4.6 16.6 1.0 O A:HOH1506 4.6 13.9 1.0 CA A:ASP308 4.7 14.1 1.0 CB A:TYR307 4.7 14.6 1.0 CB A:HIS408 4.7 13.9 1.0 C A:ASN409 4.8 11.1 1.0 CB A:MET309 4.8 11.9 1.0 N A:GLY433 4.9 11.9 1.0 C A:ASP432 4.9 11.2 1.0 CA A:ASP432 4.9 10.3 1.0 O A:ASN409 5.0 10.6 1.0

L.Lyhne-Iversen, T.J.Hobley, S.G.Kaasgaard, P.Harris. Structure of Bacillus Halmapalus Alpha-Amylase Crystallized with and Without the Substrate Analogue Acarbose and Maltose. Acta Crystallogr.,Sect.F V. 62 849 2006.
ISSN: ESSN 1744-3091
PubMed: 16946462
DOI: 10.1107/S174430910603096X