Calcium in PDB 2die: Alkaline Alpha-Amylase Amyk From Bacillus Sp. Ksm-1378

All present enzymatic activity of Alkaline Alpha-Amylase Amyk From Bacillus Sp. Ksm-1378:
3.2.1.1;

The structure of Alkaline Alpha-Amylase Amyk From Bacillus Sp. Ksm-1378, PDB code: 2die was solved by T.Shirai, K.Igarashi, T.Ozawa, H.Hagihara, T.Kobayashi, K.Ozaki, S.Ito, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	8.00 / 2.10
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	174.577, 41.467, 74.855, 90.00, 92.24, 90.00
R / Rfree (%)	17.7 / 23.1

The structure of Alkaline Alpha-Amylase Amyk From Bacillus Sp. Ksm-1378 also contains other interesting chemical elements:

Sodium

(Na)

1 atom

The binding sites of Calcium atom in the Alkaline Alpha-Amylase Amyk From Bacillus Sp. Ksm-1378 (pdb code 2die). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Alkaline Alpha-Amylase Amyk From Bacillus Sp. Ksm-1378, PDB code: 2die:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Alkaline Alpha-Amylase Amyk From Bacillus Sp. Ksm-1378


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Alkaline Alpha-Amylase Amyk From Bacillus Sp. Ksm-1378 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca778 b:10.7 occ:1.00 O A:ALA186 2.3 10.3 1.0 OD2 A:ASP188 2.4 11.0 1.0 OD1 A:ASP163 2.4 8.4 1.0 OD2 A:ASP163 2.5 4.5 1.0 OD1 A:ASP207 2.5 7.6 1.0 O A:HOH635 2.7 8.6 1.0 CG A:ASP163 2.8 8.0 1.0 CG A:ASP207 3.1 6.8 1.0 CG A:ASP188 3.5 8.9 1.0 C A:ALA186 3.6 9.1 1.0 OD2 A:ASP207 3.6 8.3 1.0 N A:ASP188 3.8 8.3 1.0 N A:ALA186 4.1 10.2 1.0 CB A:ASP207 4.1 7.1 1.0 C A:TRP187 4.1 8.7 1.0 CA A:ASP188 4.2 11.5 1.0 OD2 A:ASP209 4.2 17.9 1.0 OD1 A:ASP188 4.2 9.4 1.0 CA A:ASP207 4.2 7.1 1.0 CB A:ASP163 4.2 6.7 1.0 NA A:NA781 4.4 14.5 1.0 CB A:ASP188 4.4 9.7 1.0 CA A:ALA186 4.4 9.3 1.0 CA A:TRP187 4.5 6.9 1.0 N A:TRP187 4.5 6.8 1.0 CB A:ASP209 4.5 13.1 1.0 N A:MET208 4.6 9.3 1.0 C A:ASP207 4.7 7.5 1.0 O A:TRP187 4.7 8.2 1.0 O A:HOH640 4.7 12.8 1.0 N A:ASP209 4.7 11.2 1.0 OD2 A:ASP199 4.8 8.4 1.0 CG A:ASP209 4.8 13.7 1.0

Calcium binding site 2 out of 3 in the Alkaline Alpha-Amylase Amyk From Bacillus Sp. Ksm-1378


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Alkaline Alpha-Amylase Amyk From Bacillus Sp. Ksm-1378 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca779 b:6.8 occ:1.00 OD1 A:ASN106 2.3 8.9 1.0 OD2 A:ASP205 2.3 12.1 1.0 O A:ASP199 2.3 9.6 1.0 O A:HIS240 2.4 10.2 1.0 OD1 A:ASP199 2.4 9.2 1.0 O A:HOH707 2.6 5.0 1.0 CG A:ASP205 3.2 9.5 1.0 C A:ASP199 3.2 9.7 1.0 OD1 A:ASP205 3.4 10.9 1.0 CG A:ASN106 3.4 9.8 1.0 C A:HIS240 3.5 8.2 1.0 CG A:ASP199 3.6 9.9 1.0 CA A:ASP199 3.8 8.9 1.0 O A:HOH611 3.9 3.2 1.0 O A:ASN106 4.0 9.8 1.0 CB A:HIS240 4.0 8.0 1.0 NA A:NA781 4.1 14.5 1.0 ND2 A:ASN106 4.2 7.6 1.0 O A:HOH494 4.3 5.6 1.0 N A:TYR200 4.3 10.3 1.0 CB A:ASP199 4.3 8.6 1.0 CA A:HIS240 4.3 7.3 1.0 OD2 A:ASP199 4.5 8.4 1.0 N A:ILE241 4.5 8.6 1.0 CB A:ASN106 4.5 8.4 1.0 CA A:TYR200 4.6 10.2 1.0 CB A:ASP205 4.6 8.1 1.0 CA A:ILE241 4.7 6.6 1.0 CA A:ASN106 4.8 7.8 1.0 O A:ILE206 4.8 6.0 1.0 C A:ASN106 4.8 7.8 1.0 CG1 A:ILE241 4.8 4.9 1.0 O A:TYR198 4.9 8.0 1.0

Calcium binding site 3 out of 3 in the Alkaline Alpha-Amylase Amyk From Bacillus Sp. Ksm-1378


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Alkaline Alpha-Amylase Amyk From Bacillus Sp. Ksm-1378 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca780 b:15.6 occ:1.00 OD1 A:ASP409 2.4 12.9 1.0 O A:PHE307 2.4 11.2 1.0 O A:GLY305 2.4 11.5 1.0 O A:HOH765 2.4 17.0 1.0 OD1 A:ASP432 2.5 11.8 1.0 O A:HIS408 2.6 10.6 1.0 OD2 A:ASP432 2.6 14.2 1.0 CG A:ASP432 2.9 11.8 1.0 C A:GLY305 3.4 12.5 1.0 C A:HIS408 3.6 13.2 1.0 C A:PHE307 3.6 10.7 1.0 CG A:ASP409 3.6 17.6 1.0 N A:PHE307 3.8 9.6 1.0 CA A:ASP409 3.9 13.6 1.0 N A:ASP409 4.1 13.8 1.0 C A:TYR306 4.2 11.9 1.0 CA A:GLY305 4.2 12.9 1.0 N A:TYR306 4.3 12.1 1.0 CG A:MET309 4.3 10.9 1.0 CA A:PHE307 4.3 10.1 1.0 CB A:ASP409 4.3 15.2 1.0 CA A:TYR306 4.4 11.8 1.0 CB A:ASP432 4.4 10.5 1.0 N A:MET309 4.5 12.9 1.0 OD2 A:ASP409 4.5 16.1 1.0 CD2 A:HIS408 4.5 15.1 1.0 N A:ASP308 4.6 11.3 1.0 O A:HOH526 4.6 5.7 1.0 CB A:HIS408 4.7 13.0 1.0 CA A:HIS408 4.7 12.8 1.0 CA A:ASP308 4.7 12.0 1.0 O A:TYR306 4.8 11.7 1.0 C A:ASP432 4.9 11.4 1.0 CB A:PHE307 4.9 8.4 1.0 CG A:HIS408 5.0 14.9 1.0 O A:ASP432 5.0 9.9 1.0

T.Shirai, K.Igarashi, T.Ozawa, H.Hagihara, T.Kobayashi, K.Ozaki, S.Ito. Ancestral Sequence Evolutionary Trace and Crystal Structure Analyses of Alkaline Alpha-Amylase From Bacillus Sp. Ksm-1378 to Clarify the Alkaline Adaptation Process of Proteins Proteins V. 66 600 2007.
ISSN: ISSN 0887-3585
PubMed: 17154418
DOI: 10.1002/PROT.21255