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Calcium in PDB 6toz: Crystal Structure of Bacillus Paralicheniformis Alpha-Amylase in Complex with Acarbose

Enzymatic activity of Crystal Structure of Bacillus Paralicheniformis Alpha-Amylase in Complex with Acarbose

All present enzymatic activity of Crystal Structure of Bacillus Paralicheniformis Alpha-Amylase in Complex with Acarbose:
3.2.1.1;

Protein crystallography data

The structure of Crystal Structure of Bacillus Paralicheniformis Alpha-Amylase in Complex with Acarbose, PDB code: 6toz was solved by H.J.Rozeboom, D.B.Janssen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.01 / 1.94
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 83.060, 83.060, 188.050, 90.00, 90.00, 90.00
R / Rfree (%) 15.6 / 18.1

Other elements in 6toz:

The structure of Crystal Structure of Bacillus Paralicheniformis Alpha-Amylase in Complex with Acarbose also contains other interesting chemical elements:

Sodium (Na) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Bacillus Paralicheniformis Alpha-Amylase in Complex with Acarbose (pdb code 6toz). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Crystal Structure of Bacillus Paralicheniformis Alpha-Amylase in Complex with Acarbose, PDB code: 6toz:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 6toz

Go back to Calcium Binding Sites List in 6toz
Calcium binding site 1 out of 2 in the Crystal Structure of Bacillus Paralicheniformis Alpha-Amylase in Complex with Acarbose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Bacillus Paralicheniformis Alpha-Amylase in Complex with Acarbose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca501

b:14.5
occ:1.00
O A:HIS235 2.3 15.4 1.0
OD1 A:ASP194 2.3 15.3 1.0
OD1 A:ASP200 2.3 14.8 1.0
OD1 A:ASN104 2.3 13.6 1.0
O A:ASP194 2.4 14.5 1.0
O A:HOH778 2.4 12.2 1.0
CG A:ASP200 3.1 15.0 1.0
OD2 A:ASP200 3.1 15.2 1.0
C A:ASP194 3.3 14.9 1.0
CG A:ASP194 3.4 15.2 1.0
C A:HIS235 3.5 15.0 1.0
CG A:ASN104 3.5 13.5 1.0
CA A:ASP194 3.8 15.0 1.0
O A:HOH797 3.9 13.9 1.0
O A:ASN104 3.9 13.8 1.0
NA A:NA503 3.9 15.1 1.0
CB A:HIS235 4.0 14.7 1.0
ND2 A:ASN104 4.1 13.3 1.0
CB A:ASP194 4.2 15.4 1.0
OD2 A:ASP194 4.2 15.2 1.0
CA A:HIS235 4.2 14.8 1.0
O A:HOH704 4.4 12.1 1.0
N A:TYR195 4.4 15.2 1.0
N A:ILE236 4.5 14.8 1.0
CB A:ASP200 4.5 14.8 1.0
O A:ILE201 4.6 13.9 1.0
CB A:ASN104 4.6 13.3 1.0
CA A:ILE236 4.7 14.9 1.0
C A:ASN104 4.7 13.7 1.0
CA A:ASN104 4.8 13.6 1.0
CA A:TYR195 4.8 15.4 1.0
CG1 A:ILE236 4.9 14.2 1.0

Calcium binding site 2 out of 2 in 6toz

Go back to Calcium Binding Sites List in 6toz
Calcium binding site 2 out of 2 in the Crystal Structure of Bacillus Paralicheniformis Alpha-Amylase in Complex with Acarbose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Bacillus Paralicheniformis Alpha-Amylase in Complex with Acarbose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca502

b:16.2
occ:1.00
O A:ALA181 2.3 15.5 1.0
OD1 A:ASP183 2.3 16.6 1.0
OD1 A:ASP202 2.3 15.7 1.0
OD1 A:ASP161 2.4 15.6 1.0
OD2 A:ASP204 2.5 19.0 1.0
OD2 A:ASP161 2.5 15.0 1.0
O A:HOH942 2.5 11.9 1.0
CG A:ASP161 2.8 15.3 1.0
CG A:ASP202 3.3 15.7 1.0
CG A:ASP204 3.4 18.9 1.0
CG A:ASP183 3.5 16.3 1.0
C A:ALA181 3.5 16.2 1.0
OD2 A:ASP202 3.9 16.0 1.0
CB A:ASP204 3.9 18.9 1.0
N A:ASP183 4.0 16.5 1.0
OD2 A:ASP183 4.1 15.6 1.0
N A:ALA181 4.1 16.7 1.0
CB A:ASP202 4.1 15.3 1.0
CA A:ASP202 4.2 15.0 1.0
C A:TRP182 4.2 16.2 1.0
N A:ASP204 4.3 17.5 1.0
CB A:ASP161 4.3 15.2 1.0
OD1 A:ASP204 4.3 19.4 1.0
CA A:ASP183 4.4 17.2 1.0
CA A:ALA181 4.4 16.8 1.0
N A:TRP182 4.5 16.1 1.0
NA A:NA503 4.5 15.1 1.0
CA A:TRP182 4.5 15.9 1.0
CB A:ASP183 4.5 16.5 1.0
O A:HOH997 4.5 33.0 1.0
N A:TYR203 4.6 15.3 1.0
O A:HOH844 4.6 20.3 1.0
C A:ASP202 4.6 15.3 1.0
O A:TRP182 4.7 16.2 1.0
CA A:ASP204 4.8 18.3 1.0
CB A:ALA181 4.9 17.3 1.0
OD2 A:ASP194 4.9 15.2 1.0

Reference:

N.Bozic, H.J.Rozeboom, N.Loncar, M.S.Slavic, D.B.Janssen, Z.Vujcic. Characterization of the Starch Surface Binding Site on Bacillus Paralicheniformis Alpha-Amylase. Int.J.Biol.Macromol. V. 165 1529 2020.
ISSN: ISSN 0141-8130
PubMed: 33058974
DOI: 10.1016/J.IJBIOMAC.2020.10.025
Page generated: Wed Jul 9 18:14:09 2025

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