Calcium in PDB 3a6o: Crystal Structure of Thermoactinomyces Vulgaris R-47 Alpha- Amylase 2/Acarbose Complex

All present enzymatic activity of Crystal Structure of Thermoactinomyces Vulgaris R-47 Alpha- Amylase 2/Acarbose Complex:
3.2.1.135;

The structure of Crystal Structure of Thermoactinomyces Vulgaris R-47 Alpha- Amylase 2/Acarbose Complex, PDB code: 3a6o was solved by A.Ohtaki, M.Mizuno, T.Tonozuka, Y.Sakano, S.Kamitori, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.81 / 2.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	114.599, 119.258, 113.007, 90.00, 90.00, 90.00
R / Rfree (%)	15.7 / 23.1

The binding sites of Calcium atom in the Crystal Structure of Thermoactinomyces Vulgaris R-47 Alpha- Amylase 2/Acarbose Complex (pdb code 3a6o). 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 Thermoactinomyces Vulgaris R-47 Alpha- Amylase 2/Acarbose Complex, PDB code: 3a6o:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Crystal Structure of Thermoactinomyces Vulgaris R-47 Alpha- Amylase 2/Acarbose Complex


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 Thermoactinomyces Vulgaris R-47 Alpha- Amylase 2/Acarbose Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca586 b:19.7 occ:1.00 O A:GLY169 2.3 16.4 1.0 OD2 A:ASP171 2.3 21.8 1.0 OD2 A:ASP149 2.3 31.1 1.0 O A:HOH606 2.5 20.0 1.0 OD1 A:ASN143 2.5 24.6 1.0 OD1 A:ASN148 2.5 17.1 1.0 O A:ASP145 2.5 20.2 1.0 CG A:ASN143 3.2 23.8 1.0 C A:GLY169 3.3 16.9 1.0 CG A:ASP171 3.4 16.5 1.0 C A:ASP145 3.5 19.8 1.0 CG A:ASP149 3.5 27.7 1.0 ND2 A:ASN143 3.6 22.1 1.0 CA A:GLY169 3.7 17.9 1.0 CG A:ASN148 3.7 22.8 1.0 CB A:ASP171 4.0 12.2 1.0 CA A:ASP149 4.1 24.8 1.0 N A:ASP149 4.1 23.3 1.0 N A:PRO146 4.2 18.9 1.0 N A:ASP145 4.3 22.1 1.0 C A:ASN148 4.3 21.5 1.0 OD1 A:ASP149 4.3 26.1 1.0 ND2 A:ASN148 4.4 23.6 1.0 CB A:ASN143 4.4 21.4 1.0 CA A:ASP145 4.4 20.6 1.0 CB A:ASP149 4.4 24.0 1.0 CA A:PRO146 4.4 20.1 1.0 OD1 A:ASP171 4.4 14.2 1.0 O A:GLY170 4.4 17.6 1.0 C A:GLY170 4.4 15.7 1.0 N A:GLY170 4.5 15.9 1.0 CA A:ASN143 4.5 21.8 1.0 O A:GLN215 4.5 22.7 1.0 N A:ASP171 4.6 14.3 1.0 O A:ASN148 4.7 21.4 1.0 CB A:ASP145 4.8 19.5 1.0 C A:PRO146 4.9 21.3 1.0 N A:ASN148 4.9 20.4 1.0 CA A:GLY170 4.9 14.9 1.0 C A:ASN143 4.9 20.7 1.0 CA A:ASP171 4.9 14.2 1.0 CA A:ASN148 4.9 19.8 1.0 CB A:ASN148 4.9 18.6 1.0 N A:GLY144 4.9 19.8 1.0

Calcium binding site 2 out of 2 in the Crystal Structure of Thermoactinomyces Vulgaris R-47 Alpha- Amylase 2/Acarbose Complex


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 Thermoactinomyces Vulgaris R-47 Alpha- Amylase 2/Acarbose Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca586 b:28.9 occ:1.00 OD1 B:ASN148 2.2 37.6 1.0 OD1 B:ASP149 2.3 36.6 1.0 OD1 B:ASN143 2.3 30.4 1.0 OD1 B:ASP171 2.4 33.2 1.0 O B:HOH603 2.5 21.1 1.0 O B:GLY169 2.5 28.9 1.0 O B:ASP145 2.6 35.0 1.0 CG B:ASN148 3.2 38.8 1.0 CG B:ASP171 3.3 30.0 1.0 CG B:ASN143 3.4 31.1 1.0 C B:ASP145 3.4 34.7 1.0 CG B:ASP149 3.5 34.6 1.0 C B:GLY169 3.6 29.9 1.0 ND2 B:ASN148 3.7 34.5 1.0 CB B:ASP171 3.7 27.0 1.0 ND2 B:ASN143 3.9 30.6 1.0 OD2 B:ASP149 4.1 32.7 1.0 CA B:GLY169 4.1 29.6 1.0 N B:ASP149 4.2 38.7 1.0 N B:ASP145 4.2 32.5 1.0 CA B:PRO146 4.2 35.7 1.0 CA B:ASP145 4.2 33.5 1.0 N B:PRO146 4.3 35.2 1.0 CA B:ASP149 4.3 38.0 1.0 O B:GLN215 4.3 27.8 1.0 C B:ASN148 4.4 39.6 1.0 OD2 B:ASP171 4.4 31.6 1.0 CB B:ASN143 4.5 29.0 1.0 CA B:ASN143 4.5 29.6 1.0 CB B:ASP149 4.5 36.1 1.0 O B:GLY170 4.5 28.9 1.0 C B:GLY170 4.5 27.6 1.0 CB B:ASN148 4.6 39.2 1.0 CB B:ASP145 4.6 32.4 1.0 N B:ASN148 4.6 40.3 1.0 N B:ASP171 4.7 27.1 1.0 C B:PRO146 4.7 35.7 1.0 O B:HOH666 4.7 32.7 1.0 N B:GLY170 4.8 29.1 1.0 CA B:ASP171 4.8 26.2 1.0 CA B:ASN148 4.8 39.6 1.0 O B:ASN148 4.8 40.1 1.0 C B:ASN143 4.9 30.2 1.0 N B:GLY144 5.0 30.0 1.0

A.Ohtaki, M.Mizuno, T.Tonozuka, Y.Sakano, S.Kamitori. Complex Structures of Thermoactinomyces Vulgaris R-47 Alpha-Amylase 2 with Acarbose and Cyclodextrins Demonstrate the Multiple Substrate Recognition Mechanism J.Biol.Chem. V. 279 31033 2004.
ISSN: ISSN 0021-9258
PubMed: 15138257
DOI: 10.1074/JBC.M404311200