Calcium in PDB 1vfo: Crystal Structure of Thermoactinomyces Vulgaris R-47 Alpha- Amylase 2/Beta-Cyclodextrin Complex

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

The structure of Crystal Structure of Thermoactinomyces Vulgaris R-47 Alpha- Amylase 2/Beta-Cyclodextrin Complex, PDB code: 1vfo 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)	38.87 / 2.81
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	115.083, 118.812, 114.277, 90.00, 90.00, 90.00
R / Rfree (%)	20 / 25.6

The binding sites of Calcium atom in the Crystal Structure of Thermoactinomyces Vulgaris R-47 Alpha- Amylase 2/Beta-Cyclodextrin Complex (pdb code 1vfo). 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/Beta-Cyclodextrin Complex, PDB code: 1vfo:
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/Beta-Cyclodextrin 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/Beta-Cyclodextrin Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1001 b:35.4 occ:1.00 OD1 A:ASN143 2.3 33.3 1.0 OD1 A:ASN148 2.3 39.0 1.0 OD2 A:ASP149 2.4 33.1 1.0 O A:GLY169 2.4 36.9 1.0 O A:ASP145 2.5 35.7 1.0 OD2 A:ASP171 2.5 28.3 1.0 CG A:ASN143 3.2 32.3 1.0 C A:GLY169 3.4 35.4 1.0 CG A:ASN148 3.5 36.4 1.0 CG A:ASP149 3.5 32.7 1.0 C A:ASP145 3.5 35.1 1.0 CG A:ASP171 3.6 30.0 1.0 ND2 A:ASN143 3.6 28.2 1.0 CA A:GLY169 3.8 35.0 1.0 N A:ASP149 3.9 33.8 1.0 CB A:ASP171 4.0 28.8 1.0 CA A:ASP149 4.1 33.5 1.0 ND2 A:ASN148 4.1 36.3 1.0 C A:ASN148 4.1 34.2 1.0 O A:GLN215 4.3 35.3 1.0 OD1 A:ASP149 4.3 31.2 1.0 N A:PRO146 4.3 33.8 1.0 CB A:ASN143 4.4 30.5 1.0 CB A:ASP149 4.4 32.4 1.0 N A:ASP145 4.4 34.5 1.0 CA A:ASP145 4.4 34.5 1.0 CA A:PRO146 4.5 32.5 1.0 O A:ASN148 4.5 33.8 1.0 N A:ASN148 4.6 34.8 1.0 CA A:ASN143 4.6 31.4 1.0 N A:GLY170 4.6 35.6 1.0 CB A:ASN148 4.6 34.8 1.0 OD1 A:ASP171 4.7 26.5 1.0 CA A:ASN148 4.7 34.7 1.0 C A:GLY170 4.7 32.2 1.0 CB A:ASP145 4.7 37.1 1.0 C A:PRO146 4.7 33.0 1.0 N A:ASP171 4.8 29.7 1.0 O A:GLY170 4.8 31.5 1.0 O A:PRO146 4.9 33.3 1.0 C A:ASN143 5.0 31.4 1.0

Calcium binding site 2 out of 2 in the Crystal Structure of Thermoactinomyces Vulgaris R-47 Alpha- Amylase 2/Beta-Cyclodextrin 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/Beta-Cyclodextrin Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1002 b:66.4 occ:1.00 O B:GLY169 2.1 69.2 1.0 O B:ASP145 2.1 61.6 1.0 OD1 B:ASN148 2.2 69.7 1.0 OD1 B:ASP149 2.5 76.2 1.0 OD1 B:ASN143 2.5 60.3 1.0 OD1 B:ASP171 3.1 60.6 1.0 CG B:ASN148 3.2 69.5 1.0 C B:ASP145 3.2 62.2 1.0 CG B:ASN143 3.3 60.1 1.0 C B:GLY169 3.3 69.1 1.0 CG B:ASP149 3.5 74.7 1.0 ND2 B:ASN143 3.6 58.5 1.0 CG B:ASP171 3.7 62.0 1.0 ND2 B:ASN148 3.7 68.8 1.0 CA B:GLY169 3.9 70.3 1.0 CB B:ASP171 4.0 60.7 1.0 N B:PRO146 4.1 63.2 1.0 N B:ASP149 4.1 71.2 1.0 N B:ASP145 4.2 61.0 1.0 OD2 B:ASP149 4.2 75.7 1.0 CA B:PRO146 4.2 63.1 1.0 CA B:ASP145 4.2 60.7 1.0 O B:GLN215 4.2 58.3 1.0 CA B:ASP149 4.3 71.8 1.0 C B:ASN148 4.3 70.3 1.0 N B:GLY170 4.4 67.7 1.0 C B:GLY170 4.4 62.1 1.0 OD2 B:ASP171 4.4 63.0 1.0 CB B:ASN143 4.5 59.5 1.0 CB B:ASP149 4.5 72.9 1.0 CB B:ASN148 4.5 69.8 1.0 N B:ASP171 4.6 60.9 1.0 O B:GLY170 4.6 60.3 1.0 CA B:ASN143 4.6 61.0 1.0 CA B:GLY170 4.7 64.4 1.0 CB B:ASP145 4.7 59.4 1.0 O B:ASN148 4.7 69.4 1.0 C B:PRO146 4.8 63.5 1.0 N B:ASN148 4.8 68.7 1.0 CA B:ASN148 4.8 69.9 1.0 C B:ASN143 4.9 61.1 1.0 CA B:ASP171 5.0 59.8 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