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

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

The structure of Crystal Structure of Thermoactinomyces Vulgaris R-47 Alpha- Amylase 2/Alpha-Cyclodextrin Complex, PDB code: 1vfm 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)	40.49 / 2.90
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	115.395, 118.428, 113.690, 90.00, 90.00, 90.00
R / Rfree (%)	19.1 / 24.8

The binding sites of Calcium atom in the Crystal Structure of Thermoactinomyces Vulgaris R-47 Alpha- Amylase 2/Alpha-Cyclodextrin Complex (pdb code 1vfm). 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/Alpha-Cyclodextrin Complex, PDB code: 1vfm:
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/Alpha-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/Alpha-Cyclodextrin Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1001 b:45.5 occ:1.00 OD2 A:ASP149 2.2 47.4 1.0 OD1 A:ASN143 2.3 41.0 1.0 OD1 A:ASN148 2.4 55.7 1.0 OD2 A:ASP171 2.5 48.7 1.0 O A:GLY169 2.5 49.2 1.0 O A:ASP145 2.6 46.2 1.0 CG A:ASN143 3.1 41.2 1.0 ND2 A:ASN143 3.4 41.3 1.0 CG A:ASP149 3.4 47.8 1.0 CG A:ASP171 3.5 47.8 1.0 C A:GLY169 3.5 48.7 1.0 CG A:ASN148 3.6 55.2 1.0 C A:ASP145 3.6 45.2 1.0 N A:ASP149 3.8 52.3 1.0 CB A:ASP171 3.8 45.2 1.0 CA A:GLY169 4.0 49.0 1.0 CA A:ASP149 4.0 51.5 1.0 CA A:PRO146 4.1 46.2 1.0 O A:GLN215 4.1 50.7 1.0 N A:PRO146 4.2 45.6 1.0 OD1 A:ASP149 4.3 47.1 1.0 ND2 A:ASN148 4.3 55.9 1.0 CB A:ASP149 4.3 49.5 1.0 C A:ASN148 4.3 53.1 1.0 CB A:ASN143 4.3 40.6 1.0 C A:GLY170 4.5 45.5 1.0 CA A:ASN143 4.5 42.0 1.0 N A:ASP145 4.5 42.6 1.0 N A:ASP171 4.6 44.3 1.0 N A:GLY170 4.6 47.6 1.0 CA A:ASP145 4.6 43.6 1.0 OD1 A:ASP171 4.6 48.1 1.0 O A:GLY170 4.7 46.1 1.0 N A:ASN148 4.7 53.0 1.0 CB A:ASN148 4.7 54.4 1.0 C A:PRO146 4.7 46.7 1.0 CA A:ASN148 4.8 53.4 1.0 CA A:ASP171 4.8 43.2 1.0 CA A:GLY170 4.9 46.3 1.0 O A:ASN148 4.9 54.0 1.0

Calcium binding site 2 out of 2 in the Crystal Structure of Thermoactinomyces Vulgaris R-47 Alpha- Amylase 2/Alpha-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/Alpha-Cyclodextrin Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1002 b:73.6 occ:1.00 OD1 B:ASN143 2.4 74.8 1.0 O B:GLY169 2.5 81.1 1.0 OD1 B:ASN148 2.5 81.9 1.0 OD1 B:ASP149 2.6 86.5 1.0 O B:ASP145 2.7 77.4 1.0 CG B:ASN143 2.9 75.2 1.0 ND2 B:ASN143 3.0 75.8 1.0 OD1 B:ASP171 3.1 67.7 1.0 CG B:ASP149 3.4 86.3 1.0 C B:GLY169 3.4 81.0 1.0 CG B:ASP171 3.5 69.1 1.0 C B:ASP145 3.6 77.8 1.0 CG B:ASN148 3.7 82.2 1.0 OD2 B:ASP149 3.8 86.2 1.0 CA B:GLY169 3.9 83.0 1.0 CB B:ASP171 3.9 68.3 1.0 N B:ASP149 4.1 84.8 1.0 OD2 B:ASP171 4.2 70.8 1.0 CA B:PRO146 4.2 79.1 1.0 N B:PRO146 4.2 78.5 1.0 CB B:ASN143 4.2 74.8 1.0 ND2 B:ASN148 4.2 82.3 1.0 CA B:ASP149 4.3 86.7 1.0 N B:ASP145 4.3 77.3 1.0 CB B:ASP149 4.5 86.0 1.0 CA B:ASP145 4.5 77.0 1.0 O B:GLN215 4.5 70.1 1.0 C B:ASN148 4.5 84.0 1.0 CA B:ASN143 4.6 75.7 1.0 N B:GLY170 4.6 78.6 1.0 C B:GLY170 4.6 72.4 1.0 N B:ASP171 4.7 69.6 1.0 N B:ASN148 4.7 82.7 1.0 C B:PRO146 4.8 79.2 1.0 O B:GLY170 4.8 72.0 1.0 CB B:ASN148 4.8 82.4 1.0 N B:GLY144 4.9 75.5 1.0 CB B:ASP145 4.9 77.0 1.0 CA B:ASP171 4.9 67.7 1.0 CA B:ASN148 4.9 83.3 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