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

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

The structure of Crystal Structure of Thermoactinomyces Vulgaris R-47 Amylase 2/Gamma-Cyclodextrin Complex, PDB code: 1vfu 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)	47.71 / 3.10
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	113.454, 118.496, 114.080, 90.00, 90.00, 90.00
R / Rfree (%)	20.8 / 28.4

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

Calcium binding site 1 out of 2 in the Crystal Structure of Thermoactinomyces Vulgaris R-47 Amylase 2/Gamma-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 Amylase 2/Gamma-Cyclodextrin Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1001 b:32.0 occ:1.00 OD1 A:ASN148 2.2 58.9 1.0 OD2 A:ASP171 2.4 40.4 1.0 O A:GLY169 2.4 55.6 1.0 OD2 A:ASP149 2.4 58.5 1.0 OD1 A:ASN143 2.7 51.3 1.0 O A:ASP145 2.8 42.8 1.0 CG A:ASN148 3.0 58.0 1.0 CG A:ASN143 3.1 50.3 1.0 ND2 A:ASN143 3.2 51.5 1.0 ND2 A:ASN148 3.3 59.1 1.0 CG A:ASP171 3.4 42.3 1.0 C A:GLY169 3.4 55.6 1.0 CG A:ASP149 3.6 59.0 1.0 C A:ASP145 3.6 43.8 1.0 CB A:ASP171 3.7 42.6 1.0 CA A:GLY169 3.8 58.1 1.0 N A:ASP149 3.9 58.9 1.0 N A:PRO146 4.3 42.7 1.0 O A:GLN215 4.3 49.9 1.0 CA A:ASP149 4.3 60.4 1.0 CA A:PRO146 4.3 44.3 1.0 OD1 A:ASP149 4.3 58.0 1.0 C A:ASN148 4.4 59.0 1.0 CB A:ASN143 4.4 48.2 1.0 CB A:ASN148 4.4 57.8 1.0 N A:ASP145 4.4 46.5 1.0 OD1 A:ASP171 4.5 42.2 1.0 C A:GLY170 4.5 49.7 1.0 CA A:ASP145 4.5 45.5 1.0 N A:ASP171 4.6 45.9 1.0 CB A:ASP149 4.6 58.7 1.0 N A:GLY170 4.6 53.6 1.0 O A:GLY170 4.7 50.2 1.0 CA A:ASN143 4.7 47.3 1.0 CA A:ASN148 4.8 57.9 1.0 CA A:ASP171 4.8 42.8 1.0 N A:ASN148 4.8 56.7 1.0 C A:PRO146 4.8 46.8 1.0 CB A:ASP145 4.9 46.6 1.0 CA A:GLY170 5.0 51.7 1.0

Calcium binding site 2 out of 2 in the Crystal Structure of Thermoactinomyces Vulgaris R-47 Amylase 2/Gamma-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 Amylase 2/Gamma-Cyclodextrin Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1002 b:85.9 occ:1.00 OD1 B:ASN148 2.1 0.9 1.0 O B:GLY169 2.5 94.5 1.0 ND2 B:ASN143 2.8 95.2 1.0 OD1 B:ASP149 3.1 0.0 1.0 O B:ASP145 3.2 98.6 1.0 OD1 B:ASP171 3.2 89.7 1.0 C B:GLY169 3.2 94.3 1.0 CG B:ASN148 3.3 0.7 1.0 CG B:ASN143 3.3 95.5 1.0 OD1 B:ASN143 3.5 94.3 1.0 O B:GLN215 3.8 88.1 1.0 C B:GLY170 3.8 90.5 1.0 N B:GLY170 3.9 93.0 1.0 CG B:ASP149 3.9 0.1 1.0 CA B:GLY170 3.9 91.5 1.0 ND2 B:ASN148 3.9 0.2 1.0 O B:GLY170 4.1 90.4 1.0 N B:ASP171 4.1 88.6 1.0 CG B:ASP171 4.1 89.6 1.0 CB B:ASP171 4.1 88.5 1.0 CA B:GLY169 4.1 94.6 1.0 N B:ASP149 4.2 0.3 1.0 CA B:ASP149 4.3 0.1 1.0 C B:ASN148 4.3 0.8 1.0 CB B:ASN143 4.4 96.5 1.0 C B:ASP145 4.4 100.0 1.0 OD2 B:ASP149 4.4 0.4 1.0 CB B:ASN148 4.5 0.3 1.0 O B:ASN148 4.5 0.1 1.0 CB B:ASP149 4.7 0.5 1.0 CA B:ASP171 4.7 86.5 1.0 CA B:ASN143 4.8 97.6 1.0 C B:GLN215 4.9 87.9 1.0 CA B:ASN148 4.9 0.2 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