Calcium in PDB 1jf6: Crystal Structure of Thermoactinomyces Vulgaris R-47 Alpha- Amylase Mutant F286Y

All present enzymatic activity of Crystal Structure of Thermoactinomyces Vulgaris R-47 Alpha- Amylase Mutant F286Y:
3.2.1.135;

The structure of Crystal Structure of Thermoactinomyces Vulgaris R-47 Alpha- Amylase Mutant F286Y, PDB code: 1jf6 was solved by A.Ohtaki, S.Kondo, Y.Shimura, 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)	38.39 / 3.20
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	112.250, 117.940, 113.320, 90.00, 90.00, 90.00
R / Rfree (%)	20.4 / 28.2

The binding sites of Calcium atom in the Crystal Structure of Thermoactinomyces Vulgaris R-47 Alpha- Amylase Mutant F286Y (pdb code 1jf6). 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 Mutant F286Y, PDB code: 1jf6:
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 Mutant F286Y


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 Mutant F286Y within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca601 b:11.7 occ:1.00 OD1 A:ASN148 2.1 30.1 1.0 OD2 A:ASP171 2.3 22.1 1.0 OD2 A:ASP149 2.3 29.2 1.0 O A:GLY169 2.4 34.7 1.0 OD1 A:ASN143 2.4 18.8 1.0 O A:ASP145 2.5 14.2 1.0 CG A:ASN148 3.1 28.4 1.0 CG A:ASP171 3.3 22.2 1.0 CG A:ASN143 3.4 21.8 1.0 C A:GLY169 3.4 33.8 1.0 C A:ASP145 3.5 14.8 1.0 CG A:ASP149 3.5 28.9 1.0 ND2 A:ASN148 3.6 29.6 1.0 CB A:ASP171 3.7 21.6 1.0 ND2 A:ASN143 3.8 22.5 1.0 N A:ASP149 3.8 28.4 1.0 CA A:GLY169 3.8 35.2 1.0 C A:ASN148 4.1 28.9 1.0 CA A:ASP149 4.2 30.3 1.0 OD1 A:ASP149 4.2 27.6 1.0 N A:PRO146 4.2 13.4 1.0 O A:GLN215 4.2 22.9 1.0 N A:ASP145 4.3 17.1 1.0 CA A:ASP145 4.3 16.1 1.0 CB A:ASN148 4.4 27.8 1.0 CB A:ASP149 4.4 28.6 1.0 OD1 A:ASP171 4.4 20.9 1.0 CA A:PRO146 4.4 14.8 1.0 N A:ASN148 4.4 27.5 1.0 CA A:ASN148 4.5 28.4 1.0 C A:GLY170 4.5 27.7 1.0 O A:GLY170 4.6 27.9 1.0 CB A:ASN143 4.6 22.8 1.0 N A:GLY170 4.6 32.2 1.0 N A:ASP171 4.7 24.6 1.0 O A:ASN148 4.7 30.6 1.0 CA A:ASN143 4.7 23.1 1.0 CB A:ASP145 4.8 17.5 1.0 C A:PRO146 4.8 17.7 1.0 CA A:ASP171 4.9 21.3 1.0

Calcium binding site 2 out of 2 in the Crystal Structure of Thermoactinomyces Vulgaris R-47 Alpha- Amylase Mutant F286Y


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 Mutant F286Y within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca602 b:37.9 occ:1.00 O B:ASP145 2.2 46.1 1.0 OD1 B:ASN148 2.2 46.6 1.0 OD1 B:ASN143 2.4 40.4 1.0 OD1 B:ASP149 2.4 48.5 1.0 OD1 B:ASP171 2.7 36.7 1.0 O B:GLY169 2.8 43.9 1.0 CG B:ASN148 2.9 47.4 1.0 CG B:ASN143 3.0 42.8 1.0 ND2 B:ASN148 3.1 47.9 1.0 ND2 B:ASN143 3.1 42.8 1.0 C B:ASP145 3.1 46.7 1.0 CG B:ASP149 3.4 48.0 1.0 CG B:ASP171 3.5 38.2 1.0 C B:GLY169 3.8 43.4 1.0 N B:PRO146 3.9 46.9 1.0 CA B:PRO146 3.9 46.8 1.0 OD2 B:ASP149 3.9 47.7 1.0 CB B:ASP171 3.9 39.0 1.0 N B:ASP149 3.9 47.7 1.0 CA B:GLY169 4.1 43.6 1.0 CA B:ASP145 4.1 47.0 1.0 N B:ASP145 4.1 47.4 1.0 C B:ASN148 4.2 47.3 1.0 CB B:ASN148 4.2 46.8 1.0 N B:ASN148 4.3 47.1 1.0 CB B:ASN143 4.3 43.9 1.0 CA B:ASP149 4.4 49.3 1.0 C B:PRO146 4.4 46.5 1.0 CB B:ASP149 4.5 48.7 1.0 CA B:ASN148 4.5 47.3 1.0 OD2 B:ASP171 4.5 39.0 1.0 CA B:ASN143 4.6 45.6 1.0 O B:PRO146 4.7 46.9 1.0 CB B:ASP145 4.7 46.1 1.0 O B:ASN148 4.8 47.1 1.0 O B:GLN215 4.8 33.0 1.0 N B:SER147 4.9 45.2 1.0 N B:ASP171 5.0 38.2 1.0 C B:GLY170 5.0 39.3 1.0 C B:ASN143 5.0 46.3 1.0 N B:GLY144 5.0 46.2 1.0

A.Ohtaki, S.Kondo, Y.Shimura, T.Tonozuka, Y.Sakano, S.Kamitori. Role of PHE286 in the Recognition Mechanism of Cyclomaltooligosaccharides (Cyclodextrins) By Thermoactinomyces Vulgaris R-47 Alpha-Amylase 2 (Tvaii). X-Ray Structures of the Mutant Tvaiis, F286A and F286Y, and Kinetic Analyses of the PHE286-Replaced Mutant Tvaiis Carbohydr.Res. V. 334 309 2001.
ISSN: ISSN 0008-6215
PubMed: 11527532
DOI: 10.1016/S0008-6215(01)00190-2