Calcium in PDB 1ji2: Improved X-Ray Structure of Thermoactinomyces Vulgaris R-47 Alpha- Amylase 2

All present enzymatic activity of Improved X-Ray Structure of Thermoactinomyces Vulgaris R-47 Alpha- Amylase 2:
3.2.1.135;

The structure of Improved X-Ray Structure of Thermoactinomyces Vulgaris R-47 Alpha- Amylase 2, PDB code: 1ji2 was solved by S.Kamitori, A.Abe, A.Ohtaki, A.Kaji, T.Tonozuka, Y.Sakano, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.05 / 2.30
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	112.457, 117.684, 112.674, 90.00, 90.00, 90.00
R / Rfree (%)	17.9 / 22.4

The binding sites of Calcium atom in the Improved X-Ray Structure of Thermoactinomyces Vulgaris R-47 Alpha- Amylase 2 (pdb code 1ji2). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Improved X-Ray Structure of Thermoactinomyces Vulgaris R-47 Alpha- Amylase 2, PDB code: 1ji2:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Improved X-Ray Structure of Thermoactinomyces Vulgaris R-47 Alpha- Amylase 2


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Improved X-Ray Structure of Thermoactinomyces Vulgaris R-47 Alpha- Amylase 2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1001 b:24.0 occ:1.00 OD2 A:ASP149 2.3 27.9 1.0 OD1 A:ASN148 2.3 22.9 1.0 OD1 A:ASN143 2.4 22.5 1.0 OD2 A:ASP171 2.4 24.6 1.0 O A:ASP145 2.4 26.8 1.0 O A:GLY169 2.5 23.1 1.0 O A:HOH1118 2.5 23.3 1.0 CG A:ASN143 3.3 25.8 1.0 C A:ASP145 3.4 27.2 1.0 CG A:ASN148 3.4 23.6 1.0 CG A:ASP171 3.5 24.5 1.0 C A:GLY169 3.5 25.6 1.0 CG A:ASP149 3.5 28.3 1.0 ND2 A:ASN143 3.8 25.0 1.0 CA A:GLY169 3.9 27.4 1.0 CB A:ASP171 3.9 23.6 1.0 ND2 A:ASN148 4.0 24.6 1.0 N A:ASP149 4.0 28.8 1.0 N A:PRO146 4.2 27.6 1.0 C A:ASN148 4.2 27.9 1.0 CA A:ASP149 4.2 30.1 1.0 N A:ASP145 4.2 26.5 1.0 CA A:ASP145 4.2 26.5 1.0 O A:GLN215 4.3 20.9 1.0 OD1 A:ASP149 4.3 27.8 1.0 CA A:PRO146 4.3 27.0 1.0 CB A:ASN143 4.5 23.9 1.0 CB A:ASP149 4.5 29.0 1.0 OD1 A:ASP171 4.5 26.0 1.0 CB A:ASP145 4.5 27.8 1.0 O A:ASN148 4.6 27.6 1.0 N A:ASN148 4.6 25.8 1.0 CA A:ASN143 4.6 25.9 1.0 CB A:ASN148 4.6 24.8 1.0 C A:GLY170 4.7 22.5 1.0 N A:GLY170 4.7 24.6 1.0 C A:PRO146 4.7 26.4 1.0 O A:GLY170 4.7 21.2 1.0 CA A:ASN148 4.7 27.1 1.0 N A:ASP171 4.8 22.1 1.0 O A:PRO146 4.8 27.4 1.0 O A:HOH1111 4.9 21.2 1.0 C A:ASN143 5.0 26.5 1.0

Calcium binding site 2 out of 2 in the Improved X-Ray Structure of Thermoactinomyces Vulgaris R-47 Alpha- Amylase 2


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Improved X-Ray Structure of Thermoactinomyces Vulgaris R-47 Alpha- Amylase 2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1002 b:27.9 occ:1.00 OD1 B:ASP149 2.2 36.9 1.0 OD1 B:ASN148 2.2 29.4 1.0 OD1 B:ASN143 2.4 28.5 1.0 OD1 B:ASP171 2.5 29.3 1.0 O B:ASP145 2.5 35.8 1.0 O B:GLY169 2.5 28.2 1.0 O B:HOH1377 2.6 14.3 1.0 CG B:ASN143 3.2 28.7 1.0 CG B:ASN148 3.4 30.7 1.0 C B:ASP145 3.4 34.9 1.0 CG B:ASP171 3.4 29.6 1.0 CG B:ASP149 3.4 36.6 1.0 C B:GLY169 3.6 29.1 1.0 ND2 B:ASN143 3.7 27.1 1.0 CB B:ASP171 3.9 29.4 1.0 ND2 B:ASN148 3.9 27.4 1.0 N B:ASP149 4.0 35.1 1.0 CA B:GLY169 4.0 30.3 1.0 OD2 B:ASP149 4.2 36.8 1.0 N B:ASP145 4.2 33.3 1.0 N B:PRO146 4.2 34.5 1.0 CA B:ASP149 4.3 36.8 1.0 C B:ASN148 4.3 34.6 1.0 CA B:ASP145 4.3 34.2 1.0 CA B:PRO146 4.3 34.2 1.0 CB B:ASN143 4.3 28.1 1.0 O B:GLN215 4.4 25.2 1.0 CB B:ASP149 4.4 36.7 1.0 OD2 B:ASP171 4.5 28.9 1.0 CA B:ASN143 4.5 29.4 1.0 CB B:ASN148 4.6 31.8 1.0 N B:ASN148 4.7 34.0 1.0 C B:GLY170 4.7 28.7 1.0 O B:ASN148 4.7 35.7 1.0 N B:GLY170 4.7 29.1 1.0 O B:GLY170 4.7 28.2 1.0 C B:PRO146 4.7 33.4 1.0 CA B:ASN148 4.7 33.9 1.0 CB B:ASP145 4.7 34.4 1.0 N B:ASP171 4.8 28.2 1.0 O B:HOH1238 4.9 22.3 1.0 C B:ASN143 4.9 30.0 1.0 N B:GLY144 4.9 30.1 1.0 O B:PRO146 4.9 32.4 1.0 CA B:ASP171 5.0 28.6 1.0

S.Kamitori, A.Abe, A.Ohtaki, A.Kaji, T.Tonozuka, Y.Sakano. Crystal Structures and Structural Comparison of Thermoactinomyces Vulgaris R-47 Alpha-Amylase 1 (Tvai) at 1.6 A Resolution and Alpha-Amylase 2 (Tvaii) at 2.3 A Resolution. J.Mol.Biol. V. 318 443 2002.
ISSN: ISSN 0022-2836
PubMed: 12051850
DOI: 10.1016/S0022-2836(02)00111-0