Calcium in PDB 1vb9: Crystal Structure of Thermoactinomyces Vulgaris R-47 Alpha- Amylase II (Tva II) Complexed with Transglycosylated Product

All present enzymatic activity of Crystal Structure of Thermoactinomyces Vulgaris R-47 Alpha- Amylase II (Tva II) Complexed with Transglycosylated Product:
3.2.1.1;

The structure of Crystal Structure of Thermoactinomyces Vulgaris R-47 Alpha- Amylase II (Tva II) Complexed with Transglycosylated Product, PDB code: 1vb9 was solved by M.Mizuno, T.Tonozuka, A.Uechi, A.Ohtaki, K.Ichikawa, S.Kamitori, A.Nishikawa, Y.Sakano, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	33.99 / 2.20
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	113.049, 118.274, 112.107, 90.00, 90.00, 90.00
R / Rfree (%)	19.4 / 23.3

The binding sites of Calcium atom in the Crystal Structure of Thermoactinomyces Vulgaris R-47 Alpha- Amylase II (Tva II) Complexed with Transglycosylated Product (pdb code 1vb9). 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 II (Tva II) Complexed with Transglycosylated Product, PDB code: 1vb9:
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 II (Tva II) Complexed with Transglycosylated Product


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 II (Tva II) Complexed with Transglycosylated Product within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca601 b:26.8 occ:1.00 OD2 A:ASP149 2.2 28.2 1.0 OD2 A:ASP171 2.4 27.4 1.0 OD1 A:ASN148 2.4 19.7 1.0 O A:HOH763 2.4 25.7 1.0 O A:ASP145 2.5 26.9 1.0 O A:GLY169 2.5 22.7 1.0 OD1 A:ASN143 2.5 22.4 1.0 CG A:ASN143 3.3 24.1 1.0 C A:ASP145 3.4 27.8 1.0 CG A:ASP171 3.4 28.0 1.0 CG A:ASP149 3.5 28.3 1.0 CG A:ASN148 3.5 22.8 1.0 C A:GLY169 3.5 24.7 1.0 ND2 A:ASN143 3.8 22.7 1.0 CB A:ASP171 3.9 26.2 1.0 CA A:GLY169 4.0 25.9 1.0 N A:ASP149 4.0 27.4 1.0 ND2 A:ASN148 4.1 20.3 1.0 N A:PRO146 4.2 28.2 1.0 CA A:ASP149 4.2 30.5 1.0 CA A:PRO146 4.2 27.4 1.0 N A:ASP145 4.2 25.9 1.0 OD1 A:ASP149 4.2 25.8 1.0 CA A:ASP145 4.3 26.5 1.0 O A:GLN215 4.3 26.5 1.0 C A:ASN148 4.3 26.8 1.0 CB A:ASN143 4.4 25.9 1.0 CB A:ASP149 4.4 28.9 1.0 OD1 A:ASP171 4.5 28.3 1.0 CA A:ASN143 4.5 25.9 1.0 N A:ASN148 4.6 26.9 1.0 C A:GLY170 4.6 23.1 1.0 O A:GLY170 4.6 23.0 1.0 CB A:ASP145 4.6 28.6 1.0 C A:PRO146 4.7 26.2 1.0 N A:GLY170 4.7 24.6 1.0 CB A:ASN148 4.7 24.3 1.0 O A:ASN148 4.7 27.1 1.0 N A:ASP171 4.7 25.0 1.0 CA A:ASN148 4.8 25.6 1.0 C A:ASN143 4.9 26.5 1.0 CA A:ASP171 5.0 25.2 1.0 N A:GLY144 5.0 27.3 1.0

Calcium binding site 2 out of 2 in the Crystal Structure of Thermoactinomyces Vulgaris R-47 Alpha- Amylase II (Tva II) Complexed with Transglycosylated Product


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 II (Tva II) Complexed with Transglycosylated Product within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca602 b:34.6 occ:1.00 OD1 B:ASP149 2.3 40.5 1.0 OD1 B:ASN148 2.3 25.3 1.0 O B:GLY169 2.4 30.3 1.0 O B:HOH757 2.4 30.9 1.0 OD1 B:ASP171 2.5 34.8 1.0 O B:ASP145 2.5 39.7 1.0 OD1 B:ASN143 2.5 31.4 1.0 C B:ASP145 3.3 40.9 1.0 CG B:ASN143 3.4 32.1 1.0 CG B:ASP171 3.4 33.5 1.0 C B:GLY169 3.4 31.3 1.0 CG B:ASN148 3.4 27.0 1.0 CG B:ASP149 3.5 40.4 1.0 CA B:GLY169 3.9 31.6 1.0 ND2 B:ASN143 3.9 32.9 1.0 CB B:ASP171 3.9 30.7 1.0 N B:ASP149 4.0 35.5 1.0 ND2 B:ASN148 4.0 25.8 1.0 N B:PRO146 4.1 42.0 1.0 N B:ASP145 4.1 39.3 1.0 CA B:PRO146 4.2 42.4 1.0 CA B:ASP149 4.2 38.1 1.0 CA B:ASP145 4.2 39.7 1.0 OD2 B:ASP149 4.3 41.1 1.0 C B:ASN148 4.3 33.6 1.0 O B:GLN215 4.4 26.8 1.0 OD2 B:ASP171 4.4 33.6 1.0 CB B:ASN143 4.5 30.2 1.0 CA B:ASN143 4.5 31.3 1.0 CB B:ASP149 4.5 39.3 1.0 C B:GLY170 4.6 28.5 1.0 O B:GLY170 4.6 30.0 1.0 N B:GLY170 4.6 31.1 1.0 N B:ASN148 4.7 36.7 1.0 CB B:ASP145 4.7 39.5 1.0 CB B:ASN148 4.7 31.0 1.0 C B:PRO146 4.7 41.8 1.0 N B:ASP171 4.7 28.4 1.0 O B:ASN148 4.8 33.1 1.0 CA B:ASN148 4.8 33.8 1.0 C B:ASN143 4.8 32.4 1.0 N B:GLY144 4.8 34.6 1.0 CA B:GLY170 5.0 29.2 1.0

M.Mizuno, T.Tonozuka, A.Uechi, A.Ohtaki, K.Ichikawa, S.Kamitori, A.Nishikawa, Y.Sakano. The Crystal Structure of Thermoactinomyces Vulgaris R-47 Alpha-Amylase II (Tva II) Complexed with Transglycosylated Product Eur.J.Biochem. V. 271 2530 2004.
ISSN: ISSN 0014-2956
PubMed: 15182368
DOI: 10.1111/J.1432-1033.2004.04183.X