Calcium in PDB 1izk: Thermoactinomyces Vulgaris R-47 Alpha-Amylase 1 Mutant Enzyme W398V

All present enzymatic activity of Thermoactinomyces Vulgaris R-47 Alpha-Amylase 1 Mutant Enzyme W398V:
3.2.1.1;

The structure of Thermoactinomyces Vulgaris R-47 Alpha-Amylase 1 Mutant Enzyme W398V, PDB code: 1izk was solved by A.Ohtaki, A.Iguchi, 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)	25.41 / 2.20
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	122.720, 50.820, 108.820, 90.00, 104.19, 90.00
R / Rfree (%)	19.2 / 23.8

The binding sites of Calcium atom in the Thermoactinomyces Vulgaris R-47 Alpha-Amylase 1 Mutant Enzyme W398V (pdb code 1izk). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Thermoactinomyces Vulgaris R-47 Alpha-Amylase 1 Mutant Enzyme W398V, PDB code: 1izk:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Thermoactinomyces Vulgaris R-47 Alpha-Amylase 1 Mutant Enzyme W398V


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Thermoactinomyces Vulgaris R-47 Alpha-Amylase 1 Mutant Enzyme W398V within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca701 b:10.3 occ:1.00 O A:HOH738 2.2 8.1 1.0 O A:ALA2 2.3 12.1 1.0 O A:ASN6 2.3 7.7 1.0 OD1 A:ASP42 2.4 11.7 1.0 OD2 A:ASP96 2.5 10.4 1.0 OD1 A:ASP4 2.5 5.0 1.0 O A:ASP42 2.6 11.1 1.0 CG A:ASP42 3.2 13.2 1.0 C A:ASN6 3.4 9.3 1.0 CG A:ASP96 3.4 10.9 1.0 C A:ALA2 3.5 12.1 1.0 C A:ASP42 3.5 9.8 1.0 CG A:ASP4 3.5 10.2 1.0 CA A:ASP42 3.8 11.8 1.0 OD2 A:ASP42 3.9 10.2 1.0 N A:ASP4 3.9 13.5 1.0 OD2 A:ASP4 4.0 12.0 1.0 CB A:ASP42 4.1 11.4 1.0 N A:ASN6 4.1 10.8 1.0 CA A:ASN6 4.1 10.4 1.0 N A:ALA2 4.2 14.6 1.0 OD1 A:ASP96 4.2 9.3 1.0 CB A:ASP96 4.2 8.4 1.0 N A:ASN3 4.4 11.4 1.0 CA A:ASN3 4.4 13.1 1.0 N A:VAL7 4.4 8.0 1.0 CA A:ALA2 4.4 13.2 1.0 CB A:ASN6 4.4 11.6 1.0 OE1 A:GLU8 4.6 11.1 1.0 CG A:GLU8 4.6 10.8 1.0 CA A:VAL7 4.6 8.0 1.0 N A:ALA1 4.7 15.6 1.0 C A:ASN3 4.7 14.0 1.0 CB A:ASP4 4.7 9.9 1.0 N A:ILE43 4.8 9.6 1.0 CA A:ASP4 4.8 12.1 1.0 N A:GLU8 4.9 7.6 1.0

Calcium binding site 2 out of 3 in the Thermoactinomyces Vulgaris R-47 Alpha-Amylase 1 Mutant Enzyme W398V


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Thermoactinomyces Vulgaris R-47 Alpha-Amylase 1 Mutant Enzyme W398V within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca702 b:18.6 occ:1.00 OD1 A:ASN279 2.3 15.9 1.0 O A:SER283 2.3 11.7 1.0 O A:PHE281 2.3 17.0 1.0 OD2 A:ASP276 2.4 12.9 1.0 OE1 A:GLU288 2.4 13.4 1.0 OE2 A:GLU288 2.6 15.1 1.0 CD A:GLU288 2.8 14.8 1.0 CG A:ASN279 3.4 15.0 1.0 C A:PHE281 3.5 17.6 1.0 C A:SER283 3.6 13.1 1.0 CG A:ASP276 3.6 10.2 1.0 CA A:ASN279 4.0 13.6 1.0 O A:HOH871 4.1 9.3 1.0 C A:SER282 4.1 16.6 1.0 CB A:ASN279 4.1 14.1 1.0 O A:SER282 4.2 15.6 1.0 N A:PHE281 4.2 16.1 1.0 CA A:GLN284 4.3 17.0 1.0 N A:SER283 4.3 14.4 1.0 CG A:GLU288 4.3 12.2 1.0 CB A:ASP276 4.4 10.0 1.0 CA A:PHE281 4.4 16.6 1.0 N A:GLN284 4.4 14.9 1.0 ND2 A:ASN279 4.4 14.6 1.0 N A:SER282 4.4 17.7 1.0 OD1 A:ASP276 4.4 9.3 1.0 C A:ASN279 4.5 14.8 1.0 CA A:SER282 4.5 18.2 1.0 CA A:SER283 4.6 13.6 1.0 N A:GLY285 4.6 14.8 1.0 CB A:PHE281 4.7 15.6 1.0 N A:ASN280 4.8 14.9 1.0 O A:ASN279 5.0 15.3 1.0

Calcium binding site 3 out of 3 in the Thermoactinomyces Vulgaris R-47 Alpha-Amylase 1 Mutant Enzyme W398V


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Thermoactinomyces Vulgaris R-47 Alpha-Amylase 1 Mutant Enzyme W398V within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca703 b:33.6 occ:1.00 O A:ASP147 2.2 30.1 1.0 OD2 A:ASP151 2.4 30.8 1.0 OD1 A:ASN150 2.5 21.8 1.0 O A:HOH788 2.5 16.0 1.0 O A:GLY187 2.6 18.0 1.0 OD2 A:ASP189 2.7 28.7 1.0 OD1 A:ASN145 2.9 24.5 1.0 C A:ASP147 3.2 31.6 1.0 CG A:ASN145 3.5 22.7 1.0 CG A:ASP189 3.5 28.9 1.0 CG A:ASN150 3.6 23.4 1.0 CG A:ASP151 3.6 32.1 1.0 C A:GLY187 3.7 20.4 1.0 CB A:ASP189 3.8 26.4 1.0 ND2 A:ASN145 3.8 20.2 1.0 N A:ASP147 3.9 30.4 1.0 N A:SER148 4.0 30.9 1.0 ND2 A:ASN150 4.1 20.8 1.0 CA A:ASP147 4.1 31.1 1.0 CA A:SER148 4.2 30.9 1.0 N A:ASP151 4.2 29.8 1.0 O A:ALA234 4.3 26.0 1.0 OD1 A:ASP151 4.3 30.9 1.0 CA A:GLY187 4.4 19.9 1.0 CA A:ASP151 4.4 31.2 1.0 C A:GLY188 4.5 22.1 1.0 N A:ASP189 4.5 23.0 1.0 C A:ASN150 4.5 28.4 1.0 CB A:ASP147 4.5 32.1 1.0 OD1 A:ASP189 4.5 30.4 1.0 CB A:ASN145 4.5 23.3 1.0 CA A:ASN145 4.6 23.5 1.0 CB A:ASP151 4.6 31.5 1.0 N A:GLY146 4.7 25.4 1.0 C A:SER148 4.7 29.4 1.0 O A:GLY188 4.7 24.1 1.0 CA A:ASP189 4.8 23.1 1.0 N A:GLY188 4.8 21.6 1.0 N A:ASN150 4.8 28.9 1.0 CB A:ASN150 4.8 25.7 1.0 C A:ASN145 4.9 23.4 1.0 CA A:GLY188 4.9 21.7 1.0 O A:ASN150 4.9 28.6 1.0 CA A:ASN150 5.0 27.6 1.0 O A:HOH779 5.0 13.7 1.0

A.Ohtaki, A.Iguchi, M.Mizuno, T.Tonozuka, Y.Sakano, S.Kamitori. Mutual Conversion of Substrate Specificities of Thermoactinomyces Vulgaris R-47 Alpha-Amylases Tvai and Tvaii By Site-Directed Mutagenesis Carbohydr.Res. V. 338 1553 2003.
ISSN: ISSN 0008-6215
PubMed: 12860426
DOI: 10.1016/S0008-6215(03)00219-2