Calcium in PDB 1izj: Thermoactinomyces Vulgaris R-47 Alpha-Amylase 1 Mutant Enzyme F313A

All present enzymatic activity of Thermoactinomyces Vulgaris R-47 Alpha-Amylase 1 Mutant Enzyme F313A:
3.2.1.1;

The structure of Thermoactinomyces Vulgaris R-47 Alpha-Amylase 1 Mutant Enzyme F313A, PDB code: 1izj 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)	58.79 / 2.20
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	120.944, 50.417, 107.920, 90.00, 103.56, 90.00
R / Rfree (%)	17.9 / 22

The binding sites of Calcium atom in the Thermoactinomyces Vulgaris R-47 Alpha-Amylase 1 Mutant Enzyme F313A (pdb code 1izj). 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 F313A, PDB code: 1izj:
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 F313A


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 F313A within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1001 b:11.0 occ:1.00 O A:ASN6 2.2 11.0 1.0 OD1 A:ASP42 2.3 10.4 1.0 O A:ALA2 2.3 13.0 1.0 OD1 A:ASP4 2.4 5.4 1.0 O A:HOH1082 2.4 10.7 1.0 OD2 A:ASP96 2.4 11.1 1.0 O A:ASP42 2.6 8.2 1.0 CG A:ASP42 3.3 11.9 1.0 CG A:ASP96 3.3 11.7 1.0 C A:ASN6 3.4 10.8 1.0 CG A:ASP4 3.5 10.6 1.0 C A:ALA2 3.6 13.1 1.0 C A:ASP42 3.6 7.5 1.0 CA A:ASP42 3.8 8.6 1.0 N A:ASP4 3.9 11.3 1.0 OD2 A:ASP42 4.1 8.6 1.0 N A:ASN6 4.1 10.3 1.0 OD2 A:ASP4 4.1 8.8 1.0 OD1 A:ASP96 4.1 10.7 1.0 CB A:ASP42 4.1 9.1 1.0 CA A:ASN6 4.1 11.4 1.0 CB A:ASP96 4.2 10.7 1.0 N A:ALA2 4.2 14.8 1.0 CA A:ASN3 4.4 13.3 1.0 N A:VAL7 4.4 9.3 1.0 CB A:ASN6 4.4 13.0 1.0 N A:ASN3 4.4 12.4 1.0 CA A:ALA2 4.5 13.7 1.0 O A:HOH1117 4.5 25.2 1.0 CA A:VAL7 4.6 9.1 1.0 C A:ASN3 4.7 13.0 1.0 CB A:ASP4 4.7 8.5 1.0 CG A:GLU8 4.7 9.3 1.0 N A:ALA1 4.7 15.3 1.0 CA A:ASP4 4.7 10.2 1.0 OE1 A:GLU8 4.8 8.7 1.0 N A:ILE43 4.8 6.5 1.0 C A:ASP4 4.9 9.8 1.0 N A:GLU8 4.9 8.4 1.0

Calcium binding site 2 out of 3 in the Thermoactinomyces Vulgaris R-47 Alpha-Amylase 1 Mutant Enzyme F313A


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 F313A within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1002 b:14.9 occ:1.00 OD1 A:ASN279 2.2 19.5 1.0 OD2 A:ASP276 2.3 10.7 1.0 O A:PHE281 2.4 15.8 1.0 O A:SER283 2.4 12.2 1.0 OE2 A:GLU288 2.5 15.7 1.0 OE1 A:GLU288 2.5 14.5 1.0 CD A:GLU288 2.8 13.8 1.0 CG A:ASN279 3.4 19.2 1.0 CG A:ASP276 3.5 12.0 1.0 C A:PHE281 3.5 16.3 1.0 C A:SER283 3.6 14.1 1.0 CA A:ASN279 3.8 17.0 1.0 CB A:ASN279 4.1 17.2 1.0 N A:PHE281 4.2 14.7 1.0 O A:HOH1101 4.2 17.4 1.0 C A:SER282 4.2 16.4 1.0 CA A:GLN284 4.2 16.2 1.0 CB A:ASP276 4.3 10.3 1.0 O A:SER282 4.3 18.4 1.0 N A:SER283 4.3 14.8 1.0 CA A:PHE281 4.3 15.8 1.0 N A:GLN284 4.3 13.8 1.0 C A:ASN279 4.3 17.5 1.0 CG A:GLU288 4.4 14.0 1.0 OD1 A:ASP276 4.4 13.1 1.0 ND2 A:ASN279 4.4 18.4 1.0 N A:SER282 4.5 16.1 1.0 CA A:SER283 4.6 14.7 1.0 CA A:SER282 4.6 16.2 1.0 N A:GLY285 4.6 13.8 1.0 CB A:PHE281 4.7 15.7 1.0 N A:ASN280 4.7 16.6 1.0 O A:ASN279 4.8 17.5 1.0 N A:ASN279 5.0 15.9 1.0 C A:GLN284 5.0 15.7 1.0 O A:ASP276 5.0 12.3 1.0

Calcium binding site 3 out of 3 in the Thermoactinomyces Vulgaris R-47 Alpha-Amylase 1 Mutant Enzyme F313A


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 F313A within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1003 b:16.9 occ:1.00 OD2 A:ASP151 2.1 15.1 1.0 OD2 A:ASP189 2.4 18.2 1.0 OD1 A:ASN150 2.4 11.9 1.0 O A:HOH1019 2.4 11.4 1.0 O A:ASP147 2.4 14.5 1.0 OD1 A:ASN145 2.5 15.3 1.0 O A:GLY187 2.5 13.9 1.0 CG A:ASN145 3.3 15.1 1.0 CG A:ASP189 3.3 15.6 1.0 C A:ASP147 3.4 15.5 1.0 CG A:ASP151 3.4 17.6 1.0 CG A:ASN150 3.5 15.2 1.0 C A:GLY187 3.6 14.8 1.0 ND2 A:ASN145 3.8 12.0 1.0 CB A:ASP189 3.9 13.0 1.0 ND2 A:ASN150 3.9 14.6 1.0 N A:ASP151 4.0 16.9 1.0 CA A:GLY187 4.0 15.2 1.0 N A:ASP147 4.1 15.7 1.0 OD1 A:ASP151 4.1 18.0 1.0 N A:SER148 4.2 15.3 1.0 CA A:ASP147 4.2 15.2 1.0 CA A:ASP151 4.2 16.6 1.0 O A:ALA234 4.3 13.4 1.0 CA A:SER148 4.3 16.2 1.0 OD1 A:ASP189 4.3 14.8 1.0 CB A:ASN145 4.4 14.8 1.0 C A:ASN150 4.4 17.8 1.0 CB A:ASP151 4.4 17.6 1.0 CA A:ASN145 4.5 14.9 1.0 CB A:ASP147 4.6 15.8 1.0 C A:GLY188 4.7 11.5 1.0 N A:ASN150 4.7 17.3 1.0 N A:ASP189 4.7 11.9 1.0 C A:SER148 4.7 15.2 1.0 CB A:ASN150 4.7 15.2 1.0 N A:GLY188 4.8 14.3 1.0 O A:ASN150 4.8 16.9 1.0 C A:ASN145 4.8 14.7 1.0 N A:GLY146 4.8 15.1 1.0 CA A:ASN150 4.9 16.3 1.0 O A:GLY188 4.9 12.0 1.0 O A:HOH1031 4.9 9.6 1.0 CA A:ASP189 4.9 12.0 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