Calcium in PDB 1uh3: Thermoactinomyces Vulgaris R-47 Alpha-Amylase/Acarbose Complex

All present enzymatic activity of Thermoactinomyces Vulgaris R-47 Alpha-Amylase/Acarbose Complex:
3.2.1.1;

The structure of Thermoactinomyces Vulgaris R-47 Alpha-Amylase/Acarbose Complex, PDB code: 1uh3 was solved by A.Abe, 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)	33.00 / 2.60
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	121.611, 50.600, 108.555, 90.00, 103.77, 90.00
R / Rfree (%)	18.5 / 25.5

The binding sites of Calcium atom in the Thermoactinomyces Vulgaris R-47 Alpha-Amylase/Acarbose Complex (pdb code 1uh3). 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/Acarbose Complex, PDB code: 1uh3:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Thermoactinomyces Vulgaris R-47 Alpha-Amylase/Acarbose Complex


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/Acarbose Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1001 b:9.4 occ:1.00 O A:ALA2 2.2 8.4 1.0 OD1 A:ASP42 2.2 12.1 1.0 OD1 A:ASP4 2.4 10.4 1.0 O A:ASN6 2.4 6.3 1.0 O A:ASP42 2.6 10.2 1.0 OD2 A:ASP96 2.7 7.3 1.0 CG A:ASP42 3.2 9.4 1.0 C A:ALA2 3.4 8.7 1.0 CG A:ASP96 3.4 6.4 1.0 C A:ASP42 3.5 10.6 1.0 C A:ASN6 3.6 8.0 1.0 CG A:ASP4 3.6 11.4 1.0 CA A:ASP42 3.7 9.5 1.0 N A:ASP4 3.8 7.9 1.0 OD1 A:ASP96 4.0 3.8 1.0 OD2 A:ASP42 4.0 7.4 1.0 CB A:ASP42 4.0 8.8 1.0 N A:ALA2 4.1 11.6 1.0 N A:ASN6 4.2 12.3 1.0 CA A:ASN3 4.2 7.5 1.0 OD2 A:ASP4 4.2 12.8 1.0 N A:ASN3 4.3 7.2 1.0 CB A:ASP96 4.3 7.4 1.0 CA A:ASN6 4.3 11.5 1.0 CA A:ALA2 4.4 9.8 1.0 C A:ASN3 4.5 8.1 1.0 N A:VAL7 4.6 7.4 1.0 CB A:ASN6 4.6 13.8 1.0 CA A:ASP4 4.7 8.9 1.0 CB A:ASP4 4.7 9.7 1.0 N A:ILE43 4.7 9.9 1.0 CA A:VAL7 4.7 7.5 1.0 CG A:GLU8 4.8 7.3 1.0 N A:ALA1 4.9 14.6 1.0 C A:ASP4 5.0 11.4 1.0 N A:GLU8 5.0 6.6 1.0 O A:GLY41 5.0 9.5 1.0

Calcium binding site 2 out of 3 in the Thermoactinomyces Vulgaris R-47 Alpha-Amylase/Acarbose Complex


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/Acarbose Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1002 b:22.2 occ:1.00 OD2 A:ASP189 2.2 14.2 1.0 OD2 A:ASP151 2.3 9.5 1.0 O A:ASP147 2.3 15.2 1.0 OD1 A:ASN150 2.5 2.4 1.0 O A:GLY187 2.5 4.5 1.0 OD1 A:ASN145 2.9 18.5 1.0 CG A:ASP189 3.3 11.9 1.0 CG A:ASN145 3.3 17.3 1.0 C A:ASP147 3.4 13.5 1.0 CG A:ASP151 3.5 10.7 1.0 ND2 A:ASN145 3.5 16.7 1.0 CG A:ASN150 3.6 3.0 1.0 C A:GLY187 3.6 7.1 1.0 CB A:ASP189 3.9 11.3 1.0 CA A:GLY187 4.0 5.8 1.0 ND2 A:ASN150 4.0 1.0 1.0 N A:ASP147 4.1 14.7 1.0 N A:ASP151 4.2 8.7 1.0 OD1 A:ASP151 4.2 13.1 1.0 CA A:ASP147 4.3 14.2 1.0 N A:SER148 4.3 12.2 1.0 CA A:SER148 4.3 11.9 1.0 CA A:ASP151 4.4 9.0 1.0 O A:ALA234 4.4 8.4 1.0 OD1 A:ASP189 4.4 12.1 1.0 CA A:ASN145 4.4 15.4 1.0 CB A:ASN145 4.4 16.3 1.0 C A:ASN150 4.5 8.8 1.0 CB A:ASP151 4.5 7.7 1.0 CB A:ASP147 4.6 15.7 1.0 C A:GLY188 4.7 8.4 1.0 N A:GLY146 4.7 12.7 1.0 O A:GLY188 4.7 7.1 1.0 C A:ASN145 4.8 14.0 1.0 N A:GLY188 4.8 8.5 1.0 N A:ASP189 4.8 9.3 1.0 N A:ASN150 4.8 7.0 1.0 CB A:ASN150 4.9 3.2 1.0 O A:HOH1029 4.9 8.0 1.0 O A:ASN150 4.9 7.8 1.0 C A:SER148 4.9 10.4 1.0 CA A:ASN150 5.0 6.4 1.0 CA A:ASP189 5.0 9.1 1.0

Calcium binding site 3 out of 3 in the Thermoactinomyces Vulgaris R-47 Alpha-Amylase/Acarbose Complex


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/Acarbose Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1003 b:14.2 occ:1.00 OD1 A:ASN279 2.1 16.6 1.0 OE2 A:GLU288 2.2 13.8 1.0 OD2 A:ASP276 2.3 8.4 1.0 O A:HOH1201 2.3 16.2 1.0 O A:PHE281 2.4 15.8 1.0 O A:SER283 2.5 11.5 1.0 OE1 A:GLU288 2.8 13.0 1.0 CD A:GLU288 2.9 12.8 1.0 CG A:ASN279 3.3 15.5 1.0 CG A:ASP276 3.5 8.1 1.0 C A:PHE281 3.6 14.7 1.0 C A:SER283 3.7 11.8 1.0 CA A:ASN279 3.9 15.0 1.0 CB A:ASN279 4.0 15.0 1.0 N A:PHE281 4.2 14.1 1.0 O A:SER282 4.2 12.0 1.0 C A:SER282 4.2 13.0 1.0 CA A:GLN284 4.3 13.5 1.0 CB A:ASP276 4.3 7.5 1.0 ND2 A:ASN279 4.3 14.6 1.0 CA A:PHE281 4.4 14.0 1.0 C A:ASN279 4.4 14.8 1.0 CG A:GLU288 4.4 12.9 1.0 OD1 A:ASP276 4.4 5.7 1.0 N A:SER283 4.5 12.3 1.0 N A:GLN284 4.5 10.7 1.0 N A:SER282 4.6 14.6 1.0 N A:GLY285 4.7 12.5 1.0 CA A:SER282 4.7 13.5 1.0 CA A:SER283 4.8 11.8 1.0 CB A:PHE281 4.8 13.8 1.0 O A:ASN279 4.8 14.8 1.0 N A:ASN280 4.9 14.7 1.0 O A:ASP276 5.0 10.3 1.0

A.Abe, T.Tonozuka, Y.Sakano, S.Kamitori. Complex Structures of Thermoactinomyces Vulgaris R-47 Alpha-Amylase 1 with Malto-Oligosaccharides Demonstrate the Role of Domain N Acting As A Starch-Binding Domain J.Mol.Biol. V. 335 811 2004.
ISSN: ISSN 0022-2836
PubMed: 14687576
DOI: 10.1016/J.JMB.2003.10.078