Calcium in PDB 1uh2: Thermoactinomyces Vulgaris R-47 Alpha-Amylase/Malto-Hexaose Complex

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

The structure of Thermoactinomyces Vulgaris R-47 Alpha-Amylase/Malto-Hexaose Complex, PDB code: 1uh2 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)	27.00 / 2.00
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	121.630, 50.491, 108.015, 90.00, 103.82, 90.00
R / Rfree (%)	18.4 / 21.7

The binding sites of Calcium atom in the Thermoactinomyces Vulgaris R-47 Alpha-Amylase/Malto-Hexaose Complex (pdb code 1uh2). 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/Malto-Hexaose Complex, PDB code: 1uh2:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Thermoactinomyces Vulgaris R-47 Alpha-Amylase/Malto-Hexaose 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/Malto-Hexaose Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1001 b:16.1 occ:1.00 O A:ASN6 2.3 11.4 1.0 O A:ALA2 2.3 16.9 1.0 OD1 A:ASP42 2.3 16.7 1.0 OD2 A:ASP96 2.4 14.1 1.0 O A:HOH1017 2.5 17.3 1.0 OD1 A:ASP4 2.5 12.2 1.0 O A:ASP42 2.5 15.5 1.0 CG A:ASP96 3.3 14.8 1.0 CG A:ASP42 3.3 18.4 1.0 C A:ASP42 3.5 15.5 1.0 CG A:ASP4 3.5 17.1 1.0 C A:ASN6 3.5 14.1 1.0 C A:ALA2 3.5 18.2 1.0 CA A:ASP42 3.7 16.1 1.0 OD2 A:ASP4 3.9 18.4 1.0 N A:ASP4 4.0 16.7 1.0 OD1 A:ASP96 4.0 13.7 1.0 CB A:ASP42 4.1 17.4 1.0 CB A:ASP96 4.1 13.2 1.0 N A:ALA2 4.1 19.2 1.0 OD2 A:ASP42 4.1 12.8 1.0 N A:ASN6 4.2 13.5 1.0 CA A:ASN6 4.2 13.8 1.0 CA A:ASN3 4.4 17.8 1.0 N A:ASN3 4.4 17.9 1.0 N A:VAL7 4.5 14.6 1.0 CA A:ALA2 4.5 18.6 1.0 CB A:ASN6 4.6 15.0 1.0 OE1 A:GLU8 4.6 18.6 1.0 CG A:GLU8 4.6 17.9 1.0 CA A:VAL7 4.7 13.6 1.0 CB A:ASP4 4.7 15.9 1.0 N A:ILE43 4.7 14.2 1.0 C A:ASN3 4.7 18.7 1.0 CA A:ASP4 4.8 16.1 1.0 N A:GLU8 4.9 14.3 1.0 C A:ASP4 5.0 13.7 1.0

Calcium binding site 2 out of 3 in the Thermoactinomyces Vulgaris R-47 Alpha-Amylase/Malto-Hexaose 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/Malto-Hexaose Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1002 b:37.7 occ:1.00 OD2 A:ASP189 2.2 38.0 1.0 OD2 A:ASP151 2.3 38.0 1.0 O A:ASP147 2.4 37.7 1.0 O A:HOH1369 2.4 30.0 1.0 OD1 A:ASN150 2.4 29.5 1.0 O A:GLY187 2.5 27.4 1.0 ND2 A:ASN145 2.6 29.1 1.0 CG A:ASN145 3.1 29.7 1.0 CG A:ASP189 3.3 35.1 1.0 OD1 A:ASN145 3.3 31.5 1.0 C A:ASP147 3.4 38.1 1.0 CG A:ASP151 3.5 37.0 1.0 C A:GLY187 3.5 27.6 1.0 CG A:ASN150 3.6 28.5 1.0 CB A:ASP189 3.9 33.0 1.0 CA A:GLY187 4.0 28.1 1.0 ND2 A:ASN150 4.1 27.1 1.0 N A:ASP151 4.2 33.8 1.0 CB A:ASN145 4.2 31.6 1.0 OD1 A:ASP151 4.2 38.5 1.0 N A:SER148 4.2 37.1 1.0 CA A:SER148 4.2 35.8 1.0 N A:ASP147 4.3 36.1 1.0 O A:ALA234 4.3 30.1 1.0 OD1 A:ASP189 4.3 34.9 1.0 CA A:ASP147 4.4 37.7 1.0 CA A:ASP151 4.4 34.9 1.0 CA A:ASN145 4.4 31.2 1.0 C A:ASN150 4.5 33.5 1.0 CB A:ASP151 4.5 36.5 1.0 C A:GLY188 4.7 28.7 1.0 O A:GLY188 4.7 28.5 1.0 N A:GLY188 4.7 28.8 1.0 CB A:ASP147 4.8 38.9 1.0 N A:ASN150 4.8 34.8 1.0 C A:SER148 4.8 34.7 1.0 CB A:ASN150 4.8 31.8 1.0 N A:ASP189 4.8 28.3 1.0 O A:HOH1471 4.8 23.2 1.0 O A:ASN150 4.9 33.3 1.0 C A:ASN145 4.9 32.1 1.0 N A:GLY146 4.9 32.5 1.0 CA A:ASN150 4.9 33.0 1.0

Calcium binding site 3 out of 3 in the Thermoactinomyces Vulgaris R-47 Alpha-Amylase/Malto-Hexaose 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/Malto-Hexaose Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1003 b:18.2 occ:1.00 O A:SER283 2.3 17.8 1.0 O A:PHE281 2.4 21.0 1.0 OD2 A:ASP276 2.4 18.4 1.0 OE2 A:GLU288 2.4 19.1 1.0 O A:HOH1124 2.4 23.9 1.0 OD1 A:ASN279 2.4 24.2 1.0 OE1 A:GLU288 2.5 19.9 1.0 CD A:GLU288 2.8 18.3 1.0 C A:SER283 3.5 19.5 1.0 CG A:ASP276 3.5 16.1 1.0 C A:PHE281 3.5 22.3 1.0 CG A:ASN279 3.5 25.0 1.0 CA A:ASN279 3.9 22.0 1.0 C A:SER282 4.1 23.2 1.0 CB A:ASN279 4.1 22.6 1.0 O A:HOH1089 4.1 17.7 1.0 O A:SER282 4.2 22.6 1.0 N A:PHE281 4.2 21.3 1.0 N A:SER283 4.2 21.6 1.0 CG A:GLU288 4.3 17.5 1.0 CB A:ASP276 4.3 15.1 1.0 CA A:GLN284 4.3 19.9 1.0 NE2 A:GLN284 4.3 33.0 1.0 CA A:PHE281 4.3 22.0 1.0 N A:GLN284 4.4 19.0 1.0 OD1 A:ASP276 4.4 15.0 1.0 C A:ASN279 4.5 22.6 1.0 O A:HOH1457 4.5 38.4 1.0 N A:SER282 4.5 22.9 1.0 CA A:SER283 4.5 20.1 1.0 N A:GLY285 4.5 17.9 1.0 CA A:SER282 4.6 23.4 1.0 ND2 A:ASN279 4.7 26.1 1.0 CB A:PHE281 4.7 22.1 1.0 N A:ASN280 4.8 22.3 1.0 C A:GLN284 5.0 17.7 1.0 O A:ASN279 5.0 23.2 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