Calcium in PDB 1uh4: Thermoactinomyces Vulgaris R-47 Alpha-Amylase 1/Malto- Tridecaose Complex

All present enzymatic activity of Thermoactinomyces Vulgaris R-47 Alpha-Amylase 1/Malto- Tridecaose Complex:
3.2.1.1;

The structure of Thermoactinomyces Vulgaris R-47 Alpha-Amylase 1/Malto- Tridecaose Complex, PDB code: 1uh4 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)	31.00 / 1.80
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	120.880, 50.519, 108.073, 90.00, 103.43, 90.00
R / Rfree (%)	16.5 / 20

The binding sites of Calcium atom in the Thermoactinomyces Vulgaris R-47 Alpha-Amylase 1/Malto- Tridecaose Complex (pdb code 1uh4). 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/Malto- Tridecaose Complex, PDB code: 1uh4:
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/Malto- Tridecaose 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 1/Malto- Tridecaose Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1001 b:14.4 occ:1.00 OD1 A:ASP42 2.3 14.5 1.0 O A:ALA2 2.3 15.2 1.0 OD1 A:ASP4 2.4 13.3 1.0 O A:ASN6 2.4 14.1 1.0 OD2 A:ASP96 2.4 16.9 1.0 O A:HOH2232 2.4 13.4 1.0 O A:ASP42 2.6 14.0 1.0 CG A:ASP42 3.3 16.7 1.0 CG A:ASP96 3.3 15.7 1.0 CG A:ASP4 3.4 16.4 1.0 C A:ASP42 3.5 14.6 1.0 C A:ASN6 3.5 13.3 1.0 C A:ALA2 3.5 17.2 1.0 CA A:ASP42 3.7 16.0 1.0 OD2 A:ASP4 3.9 15.7 1.0 N A:ASP4 3.9 15.6 1.0 CB A:ASP42 4.1 14.4 1.0 OD1 A:ASP96 4.1 16.4 1.0 OD2 A:ASP42 4.1 14.3 1.0 CB A:ASP96 4.1 14.1 1.0 N A:ALA2 4.1 17.0 1.0 N A:ASN6 4.1 13.2 1.0 CA A:ASN6 4.2 12.9 1.0 CA A:ASN3 4.4 16.6 1.0 N A:ASN3 4.4 16.6 1.0 CA A:ALA2 4.5 17.1 1.0 N A:VAL7 4.5 12.0 1.0 CB A:ASN6 4.6 13.6 1.0 CB A:ASP4 4.6 14.8 1.0 O A:HOH2466 4.6 34.1 1.0 CA A:VAL7 4.7 13.4 1.0 C A:ASN3 4.7 16.1 1.0 N A:ILE43 4.7 15.2 1.0 CA A:ASP4 4.7 13.7 1.0 CG A:GLU8 4.7 16.4 1.0 OE1 A:GLU8 4.8 16.3 1.0 C A:ASP4 4.9 13.0 1.0 N A:GLU8 5.0 13.3 1.0

Calcium binding site 2 out of 3 in the Thermoactinomyces Vulgaris R-47 Alpha-Amylase 1/Malto- Tridecaose 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 1/Malto- Tridecaose Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1002 b:20.1 occ:1.00 OD2 A:ASP189 2.3 20.1 1.0 OD2 A:ASP151 2.3 23.1 1.0 OD1 A:ASN150 2.3 15.5 1.0 O A:HOH2067 2.4 18.0 1.0 O A:ASP147 2.4 24.0 1.0 OD1 A:ASN145 2.5 20.9 1.0 O A:GLY187 2.6 17.2 1.0 CG A:ASN145 3.3 21.8 1.0 CG A:ASP189 3.4 20.6 1.0 C A:ASP147 3.4 22.7 1.0 CG A:ASN150 3.4 16.0 1.0 CG A:ASP151 3.5 23.9 1.0 C A:GLY187 3.7 17.7 1.0 ND2 A:ASN145 3.8 21.3 1.0 ND2 A:ASN150 3.9 15.7 1.0 CB A:ASP189 3.9 18.2 1.0 N A:ASP151 4.0 20.9 1.0 CA A:GLY187 4.1 19.5 1.0 N A:ASP147 4.1 21.5 1.0 N A:SER148 4.2 22.4 1.0 CA A:SER148 4.2 22.4 1.0 O A:ALA234 4.3 18.0 1.0 OD1 A:ASP151 4.3 25.8 1.0 CA A:ASP147 4.3 22.9 1.0 CA A:ASP151 4.3 20.6 1.0 CB A:ASN145 4.4 21.8 1.0 OD1 A:ASP189 4.4 22.2 1.0 C A:ASN150 4.4 20.6 1.0 CA A:ASN145 4.5 21.9 1.0 CB A:ASP151 4.5 22.6 1.0 C A:SER148 4.7 22.1 1.0 CB A:ASN150 4.7 18.2 1.0 N A:ASN150 4.7 22.8 1.0 CB A:ASP147 4.7 23.9 1.0 C A:GLY188 4.7 17.6 1.0 N A:ASP189 4.8 15.6 1.0 N A:GLY188 4.8 18.5 1.0 C A:ASN145 4.8 22.9 1.0 CA A:ASN150 4.9 19.4 1.0 O A:GLY188 4.9 19.1 1.0 N A:GLY146 4.9 21.5 1.0 O A:HOH2113 4.9 18.8 1.0 O A:SER148 4.9 23.3 1.0 O A:ASN150 5.0 19.1 1.0

Calcium binding site 3 out of 3 in the Thermoactinomyces Vulgaris R-47 Alpha-Amylase 1/Malto- Tridecaose 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 1/Malto- Tridecaose Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1003 b:17.3 occ:1.00 OD2 A:ASP276 2.3 14.5 1.0 O A:PHE281 2.4 16.9 1.0 O A:SER283 2.4 18.5 1.0 OD1 A:ASN279 2.4 21.4 1.0 O A:HOH2749 2.4 27.2 1.0 OE2 A:GLU288 2.4 19.7 1.0 OE1 A:GLU288 2.5 20.7 1.0 CD A:GLU288 2.8 20.7 1.0 CG A:ASP276 3.4 14.5 1.0 CG A:ASN279 3.5 23.3 1.0 C A:PHE281 3.5 17.8 1.0 C A:SER283 3.6 19.4 1.0 CA A:ASN279 3.9 19.6 1.0 CB A:ASN279 4.1 21.1 1.0 O A:HOH2070 4.2 16.5 1.0 C A:SER282 4.2 19.0 1.0 N A:PHE281 4.2 18.3 1.0 N A:SER283 4.3 18.4 1.0 OD1 A:ASP276 4.3 16.1 1.0 CB A:ASP276 4.3 13.7 1.0 CG A:GLU288 4.3 17.3 1.0 CA A:PHE281 4.3 18.0 1.0 CA A:GLN284 4.4 20.4 1.0 O A:SER282 4.4 19.9 1.0 O A:HOH2600 4.4 26.2 1.0 N A:GLN284 4.4 19.6 1.0 C A:ASN279 4.4 20.4 1.0 N A:SER282 4.5 17.0 1.0 NE2 A:GLN284 4.5 29.5 0.5 CA A:SER283 4.6 18.6 1.0 ND2 A:ASN279 4.6 25.2 1.0 CA A:SER282 4.6 17.4 1.0 N A:GLY285 4.6 19.1 1.0 CB A:PHE281 4.7 16.9 1.0 N A:ASN280 4.8 19.2 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