Calcium in PDB 1rp9: Crystal Structure of Barley Alpha-Amylase Isozyme 1 (AMY1) Inactive Mutant D180A in Complex with Acarbose

All present enzymatic activity of Crystal Structure of Barley Alpha-Amylase Isozyme 1 (AMY1) Inactive Mutant D180A in Complex with Acarbose:
3.2.1.1;

The structure of Crystal Structure of Barley Alpha-Amylase Isozyme 1 (AMY1) Inactive Mutant D180A in Complex with Acarbose, PDB code: 1rp9 was solved by X.Robert, R.Haser, N.Aghajari, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.52 / 2.00
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	93.730, 73.540, 61.060, 90.00, 90.00, 90.00
R / Rfree (%)	16.6 / 22.6

The binding sites of Calcium atom in the Crystal Structure of Barley Alpha-Amylase Isozyme 1 (AMY1) Inactive Mutant D180A in Complex with Acarbose (pdb code 1rp9). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Crystal Structure of Barley Alpha-Amylase Isozyme 1 (AMY1) Inactive Mutant D180A in Complex with Acarbose, PDB code: 1rp9:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Crystal Structure of Barley Alpha-Amylase Isozyme 1 (AMY1) Inactive Mutant D180A in Complex with Acarbose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Barley Alpha-Amylase Isozyme 1 (AMY1) Inactive Mutant D180A in Complex with Acarbose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca500 b:17.9 occ:1.00 OD2 A:ASP149 2.3 23.6 1.0 O A:GLY184 2.3 16.7 1.0 OD2 A:ASP139 2.4 20.4 1.0 OD1 A:ASN92 2.4 14.9 1.0 O A:ALA142 2.4 21.2 1.0 O A:HOH630 2.5 16.8 1.0 OD1 A:ASP139 2.6 19.8 1.0 CG A:ASP139 2.8 19.5 1.0 C A:GLY184 3.3 17.4 1.0 CG A:ASP149 3.4 23.8 1.0 CG A:ASN92 3.4 15.1 1.0 C A:ALA142 3.6 23.0 1.0 CA A:GLY184 3.8 19.0 1.0 ND2 A:ASN92 3.9 12.1 1.0 CB A:ASP149 3.9 20.5 1.0 O A:GLY141 4.0 22.3 1.0 C A:GLY141 4.1 21.0 1.0 CA A:ASP143 4.3 24.2 1.0 O A:ASN92 4.3 16.9 1.0 N A:ALA142 4.4 19.1 1.0 CB A:ASP139 4.4 20.8 1.0 N A:ASP143 4.4 23.7 1.0 N A:TYR185 4.5 15.7 1.0 OD1 A:ASP149 4.5 21.8 1.0 N A:GLY141 4.6 21.0 1.0 CA A:ALA142 4.6 20.0 1.0 CA A:GLY141 4.6 20.8 1.0 CB A:ASN92 4.8 13.8 1.0 O A:HOH754 4.9 15.9 1.0 O A:HOH809 4.9 20.6 1.0 CA A:TYR185 4.9 17.3 1.0 CA A:ASP149 5.0 19.9 1.0 C A:ASN92 5.0 17.5 1.0

Calcium binding site 2 out of 3 in the Crystal Structure of Barley Alpha-Amylase Isozyme 1 (AMY1) Inactive Mutant D180A in Complex with Acarbose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Barley Alpha-Amylase Isozyme 1 (AMY1) Inactive Mutant D180A in Complex with Acarbose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca501 b:23.5 occ:1.00 O A:ASP114 2.4 23.1 1.0 OD2 A:ASP118 2.4 23.1 1.0 O A:THR112 2.5 20.5 1.0 O A:HOH604 2.5 15.5 1.0 OD1 A:ASP118 2.6 21.5 1.0 O A:HOH656 2.6 23.5 1.0 OE2 A:GLU109 2.6 20.1 1.0 OE1 A:GLU109 2.7 26.8 1.0 CG A:ASP118 2.8 23.9 1.0 CD A:GLU109 3.0 23.8 1.0 C A:ASP114 3.6 23.3 1.0 C A:THR112 3.7 23.6 1.0 N A:THR112 4.1 22.8 1.0 C A:SER113 4.2 27.0 1.0 O A:SER113 4.3 29.0 1.0 CA A:GLY115 4.3 23.0 1.0 N A:GLY110 4.3 23.7 1.0 CB A:ASP118 4.3 23.0 1.0 OG1 A:THR112 4.4 26.3 1.0 N A:ASP114 4.4 25.0 1.0 N A:GLY115 4.4 21.7 1.0 O A:HOH1530 4.5 33.2 1.0 CA A:THR112 4.5 22.0 1.0 CG A:GLU109 4.5 24.5 1.0 O A:ARG116 4.6 20.5 1.0 CA A:ASP114 4.6 24.8 1.0 N A:GLY111 4.6 25.7 1.0 O A:HOH724 4.6 30.6 1.0 O A:HOH843 4.6 25.7 1.0 N A:SER113 4.7 24.7 1.0 C A:GLY115 4.7 22.7 1.0 CA A:SER113 4.7 27.9 1.0 N A:ARG116 4.8 23.2 1.0 CA A:GLU109 4.9 23.0 1.0

Calcium binding site 3 out of 3 in the Crystal Structure of Barley Alpha-Amylase Isozyme 1 (AMY1) Inactive Mutant D180A in Complex with Acarbose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Barley Alpha-Amylase Isozyme 1 (AMY1) Inactive Mutant D180A in Complex with Acarbose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca502 b:19.3 occ:1.00 O A:ALA147 2.3 19.5 1.0 O A:PHE144 2.3 19.3 1.0 O A:HOH788 2.4 18.1 1.0 OD2 A:ASP128 2.4 21.6 1.0 OD1 A:ASP143 2.4 24.7 1.0 OD1 A:ASP149 2.5 21.8 1.0 CG A:ASP143 3.2 27.0 1.0 CG A:ASP128 3.2 27.2 1.0 C A:PHE144 3.4 21.8 1.0 OD2 A:ASP143 3.4 27.9 1.0 CG A:ASP149 3.4 23.8 1.0 C A:ALA147 3.5 20.0 1.0 N A:ASP149 3.5 19.9 1.0 OD1 A:ASP128 3.6 26.0 1.0 N A:PHE144 3.8 24.2 1.0 CB A:ASP149 3.8 20.5 1.0 C A:PRO148 4.0 20.3 1.0 CA A:PRO148 4.1 20.5 1.0 CA A:ASP149 4.2 19.9 1.0 CA A:PHE144 4.2 22.1 1.0 N A:PRO148 4.3 22.2 1.0 N A:ALA145 4.3 22.8 1.0 N A:ALA147 4.4 23.6 1.0 CA A:ALA145 4.4 24.8 1.0 CB A:ASP128 4.5 24.0 1.0 OD2 A:ASP149 4.5 23.6 1.0 CA A:ALA147 4.5 22.1 1.0 CB A:PHE144 4.5 21.5 1.0 C A:ALA145 4.5 24.5 1.0 O A:HOH1579 4.6 33.5 1.0 O A:ALA145 4.6 24.0 1.0 CB A:ASP143 4.6 25.0 1.0 O A:HOH809 4.7 20.6 1.0 C A:ASP143 4.8 25.1 1.0 O A:PRO148 4.8 18.4 1.0 CE2 A:TYR131 4.9 27.0 1.0 CD2 A:TYR131 4.9 24.7 1.0 CA A:ASP143 5.0 24.2 1.0

X.Robert, R.Haser, H.Mori, B.Svensson, N.Aghajari. Oligosaccharide Binding to Barley {Alpha}-Amylase 1 J.Biol.Chem. V. 280 32968 2005.
ISSN: ISSN 0021-9258
PubMed: 16030022
DOI: 10.1074/JBC.M505515200