Calcium in PDB 1rpk: Crystal Structure of Barley Alpha-Amylase Isozyme 1 (AMY1) in Complex with Acarbose

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

The structure of Crystal Structure of Barley Alpha-Amylase Isozyme 1 (AMY1) in Complex with Acarbose, PDB code: 1rpk 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)	17.36 / 2.00
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	93.390, 72.920, 61.390, 90.00, 90.00, 90.00
R / Rfree (%)	18 / 23.1

The binding sites of Calcium atom in the Crystal Structure of Barley Alpha-Amylase Isozyme 1 (AMY1) in Complex with Acarbose (pdb code 1rpk). 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) in Complex with Acarbose, PDB code: 1rpk:
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) 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) in Complex with Acarbose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca500 b:10.4 occ:1.00 OD2 A:ASP149 2.4 12.0 1.0 O A:GLY184 2.4 10.9 1.0 OD2 A:ASP139 2.4 12.2 1.0 O A:HOH630 2.4 3.2 1.0 OD1 A:ASN92 2.4 12.2 1.0 O A:ALA142 2.5 8.8 1.0 OD1 A:ASP139 2.7 12.3 1.0 CG A:ASP139 2.9 11.1 1.0 C A:GLY184 3.3 11.1 1.0 CG A:ASP149 3.5 11.5 1.0 CG A:ASN92 3.5 10.2 1.0 C A:ALA142 3.6 8.3 1.0 CA A:GLY184 3.7 11.3 1.0 CB A:ASP149 3.9 9.2 1.0 ND2 A:ASN92 3.9 9.2 1.0 C A:GLY141 4.2 10.9 1.0 O A:GLY141 4.2 9.9 1.0 O A:ASN92 4.2 11.7 1.0 CA A:ASP143 4.3 11.2 1.0 N A:ALA142 4.4 10.0 1.0 CB A:ASP139 4.4 8.7 1.0 N A:ASP143 4.4 10.6 1.0 N A:TYR185 4.5 8.9 1.0 OD1 A:ASP149 4.6 11.1 1.0 N A:GLY141 4.7 12.4 1.0 CA A:ALA142 4.7 7.4 1.0 CA A:GLY141 4.7 13.3 1.0 CB A:ASN92 4.7 8.1 1.0 O A:HOH809 4.9 9.9 1.0 CA A:TYR185 4.9 10.0 1.0 O A:HOH754 4.9 14.3 1.0 SG A:CYS125 4.9 10.5 1.0 C A:ASN92 4.9 9.7 1.0 CA A:ASP149 5.0 10.1 1.0

Calcium binding site 2 out of 3 in the Crystal Structure of Barley Alpha-Amylase Isozyme 1 (AMY1) 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) in Complex with Acarbose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca501 b:16.4 occ:1.00 O A:ASP114 2.3 18.9 1.0 O A:HOH656 2.3 18.7 1.0 OD2 A:ASP118 2.4 14.4 1.0 O A:HOH604 2.5 8.1 1.0 OE2 A:GLU109 2.5 13.8 1.0 O A:THR112 2.6 19.0 1.0 OD1 A:ASP118 2.6 9.9 1.0 OE1 A:GLU109 2.7 13.4 1.0 CG A:ASP118 2.8 14.2 1.0 CD A:GLU109 3.0 13.3 1.0 C A:ASP114 3.5 18.0 1.0 C A:THR112 3.8 19.5 1.0 C A:SER113 4.2 21.9 1.0 O A:SER113 4.2 20.9 1.0 N A:THR112 4.3 18.7 1.0 N A:GLY110 4.3 13.1 1.0 CA A:GLY115 4.3 17.5 1.0 CB A:ASP118 4.3 13.9 1.0 N A:ASP114 4.3 20.6 1.0 O A:HOH1577 4.4 38.4 1.0 N A:GLY115 4.4 18.2 1.0 O A:HOH1531 4.4 33.4 1.0 OG1 A:THR112 4.4 19.9 1.0 CG A:GLU109 4.5 13.6 1.0 CA A:ASP114 4.5 20.0 1.0 N A:GLY111 4.6 16.0 1.0 CA A:THR112 4.6 19.1 1.0 O A:ARG116 4.6 12.5 1.0 N A:SER113 4.7 20.0 1.0 C A:GLY115 4.7 16.5 1.0 CA A:SER113 4.7 21.7 1.0 O A:HOH1090 4.8 28.4 1.0 O A:HOH843 4.9 27.4 1.0 CA A:GLY110 5.0 13.8 1.0 N A:ARG116 5.0 14.8 1.0

Calcium binding site 3 out of 3 in the Crystal Structure of Barley Alpha-Amylase Isozyme 1 (AMY1) 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) in Complex with Acarbose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca502 b:11.8 occ:1.00 O A:PHE144 2.3 11.3 1.0 OD2 A:ASP128 2.3 6.5 1.0 O A:ALA147 2.3 11.3 1.0 OD1 A:ASP149 2.4 11.1 1.0 OD1 A:ASP143 2.4 12.1 1.0 O A:HOH788 2.4 11.6 1.0 OD2 A:ASP143 3.0 17.6 1.0 CG A:ASP143 3.0 14.8 1.0 CG A:ASP128 3.1 9.5 1.0 C A:PHE144 3.3 12.1 1.0 CG A:ASP149 3.4 11.5 1.0 OD1 A:ASP128 3.5 9.0 1.0 C A:ALA147 3.5 11.5 1.0 N A:ASP149 3.6 9.8 1.0 N A:PHE144 3.8 10.4 1.0 CB A:ASP149 3.9 9.2 1.0 C A:PRO148 4.0 11.2 1.0 CA A:PHE144 4.2 12.7 1.0 CA A:PRO148 4.2 10.6 1.0 N A:ALA145 4.2 13.1 1.0 CA A:ASP149 4.2 10.1 1.0 O A:HOH1152 4.3 16.4 1.0 N A:PRO148 4.3 10.4 1.0 CA A:ALA145 4.3 13.9 1.0 CB A:ASP128 4.4 8.3 1.0 CB A:ASP143 4.4 12.1 1.0 N A:ALA147 4.4 12.0 1.0 OD2 A:ASP149 4.4 12.0 1.0 C A:ALA145 4.5 13.8 1.0 O A:ALA145 4.5 12.3 1.0 CA A:ALA147 4.5 11.4 1.0 C A:ASP143 4.6 12.6 1.0 CB A:PHE144 4.6 11.3 1.0 O A:HOH809 4.7 9.9 1.0 O A:PRO148 4.7 12.0 1.0 CA A:ASP143 4.7 11.2 1.0 CE2 A:TYR131 4.9 14.1 1.0 CD2 A:TYR131 5.0 11.0 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