Calcium in PDB 2qps: "Sugar Tongs" Mutant Y380A in Complex with Acarbose

All present enzymatic activity of "Sugar Tongs" Mutant Y380A in Complex with Acarbose:
3.2.1.1;

The structure of "Sugar Tongs" Mutant Y380A in Complex with Acarbose, PDB code: 2qps was solved by N.Aghajari, M.H.Jensen, S.Tranier, R.Haser, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.48 / 2.20
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	88.390, 72.420, 62.010, 90.00, 90.00, 90.00
R / Rfree (%)	24 / 30.5

The binding sites of Calcium atom in the "Sugar Tongs" Mutant Y380A in Complex with Acarbose (pdb code 2qps). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the "Sugar Tongs" Mutant Y380A in Complex with Acarbose, PDB code: 2qps:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the "Sugar Tongs" Mutant Y380A 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 "Sugar Tongs" Mutant Y380A in Complex with Acarbose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca500 b:27.7 occ:1.00 OD2 A:ASP149 2.3 32.0 1.0 O A:GLY184 2.3 29.9 1.0 O A:HOH630 2.3 27.9 1.0 OD1 A:ASN92 2.4 32.5 1.0 O A:ALA142 2.5 30.4 1.0 OD2 A:ASP139 2.5 36.3 1.0 OD1 A:ASP139 2.7 34.7 1.0 CG A:ASP139 3.0 32.7 1.0 C A:GLY184 3.3 31.2 1.0 CG A:ASN92 3.4 31.0 1.0 CG A:ASP149 3.4 32.5 1.0 C A:ALA142 3.6 31.3 1.0 ND2 A:ASN92 3.7 31.8 1.0 CA A:GLY184 3.8 30.9 1.0 CB A:ASP149 3.9 30.7 1.0 O A:GLY141 4.0 30.5 1.0 C A:GLY141 4.0 31.4 1.0 CA A:ASP143 4.2 34.9 1.0 N A:ASP143 4.3 31.8 1.0 N A:ALA142 4.3 33.7 1.0 O A:ASN92 4.3 26.9 1.0 N A:TYR185 4.4 31.6 1.0 CB A:ASP139 4.5 28.1 1.0 OD1 A:ASP149 4.5 32.3 1.0 CA A:GLY141 4.5 31.4 1.0 N A:GLY141 4.6 30.8 1.0 CA A:ALA142 4.6 32.3 1.0 CB A:ASN92 4.7 29.5 1.0 CA A:TYR185 4.9 32.1 1.0 CA A:ASP149 5.0 32.3 1.0

Calcium binding site 2 out of 3 in the "Sugar Tongs" Mutant Y380A 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 "Sugar Tongs" Mutant Y380A in Complex with Acarbose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca501 b:49.3 occ:1.00 OD2 A:ASP118 2.1 59.9 1.0 OE2 A:GLU109 2.4 42.9 1.0 OE1 A:GLU109 2.5 41.4 1.0 O A:ASP114 2.6 58.6 1.0 CD A:GLU109 2.8 41.2 1.0 O A:THR112 3.2 57.5 1.0 CG A:ASP118 3.3 57.9 1.0 O A:SER113 3.7 60.0 1.0 C A:THR112 3.8 58.0 1.0 C A:ASP114 3.8 59.2 1.0 OD1 A:ASP118 3.9 58.6 1.0 OG1 A:THR112 4.0 58.9 1.0 N A:THR112 4.1 55.6 1.0 O A:ARG116 4.1 54.0 1.0 N A:GLY110 4.1 43.7 1.0 C A:SER113 4.2 60.3 1.0 CG A:GLU109 4.3 40.6 1.0 N A:GLY111 4.3 47.6 1.0 CB A:ASP118 4.4 54.3 1.0 CA A:GLY115 4.4 56.3 1.0 CA A:THR112 4.5 56.9 1.0 N A:SER113 4.6 59.1 1.0 C A:GLY115 4.6 55.8 1.0 N A:GLY115 4.6 58.3 1.0 O A:HOH1473 4.7 49.4 1.0 N A:ASP114 4.7 60.2 1.0 N A:ARG116 4.7 54.4 1.0 CA A:SER113 4.8 60.1 1.0 CA A:GLU109 4.8 42.4 1.0 CA A:GLY110 4.8 44.5 1.0 C A:GLU109 4.9 42.8 1.0 CA A:ASP114 4.9 59.5 1.0 CB A:THR112 4.9 56.7 1.0 CB A:GLU109 5.0 41.1 1.0

Calcium binding site 3 out of 3 in the "Sugar Tongs" Mutant Y380A 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 "Sugar Tongs" Mutant Y380A in Complex with Acarbose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca502 b:37.5 occ:1.00 OD1 A:ASP143 2.1 38.3 1.0 O A:HOH788 2.2 38.3 1.0 O A:ALA147 2.2 35.0 1.0 OD1 A:ASP149 2.3 32.3 1.0 O A:PHE144 2.3 39.1 1.0 OD2 A:ASP128 2.4 42.4 1.0 CG A:ASP143 3.2 40.2 1.0 CG A:ASP128 3.3 44.0 1.0 C A:PHE144 3.3 41.1 1.0 CG A:ASP149 3.4 32.5 1.0 C A:ALA147 3.4 36.1 1.0 N A:ASP149 3.6 33.2 1.0 N A:PHE144 3.6 37.5 1.0 OD1 A:ASP128 3.7 42.8 1.0 OD2 A:ASP143 3.7 46.2 1.0 CB A:ASP149 3.9 30.7 1.0 C A:PRO148 4.0 33.7 1.0 CA A:PHE144 4.0 40.1 1.0 CA A:PRO148 4.1 34.2 1.0 CA A:ASP149 4.2 32.3 1.0 N A:PRO148 4.3 33.8 1.0 N A:ALA145 4.3 43.1 1.0 N A:ALA147 4.3 40.3 1.0 OD2 A:ASP149 4.3 32.0 1.0 CB A:PHE144 4.3 42.7 1.0 CB A:ASP143 4.5 36.4 1.0 CA A:ALA147 4.5 38.5 1.0 O A:ALA145 4.5 44.1 1.0 CB A:ASP128 4.6 43.6 1.0 CA A:ALA145 4.6 43.4 1.0 C A:ASP143 4.6 37.4 1.0 C A:ALA145 4.6 43.3 1.0 O A:PRO148 4.7 35.0 1.0 CA A:ASP143 4.8 34.9 1.0

S.Bozonnet, M.T.Jensen, M.M.Nielsen, N.Aghajari, M.H.Jensen, B.Kramhoft, M.Willemoes, S.Tranier, R.Haser, B.Svensson. The 'Pair of Sugar Tongs' Site on the Non-Catalytic Domain C of Barley Alpha-Amylase Participates in Substrate Binding and Activity Febs J. V. 274 5055 2007.
ISSN: ISSN 1742-464X
PubMed: 17803687
DOI: 10.1111/J.1742-4658.2007.06024.X