Calcium in PDB 6yq7: Taka-Amylase

All present enzymatic activity of Taka-Amylase:
3.2.1.1;

The structure of Taka-Amylase, PDB code: 6yq7 was solved by Z.Armstrong, Y.Chen, M.Artola, H.Overkleeft, G.Davies, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	59.65 / 1.58
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	65.230, 103.113, 75.229, 90.00, 103.58, 90.00
R / Rfree (%)	16.5 / 19.2

The binding sites of Calcium atom in the Taka-Amylase (pdb code 6yq7). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Taka-Amylase, PDB code: 6yq7:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Taka-Amylase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Taka-Amylase within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca504 b:16.1 occ:1.00 O A:HIS210 2.3 14.9 1.0 OD1 A:ASN121 2.3 15.1 1.0 O A:HOH714 2.4 17.0 1.0 O A:GLU162 2.4 18.1 1.0 O A:HOH771 2.4 16.8 1.0 O A:HOH716 2.5 16.1 1.0 OD2 A:ASP175 2.5 16.9 1.0 OD1 A:ASP175 2.6 15.9 1.0 CG A:ASP175 2.9 14.6 1.0 CG A:ASN121 3.5 14.8 1.0 C A:GLU162 3.5 17.1 1.0 C A:HIS210 3.5 15.2 1.0 ND2 A:ASN121 4.1 15.9 1.0 CA A:GLU162 4.1 17.6 1.0 CB A:HIS210 4.3 15.1 1.0 CB A:ASP175 4.4 14.7 1.0 ND1 A:HIS147 4.4 20.7 1.0 CA A:HIS210 4.4 14.7 1.0 N A:VAL211 4.4 15.5 1.0 O A:ASN121 4.4 14.9 1.0 CE1 A:HIS147 4.4 21.3 1.0 O A:LEU176 4.5 17.6 1.0 CG2 A:VAL211 4.5 15.9 1.0 O A:CYS164 4.5 20.3 1.0 CA A:VAL211 4.5 16.0 1.0 N A:ASP163 4.6 18.3 1.0 O A:VAL161 4.6 16.6 1.0 CB A:ASN121 4.7 14.0 1.0 O A:HOH802 4.8 21.2 1.0 CA A:ASP163 4.9 19.2 1.0 CB A:GLU162 4.9 17.8 1.0 CA A:ASN121 4.9 14.0 1.0 OG1 A:THR178 5.0 16.9 1.0

Calcium binding site 2 out of 2 in the Taka-Amylase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Taka-Amylase within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca503 b:15.8 occ:1.00 OD1 B:ASN121 2.3 16.2 1.0 O B:GLU162 2.4 17.6 1.0 O B:HIS210 2.4 15.0 1.0 O B:HOH760 2.4 18.3 1.0 OD2 B:ASP175 2.4 17.7 1.0 O B:HOH679 2.4 17.1 1.0 O B:HOH712 2.5 17.5 1.0 OD1 B:ASP175 2.6 16.8 1.0 CG B:ASP175 2.8 16.3 1.0 CG B:ASN121 3.4 14.9 1.0 C B:GLU162 3.5 17.5 1.0 C B:HIS210 3.6 14.0 1.0 ND2 B:ASN121 4.0 14.8 1.0 CA B:GLU162 4.1 17.1 1.0 CB B:HIS210 4.3 15.8 1.0 CB B:ASP175 4.3 17.0 1.0 O B:ASN121 4.4 16.4 1.0 ND1 B:HIS147 4.4 22.6 1.0 N B:VAL211 4.4 14.8 1.0 O B:LEU176 4.4 17.8 1.0 CE1 B:HIS147 4.4 24.4 1.0 CA B:HIS210 4.4 14.0 1.0 O B:CYS164 4.5 21.8 1.0 CG2 B:VAL211 4.5 15.5 1.0 N B:ASP163 4.5 20.3 1.0 CA B:VAL211 4.5 14.6 1.0 CB B:ASN121 4.6 14.2 1.0 O B:VAL161 4.7 19.1 1.0 O B:HOH816 4.8 20.0 1.0 CA B:ASP163 4.8 21.8 1.0 CA B:ASN121 4.9 15.1 1.0 CB B:GLU162 5.0 18.7 1.0

Z.Armstrong, Y.Chen, M.Artola, G.Davies, H.Overkleeft. Activity-Based Protein Profiling of Retaining Alpha-Amylases in Complex Biological Samples To Be Published.