Calcium in PDB 2amg: Structure of Hydrolase (Glycosidase)

All present enzymatic activity of Structure of Hydrolase (Glycosidase):
3.2.1.60;

The structure of Structure of Hydrolase (Glycosidase), PDB code: 2amg was solved by Y.Morishita, K.Hasegawa, Y.Matsuura, M.Kubota, S.Sakai, Y.Katsube, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	10.00 / 2.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	65.600, 170.500, 46.700, 90.00, 90.00, 90.00
R / Rfree (%)	n/a / n/a

The binding sites of Calcium atom in the Structure of Hydrolase (Glycosidase) (pdb code 2amg). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Structure of Hydrolase (Glycosidase), PDB code: 2amg:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Structure of Hydrolase (Glycosidase)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of Hydrolase (Glycosidase) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca451 b:19.7 occ:1.00 OD2 A:ASP162 2.3 15.4 1.0 OD1 A:ASN116 2.4 15.6 1.0 O A:GLY197 2.4 14.5 1.0 O A:HOH553 2.4 16.0 1.0 OD2 A:ASP151 2.5 21.2 1.0 O A:ASP154 2.5 19.7 1.0 OD1 A:ASP151 2.7 19.5 1.0 CG A:ASP151 2.9 20.6 1.0 CG A:ASP162 3.4 16.5 1.0 CG A:ASN116 3.5 14.3 1.0 C A:GLY197 3.5 14.0 1.0 C A:ASP154 3.6 20.1 1.0 CA A:GLY197 3.7 14.0 1.0 ND2 A:ASN116 3.9 12.6 1.0 CB A:ASP162 4.1 18.3 1.0 CA A:ARG155 4.2 21.9 1.0 C A:GLY153 4.2 18.9 1.0 O A:GLY153 4.2 18.4 1.0 N A:ARG155 4.3 20.9 1.0 CB A:ASP151 4.4 20.8 1.0 N A:ASP154 4.4 19.2 1.0 NH1 A:ARG137 4.4 22.6 1.0 O A:ASN116 4.4 15.4 1.0 OD1 A:ASP162 4.5 16.4 1.0 O A:HOH525 4.5 17.1 1.0 CA A:GLY153 4.6 18.8 1.0 N A:TYR198 4.7 14.3 1.0 O A:LEU163 4.7 19.0 1.0 CA A:ASP154 4.7 19.6 1.0 CB A:ASN116 4.8 14.9 1.0 N A:GLY153 4.8 19.4 1.0

Calcium binding site 2 out of 2 in the Structure of Hydrolase (Glycosidase)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of Hydrolase (Glycosidase) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca452 b:17.7 occ:1.00 OE2 A:GLU17 2.1 15.6 1.0 OD1 A:ASP1 2.1 44.0 1.0 O A:HIS13 2.2 16.9 1.0 O A:GLN2 2.3 40.9 1.0 OD1 A:ASP16 2.3 20.3 1.0 ND1 A:HIS13 2.4 20.9 1.0 CE1 A:HIS13 3.2 21.3 1.0 CD A:GLU17 3.2 15.4 1.0 CG A:ASP1 3.3 44.5 1.0 C A:HIS13 3.3 16.6 1.0 CG A:HIS13 3.4 20.2 1.0 CG A:ASP16 3.4 19.4 1.0 C A:GLN2 3.5 41.7 1.0 OD2 A:ASP1 3.7 45.2 1.0 OD2 A:ASP16 3.8 21.2 1.0 CB A:HIS13 3.8 18.4 1.0 CG A:GLU17 4.0 14.8 1.0 N A:GLN2 4.1 44.3 1.0 N A:GLY14 4.2 16.4 1.0 CA A:HIS13 4.2 16.9 1.0 OE1 A:GLU17 4.2 16.0 1.0 CE A:LYS108 4.3 21.1 1.0 CA A:GLY14 4.4 16.9 1.0 NE2 A:HIS13 4.4 21.0 1.0 CA A:ALA3 4.4 38.5 1.0 N A:ALA3 4.5 40.1 1.0 NZ A:LYS108 4.5 21.2 1.0 CA A:GLN2 4.5 43.4 1.0 CD2 A:HIS13 4.5 20.7 1.0 C A:ASP1 4.5 44.8 1.0 CB A:ASP1 4.5 45.0 1.0 N A:ASP16 4.6 16.5 1.0 CA A:ASP1 4.7 45.0 1.0 N A:GLU17 4.7 15.3 1.0 CB A:ASP16 4.7 17.7 1.0 C A:ASP16 4.8 15.7 1.0 O A:HOH581 4.8 43.9 1.0 C A:GLY14 4.9 17.6 1.0 CB A:ALA3 4.9 38.6 1.0 CA A:ASP16 4.9 16.2 1.0 N A:GLY15 5.0 17.8 1.0

Y.Morishita, K.Hasegawa, Y.Matsuura, Y.Katsube, M.Kubota, S.Sakai. Crystal Structure of A Maltotetraose-Forming Exo-Amylase From Pseudomonas Stutzeri. J.Mol.Biol. V. 267 661 1997.
ISSN: ISSN 0022-2836
PubMed: 9126844
DOI: 10.1006/JMBI.1996.0887