Calcium in PDB 1dhk: Structure of Porcine Pancreatic Alpha-Amylase

All present enzymatic activity of Structure of Porcine Pancreatic Alpha-Amylase:
3.2.1.1;

The structure of Structure of Porcine Pancreatic Alpha-Amylase, PDB code: 1dhk was solved by C.Bompard-Gilles, F.Payan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	8.00 / 1.85
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	151.600, 79.400, 68.000, 90.00, 91.54, 90.00
R / Rfree (%)	18.3 / 22

The structure of Structure of Porcine Pancreatic Alpha-Amylase also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Calcium atom in the Structure of Porcine Pancreatic Alpha-Amylase (pdb code 1dhk). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Structure of Porcine Pancreatic Alpha-Amylase, PDB code: 1dhk:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Structure of Porcine Pancreatic Alpha-Amylase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of Porcine Pancreatic Alpha-Amylase within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca500 b:9.0 occ:1.00 H1 A:HOH518 1.3 0.0 1.0 OD1 A:ASN100 1.7 11.8 1.0 OD1 A:ASP167 2.0 15.7 1.0 O A:HOH518 2.0 16.4 1.0 H1 A:HOH525 2.1 0.0 1.0 H2 A:HOH525 2.3 0.0 1.0 H2 A:HOH518 2.4 0.0 1.0 O A:HOH525 2.5 12.7 1.0 CG A:ASP167 2.6 15.3 1.0 OD2 A:ASP167 2.6 16.1 1.0 CG A:ASN100 2.7 9.7 1.0 HD21 A:ASN100 2.8 0.0 1.0 O A:HIS201 2.9 14.9 1.0 O A:HOH537 3.0 20.9 1.0 O A:ARG158 3.1 14.6 1.0 ND2 A:ASN100 3.2 12.7 1.0 H1 A:HOH537 3.2 0.0 1.0 O A:ASN100 3.5 13.5 1.0 H1 A:HOH529 3.6 0.0 1.0 H2 A:HOH537 3.6 0.0 1.0 C A:HIS201 4.0 14.9 1.0 CB A:ASP167 4.0 13.4 1.0 CB A:ASN100 4.0 12.1 1.0 HD22 A:ASN100 4.1 0.0 1.0 HD22 A:ASN137 4.2 0.0 1.0 C A:ARG158 4.3 12.7 1.0 CB A:HIS201 4.3 10.9 1.0 C A:ASN100 4.3 12.4 1.0 H1 A:HOH549 4.4 0.0 1.0 H A:LEU168 4.4 0.0 1.0 CA A:ASN100 4.5 13.0 1.0 O A:HOH529 4.5 14.1 1.0 CG A:MET202 4.5 13.5 1.0 CA A:ASP167 4.6 11.8 1.0 O A:CYS160 4.6 15.7 1.0 H2 A:HOH529 4.6 0.0 1.0 O A:LEU168 4.7 18.0 1.0 H2 A:HOH549 4.7 0.0 1.0 CA A:HIS201 4.7 12.9 1.0 H1 A:HOH504 4.8 0.0 1.0 N A:LEU168 4.8 15.0 1.0 ND2 A:ASN137 4.9 19.5 1.0 HD21 A:ASN137 4.9 0.0 1.0 CA A:ARG158 4.9 11.4 1.0 N A:MET202 4.9 13.8 1.0 C A:ASP167 5.0 15.8 1.0

Calcium binding site 2 out of 3 in the Structure of Porcine Pancreatic Alpha-Amylase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of Porcine Pancreatic Alpha-Amylase within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca497 b:44.9 occ:1.00 H1 B:HOH545 1.3 0.0 1.0 H2 B:HOH545 1.5 0.0 1.0 O B:HOH545 1.7 73.5 1.0 H2 B:HOH540 2.1 0.0 1.0 O B:HOH540 2.2 65.6 1.0 OD2 B:ASP112 2.5 38.8 1.0 OD1 B:ASP117 2.6 57.0 1.0 OE1 B:GLU101 2.7 31.2 1.0 H1 B:HOH540 2.8 0.0 1.0 OD2 B:ASP117 3.1 58.1 1.0 CG B:ASP117 3.2 56.9 1.0 OE2 B:GLU101 3.5 29.1 1.0 OE1 A:GLU149 3.5 31.1 1.0 CD B:GLU101 3.5 26.1 1.0 CG B:ASP112 3.5 33.9 1.0 O B:ASN115 4.0 64.4 1.0 CB B:ASP112 4.1 31.8 1.0 CB A:GLU149 4.1 23.8 1.0 O B:HOH569 4.2 24.7 1.0 CD A:GLU149 4.3 27.8 1.0 H2 A:HOH580 4.4 0.0 1.0 OD1 B:ASP112 4.5 34.3 1.0 CB B:ASP117 4.6 55.3 1.0 CG A:GLU149 4.6 25.4 1.0 H B:ASP117 4.6 0.0 1.0 C B:ASN115 4.6 63.6 1.0 HH21 B:ARG108 4.7 0.0 1.0 H2 B:HOH569 4.7 0.0 1.0 HE B:ARG108 4.7 0.0 1.0 N B:ASP117 4.8 54.0 1.0 H1 B:HOH569 4.8 0.0 1.0 O A:GLU149 4.9 23.2 1.0 CG B:GLU101 4.9 21.7 1.0 CA B:ASP117 5.0 53.7 1.0

Calcium binding site 3 out of 3 in the Structure of Porcine Pancreatic Alpha-Amylase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure of Porcine Pancreatic Alpha-Amylase within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca499 b:42.0 occ:1.00 H2 B:HOH555 1.4 0.0 1.0 H1 B:HOH555 1.9 0.0 1.0 H1 B:HOH554 1.9 0.0 1.0 O B:SER36 2.0 13.0 1.0 O B:HOH555 2.0 23.5 1.0 O B:HOH556 2.2 13.3 1.0 H1 B:HOH556 2.2 0.0 1.0 O B:SER189 2.2 16.5 1.0 H2 B:HOH556 2.4 0.0 1.0 O B:HOH554 2.4 25.6 1.0 H1 A:HOH708 2.8 0.0 1.0 C B:SER36 3.1 12.1 1.0 H2 B:HOH554 3.2 0.0 1.0 C B:SER189 3.5 13.6 1.0 O B:SER33 3.5 13.4 1.0 O A:HOH708 3.7 32.2 1.0 OG B:SER183 3.7 23.2 1.0 H B:SER36 3.8 0.0 1.0 N B:TYR37 4.0 13.2 1.0 CA B:TYR190 4.0 14.9 1.0 CB B:TYR37 4.0 9.9 1.0 N B:SER36 4.0 13.7 1.0 CA B:TYR37 4.0 11.8 1.0 HG B:SER183 4.0 0.0 1.0 CA B:SER36 4.1 14.6 1.0 H2 A:HOH708 4.1 0.0 1.0 N B:TYR190 4.2 13.5 1.0 H2 A:HOH707 4.2 0.0 1.0 O A:HOH707 4.3 20.2 1.0 CD1 B:TYR190 4.3 9.3 1.0 CA B:SER189 4.5 11.4 1.0 C B:TYR190 4.6 15.6 1.0 CB B:SER189 4.7 8.1 1.0 O B:TYR34 4.7 13.8 1.0 C B:SER33 4.7 14.1 1.0 CB B:SER183 4.8 16.5 1.0 C B:ASN35 4.8 13.7 1.0 H B:TYR37 4.9 0.0 1.0 O B:GLU191 4.9 16.3 1.0 CE1 B:TYR190 4.9 9.9 1.0 H B:GLU191 4.9 0.0 1.0 C B:TYR34 5.0 11.9 1.0 N B:GLU191 5.0 13.8 1.0

C.Bompard-Gilles, P.Rousseau, P.Rouge, F.Payan. Substrate Mimicry in the Active Center of A Mammalian Alpha-Amylase: Structural Analysis of An Enzyme-Inhibitor Complex. Structure V. 4 1441 1996.
ISSN: ISSN 0969-2126
PubMed: 8994970
DOI: 10.1016/S0969-2126(96)00151-7