Calcium in PDB 5va9: Human Pancreatic Alpha Amylase in Complex with Peptide Inhibitor Piha- L5(D10Y)

All present enzymatic activity of Human Pancreatic Alpha Amylase in Complex with Peptide Inhibitor Piha- L5(D10Y):
3.2.1.1;

The structure of Human Pancreatic Alpha Amylase in Complex with Peptide Inhibitor Piha- L5(D10Y), PDB code: 5va9 was solved by S.Caner, G.D.Brayer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.60 / 2.55
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	169.920, 169.920, 79.420, 90.00, 90.00, 90.00
R / Rfree (%)	19.6 / 23

The structure of Human Pancreatic Alpha Amylase in Complex with Peptide Inhibitor Piha- L5(D10Y) also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Calcium atom in the Human Pancreatic Alpha Amylase in Complex with Peptide Inhibitor Piha- L5(D10Y) (pdb code 5va9). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Human Pancreatic Alpha Amylase in Complex with Peptide Inhibitor Piha- L5(D10Y), PDB code: 5va9:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Human Pancreatic Alpha Amylase in Complex with Peptide Inhibitor Piha- L5(D10Y)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Human Pancreatic Alpha Amylase in Complex with Peptide Inhibitor Piha- L5(D10Y) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca502 b:31.8 occ:1.00 O A:HIS201 2.3 32.5 1.0 OD1 A:ASP167 2.3 35.4 1.0 O A:ARG158 2.3 32.9 1.0 O A:HOH636 2.4 28.1 1.0 OD1 A:ASN100 2.4 31.0 1.0 OD2 A:ASP167 2.7 33.2 1.0 O A:HOH657 2.7 38.2 1.0 CG A:ASP167 2.8 36.8 1.0 C A:ARG158 3.5 32.0 1.0 C A:HIS201 3.5 28.9 1.0 CG A:ASN100 3.5 32.2 1.0 ND2 A:ASN100 4.1 32.7 1.0 CA A:ARG158 4.1 31.7 1.0 CB A:HIS201 4.3 29.1 1.0 O A:ASN100 4.3 36.6 1.0 CB A:ASP167 4.3 33.5 1.0 N A:MET202 4.4 30.3 1.0 CA A:HIS201 4.4 28.6 1.0 CA A:MET202 4.4 27.1 1.0 N A:ASP159 4.5 33.5 1.0 ND2 A:ASN137 4.5 38.1 1.0 O A:CYS160 4.6 40.0 1.0 O A:VAL157 4.6 30.5 1.0 O A:LEU168 4.7 38.6 1.0 CB A:ASN100 4.8 34.9 1.0 CG A:MET202 4.8 30.8 1.0 CA A:ASP159 4.8 34.4 1.0 O A:HOH656 4.9 35.3 1.0 CB A:ARG158 4.9 34.5 1.0

Calcium binding site 2 out of 2 in the Human Pancreatic Alpha Amylase in Complex with Peptide Inhibitor Piha- L5(D10Y)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Human Pancreatic Alpha Amylase in Complex with Peptide Inhibitor Piha- L5(D10Y) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca502 b:35.3 occ:1.00 O B:ARG158 2.3 34.7 1.0 O B:HOH624 2.3 31.4 1.0 OD1 B:ASP167 2.4 33.3 1.0 O B:HIS201 2.4 32.7 1.0 OD1 B:ASN100 2.5 34.8 1.0 O B:HOH655 2.5 34.3 1.0 OD2 B:ASP167 2.5 40.3 1.0 CG B:ASP167 2.8 37.4 1.0 C B:ARG158 3.5 33.5 1.0 CG B:ASN100 3.5 32.8 1.0 C B:HIS201 3.6 31.2 1.0 ND2 B:ASN100 4.1 29.4 1.0 CA B:ARG158 4.2 35.7 1.0 ND2 B:ASN137 4.3 39.1 1.0 O B:ASN100 4.3 33.4 1.0 CB B:ASP167 4.3 35.4 1.0 N B:MET202 4.4 32.5 1.0 CB B:HIS201 4.4 30.9 1.0 CA B:MET202 4.4 31.6 1.0 N B:ASP159 4.5 34.4 1.0 O B:CYS160 4.5 35.5 1.0 CA B:HIS201 4.6 34.4 1.0 O B:LEU168 4.6 37.8 1.0 CG B:MET202 4.7 32.8 1.0 CB B:ASN100 4.8 32.8 1.0 O B:VAL157 4.8 36.6 1.0 CA B:ASP159 4.8 36.1 1.0 O B:HOH656 4.8 31.4 1.0 CB B:ARG158 5.0 34.5 1.0

L.Goldbach, B.J.A.Vermeulen, S.Caner, M.Liu, C.Tysoe, L.Van Gijzel, R.Yoshisada, M.Trellet, H.Van Ingen, G.D.Brayer, A.M.J.J.Bonvin, S.A.K.Jongkees. Folding Then Binding Vs Folding Through Binding in Macrocyclic Peptide Inhibitors of Human Pancreatic Alpha-Amylase. Acs Chem.Biol. V. 14 1751 2019.
ISSN: ESSN 1554-8937
PubMed: 31241898
DOI: 10.1021/ACSCHEMBIO.9B00290