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Calcium in PDB 5emy: Human Pancreatic Alpha-Amylase in Complex with the Mechanism Based Inactivator Glucosyl Epi-Cyclophellitol

Enzymatic activity of Human Pancreatic Alpha-Amylase in Complex with the Mechanism Based Inactivator Glucosyl Epi-Cyclophellitol

All present enzymatic activity of Human Pancreatic Alpha-Amylase in Complex with the Mechanism Based Inactivator Glucosyl Epi-Cyclophellitol:
3.2.1.1;

Protein crystallography data

The structure of Human Pancreatic Alpha-Amylase in Complex with the Mechanism Based Inactivator Glucosyl Epi-Cyclophellitol, PDB code: 5emy 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) 36.65 / 1.23
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 52.330, 68.180, 130.380, 90.00, 90.00, 90.00
R / Rfree (%) 11.9 / 14.2

Other elements in 5emy:

The structure of Human Pancreatic Alpha-Amylase in Complex with the Mechanism Based Inactivator Glucosyl Epi-Cyclophellitol also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the Human Pancreatic Alpha-Amylase in Complex with the Mechanism Based Inactivator Glucosyl Epi-Cyclophellitol (pdb code 5emy). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total only one binding site of Calcium was determined in the Human Pancreatic Alpha-Amylase in Complex with the Mechanism Based Inactivator Glucosyl Epi-Cyclophellitol, PDB code: 5emy:

Calcium binding site 1 out of 1 in 5emy

Go back to Calcium Binding Sites List in 5emy
Calcium binding site 1 out of 1 in the Human Pancreatic Alpha-Amylase in Complex with the Mechanism Based Inactivator Glucosyl Epi-Cyclophellitol


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 the Mechanism Based Inactivator Glucosyl Epi-Cyclophellitol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca503

b:9.4
occ:1.00
 OD1 A:ASN100 2.4 9.3 1.0
O A:HIS201 2.4 9.2 1.0
O A:ARG158 2.4 10.1 1.0
O A:HOH850 2.5 10.1 1.0
OD2 A:ASP167 2.5 11.4 1.0
OD1 A:ASP167 2.5 9.7 1.0
O A:HOH953 2.5 11.0 1.0
O A:HOH683 2.6 8.8 1.0
CG A:ASP167 2.9 10.0 1.0
HB3 A:HIS201 3.4 10.3 1.0
C A:ARG158 3.5 9.7 1.0
CG A:ASN100 3.5 8.9 1.0
HD21 A:ASN100 3.6 11.9 1.0
HA A:ARG158 3.6 11.7 1.0
C A:HIS201 3.6 8.8 1.0
ND2 A:ASN100 3.9 9.9 1.0
HD22 A:ASN137 4.0 14.5 1.0
HA A:MET202 4.0 10.2 1.0
CA A:ARG158 4.1 9.8 1.0
HG2 A:MET202 4.1 11.5 1.0
CB A:HIS201 4.2 8.6 1.0
HA A:ASP159 4.3 12.9 1.0
HB2 A:HIS201 4.4 10.3 1.0
CB A:ASP167 4.4 9.5 1.0
CA A:HIS201 4.4 9.0 1.0
HD21 A:ASN137 4.4 14.5 1.0
O A:ASN100 4.4 9.1 1.0
O A:HOH775 4.5 12.4 1.0
N A:ASP159 4.5 9.7 1.0
ND2 A:ASN137 4.5 12.1 1.0
N A:MET202 4.5 9.0 1.0
HA A:HIS201 4.6 10.8 1.0
O A:CYS160 4.6 10.7 1.0
HB3 A:ARG158 4.6 12.1 1.0
O A:VAL157 4.7 8.8 1.0
CA A:MET202 4.7 8.5 1.0
HD12 A:LEU170 4.7 13.9 1.0
HD22 A:ASN100 4.8 11.9 1.0
HB3 A:ASP167 4.8 11.4 1.0
CB A:ASN100 4.8 9.1 1.0
HA A:ASP167 4.8 10.8 1.0
CA A:ASP159 4.8 10.7 1.0
O A:LEU168 4.8 9.9 1.0
HB2 A:ASP167 4.8 11.4 1.0
HA A:ASN100 4.9 10.7 1.0
CG A:MET202 4.9 9.6 1.0
CB A:ARG158 4.9 10.1 1.0
HB2 A:ASN100 5.0 10.9 1.0
O A:HOH743 5.0 10.7 1.0
HG3 A:MET202 5.0 11.5 1.0

Reference:

S.Caner, X.Zhang, J.Jiang, H.M.Chen, N.T.Nguyen, H.Overkleeft, G.D.Brayer, S.G.Withers. Glucosyl Epi-Cyclophellitol Allows Mechanism-Based Inactivation and Structural Analysis of Human Pancreatic Alpha-Amylase. Febs Lett. V. 590 1143 2016.
ISSN: ISSN 0014-5793
PubMed: 27000970
DOI: 10.1002/1873-3468.12143
Page generated: Wed Jul 9 05:35:50 2025

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