Calcium in PDB 1kxt: Camelid Vhh Domains in Complex with Porcine Pancreatic Alpha-Amylase

All present enzymatic activity of Camelid Vhh Domains in Complex with Porcine Pancreatic Alpha-Amylase:
3.2.1.1;

The structure of Camelid Vhh Domains in Complex with Porcine Pancreatic Alpha-Amylase, PDB code: 1kxt was solved by A.Desmyter, S.Spinelli, F.Payan, M.Lauwereys, L.Wyns, S.Muyldermans, C.Cambillau, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.95 / 2.00
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	52.780, 286.850, 65.980, 90.00, 93.73, 90.00
R / Rfree (%)	20.3 / 23.6

The structure of Camelid Vhh Domains in Complex with Porcine Pancreatic Alpha-Amylase also contains other interesting chemical elements:

Chlorine

(Cl)

3 atoms

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

Calcium binding site 1 out of 3 in the Camelid Vhh Domains in Complex with 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 Camelid Vhh Domains in Complex with Porcine Pancreatic Alpha-Amylase within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca4001 b:16.9 occ:1.00 OD1 A:ASN100 2.2 9.0 1.0 OD1 A:ASP167 2.4 11.2 1.0 O A:HIS201 2.4 6.5 1.0 O A:ARG158 2.6 16.5 1.0 OD2 A:ASP167 2.6 11.0 1.0 O A:HOH4221 2.6 13.6 1.0 O A:HOH4227 2.8 19.8 1.0 CG A:ASP167 2.8 11.0 1.0 CG A:ASN100 3.3 8.3 1.0 C A:ARG158 3.5 16.8 1.0 C A:HIS201 3.6 7.2 1.0 ND2 A:ASN100 3.6 8.4 1.0 CA A:ARG158 4.0 17.4 1.0 CB A:HIS201 4.2 7.3 1.0 CB A:ASP167 4.3 11.2 1.0 O A:ASN100 4.4 8.7 1.0 CG A:MET202 4.4 8.2 1.0 N A:ASP159 4.5 16.0 1.0 CA A:HIS201 4.5 8.2 1.0 ND2 A:ASN137 4.5 17.8 1.0 N A:MET202 4.5 7.2 1.0 CA A:MET202 4.5 8.0 1.0 O A:HOH4035 4.6 8.4 1.0 CB A:ASN100 4.6 8.6 1.0 O A:LEU168 4.7 11.4 1.0 O A:VAL157 4.7 17.8 1.0 O A:CYS160 4.8 12.5 1.0 CA A:ASP159 4.8 15.8 1.0 CB A:ARG158 4.9 17.2 1.0 O A:HOH4051 4.9 10.5 1.0

Calcium binding site 2 out of 3 in the Camelid Vhh Domains in Complex with 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 Camelid Vhh Domains in Complex with Porcine Pancreatic Alpha-Amylase within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca4003 b:29.7 occ:1.00 O C:ARG158 2.2 22.7 1.0 O C:HOH4141 2.3 17.9 1.0 O C:HIS201 2.3 22.1 1.0 O C:HOH4275 2.3 29.6 1.0 OD1 C:ASN100 2.3 19.4 1.0 OD1 C:ASP167 2.4 21.2 1.0 O C:HOH4140 2.6 23.3 1.0 OD2 C:ASP167 2.7 20.4 1.0 CG C:ASP167 2.9 21.2 1.0 CG C:ASN100 3.3 18.3 1.0 C C:ARG158 3.3 23.3 1.0 C C:HIS201 3.5 21.9 1.0 ND2 C:ASN100 3.6 17.9 1.0 CA C:ARG158 3.8 23.6 1.0 CB C:HIS201 4.1 20.6 1.0 O C:ASN100 4.3 20.8 1.0 CB C:ASP167 4.4 19.9 1.0 N C:ASP159 4.4 23.1 1.0 CA C:HIS201 4.4 21.0 1.0 N C:MET202 4.5 22.1 1.0 CA C:MET202 4.5 23.1 1.0 O C:HOH4066 4.5 29.6 1.0 CG C:MET202 4.5 24.8 1.0 O C:CYS160 4.6 23.1 1.0 O C:VAL157 4.6 24.4 1.0 CB C:ASN100 4.7 19.3 1.0 CD1 C:LEU170 4.7 25.8 1.0 CB C:ARG158 4.7 23.7 1.0 ND2 C:ASN137 4.8 28.3 1.0 CA C:ASP159 4.8 23.3 1.0 N C:ARG158 5.0 23.8 1.0 O C:LEU168 5.0 23.5 1.0

Calcium binding site 3 out of 3 in the Camelid Vhh Domains in Complex with 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 Camelid Vhh Domains in Complex with Porcine Pancreatic Alpha-Amylase within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca4005 b:17.8 occ:1.00 O E:HIS201 2.3 6.8 1.0 O E:HOH4242 2.3 18.9 1.0 O E:HOH4240 2.4 13.9 1.0 OD1 E:ASN100 2.5 9.6 1.0 OD1 E:ASP167 2.5 10.1 1.0 O E:ARG158 2.5 16.1 1.0 OD2 E:ASP167 2.8 9.2 1.0 CG E:ASP167 3.0 10.9 1.0 C E:ARG158 3.5 16.2 1.0 C E:HIS201 3.5 7.0 1.0 CG E:ASN100 3.6 11.4 1.0 ND2 E:ASN100 4.0 11.0 1.0 CA E:ARG158 4.0 15.9 1.0 CG E:MET202 4.3 8.1 1.0 CA E:MET202 4.3 7.7 1.0 N E:MET202 4.4 7.2 1.0 CB E:HIS201 4.4 7.0 1.0 O E:ASN100 4.5 10.4 1.0 CB E:ASP167 4.5 11.5 1.0 CA E:HIS201 4.5 7.5 1.0 N E:ASP159 4.5 16.9 1.0 O E:HOH4095 4.6 21.7 1.0 ND2 E:ASN137 4.6 16.2 1.0 O E:LEU168 4.6 13.7 1.0 CB E:ARG158 4.8 15.1 1.0 CA E:ASP159 4.9 17.3 1.0 O E:CYS160 4.9 18.3 1.0 CB E:MET202 4.9 7.8 1.0 CB E:ASN100 4.9 11.0 1.0 O E:VAL157 4.9 16.9 1.0

A.Desmyter, S.Spinelli, F.Payan, M.Lauwereys, L.Wyns, S.Muyldermans, C.Cambillau. Three Camelid Vhh Domains in Complex with Porcine Pancreatic Alpha-Amylase. Inhibition and Versatility of Binding Topology. J.Biol.Chem. V. 277 23645 2002.
ISSN: ISSN 0021-9258
PubMed: 11960990
DOI: 10.1074/JBC.M202327200