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Calcium in PDB 1kxq: Camelid Vhh Domain in Complex with Porcine Pancreatic Alpha-Amylase

Enzymatic activity of Camelid Vhh Domain in Complex with Porcine Pancreatic Alpha-Amylase

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

Protein crystallography data

The structure of Camelid Vhh Domain in Complex with Porcine Pancreatic Alpha-Amylase, PDB code: 1kxq 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) 29.79 / 1.60
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 65.170, 100.920, 103.740, 79.31, 72.63, 86.11
R / Rfree (%) 19.7 / 21.9

Other elements in 1kxq:

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

Chlorine (Cl) 4 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Camelid Vhh Domain in Complex with Porcine Pancreatic Alpha-Amylase (pdb code 1kxq). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Camelid Vhh Domain in Complex with Porcine Pancreatic Alpha-Amylase, PDB code: 1kxq:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 1kxq

Go back to Calcium Binding Sites List in 1kxq
Calcium binding site 1 out of 4 in the Camelid Vhh Domain 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 Domain in Complex with Porcine Pancreatic Alpha-Amylase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca4001

b:12.2
occ:1.00
 O A:HIS201 2.4 13.5 1.0
OD1 A:ASN100 2.4 11.6 1.0
O A:ARG158 2.4 16.2 1.0
O A:HOH4094 2.5 14.7 1.0
OD2 A:ASP167 2.5 13.3 1.0
O A:HOH4014 2.5 12.8 1.0
OD1 A:ASP167 2.5 12.7 1.0
O A:HOH4125 2.6 15.9 1.0
CG A:ASP167 2.8 13.5 1.0
C A:ARG158 3.5 16.7 1.0
CG A:ASN100 3.5 11.9 1.0
C A:HIS201 3.6 13.1 1.0
ND2 A:ASN100 4.0 11.0 1.0
CA A:ARG158 4.1 16.8 1.0
CB A:HIS201 4.3 13.1 1.0
CB A:ASP167 4.3 13.5 1.0
O A:ASN100 4.4 11.6 1.0
ND2 A:ASN137 4.4 17.6 1.0
CA A:HIS201 4.5 13.3 1.0
O A:CYS160 4.5 15.9 1.0
O A:HOH4072 4.5 17.0 1.0
CG A:MET202 4.5 12.7 1.0
N A:ASP159 4.5 16.1 1.0
N A:MET202 4.5 13.3 1.0
CA A:MET202 4.6 13.5 1.0
O A:LEU168 4.7 13.9 1.0
O A:VAL157 4.7 16.7 1.0
CA A:ASP159 4.8 16.6 1.0
CB A:ASN100 4.8 11.6 1.0
O A:HOH4008 4.9 13.8 1.0
CB A:ARG158 5.0 17.1 1.0

Calcium binding site 2 out of 4 in 1kxq

Go back to Calcium Binding Sites List in 1kxq
Calcium binding site 2 out of 4 in the Camelid Vhh Domain 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 Domain in Complex with Porcine Pancreatic Alpha-Amylase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca4003

b:13.1
occ:1.00
 O B:ARG158 2.4 14.2 1.0
O B:HOH4030 2.4 14.2 1.0
O B:HIS201 2.4 14.1 1.0
OD1 B:ASN100 2.4 12.2 1.0
OD2 B:ASP167 2.5 15.4 1.0
OD1 B:ASP167 2.5 14.8 1.0
O B:HOH4307 2.5 14.6 1.0
O B:HOH4012 2.6 14.8 1.0
CG B:ASP167 2.8 15.4 1.0
C B:ARG158 3.4 14.9 1.0
CG B:ASN100 3.5 12.9 1.0
C B:HIS201 3.6 14.1 1.0
ND2 B:ASN100 4.0 12.6 1.0
CA B:ARG158 4.0 14.9 1.0
CB B:HIS201 4.3 14.1 1.0
CB B:ASP167 4.3 15.4 1.0
O B:HOH4056 4.4 17.4 1.0
O B:ASN100 4.4 12.6 1.0
ND2 B:ASN137 4.4 20.2 1.0
N B:ASP159 4.5 15.0 1.0
CA B:HIS201 4.5 14.2 1.0
CG B:MET202 4.5 14.7 1.0
N B:MET202 4.5 14.2 1.0
O B:CYS160 4.6 14.9 1.0
CA B:MET202 4.6 14.6 1.0
O B:VAL157 4.7 14.0 1.0
CA B:ASP159 4.8 15.3 1.0
CB B:ASN100 4.8 12.7 1.0
O B:HOH4049 4.8 13.8 1.0
CB B:ARG158 4.9 15.5 1.0
O B:LEU168 4.9 16.8 1.0

Calcium binding site 3 out of 4 in 1kxq

Go back to Calcium Binding Sites List in 1kxq
Calcium binding site 3 out of 4 in the Camelid Vhh Domain 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 Domain in Complex with Porcine Pancreatic Alpha-Amylase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca4005

b:11.4
occ:1.00
 O C:HIS201 2.4 11.8 1.0
OD1 C:ASN100 2.4 11.5 1.0
O C:ARG158 2.4 13.9 1.0
O C:HOH4047 2.4 13.5 1.0
OD2 C:ASP167 2.5 12.5 1.0
OD1 C:ASP167 2.5 12.5 1.0
O C:HOH4060 2.5 15.7 1.0
O C:HOH4022 2.5 12.7 1.0
CG C:ASP167 2.8 12.8 1.0
C C:ARG158 3.4 14.1 1.0
CG C:ASN100 3.5 11.6 1.0
C C:HIS201 3.6 12.4 1.0
ND2 C:ASN100 3.9 11.5 1.0
CA C:ARG158 4.0 14.6 1.0
CB C:HIS201 4.3 12.9 1.0
CB C:ASP167 4.3 12.9 1.0
O C:ASN100 4.4 11.2 1.0
ND2 C:ASN137 4.4 15.1 1.0
N C:ASP159 4.5 13.8 1.0
CG C:MET202 4.5 13.7 1.0
O C:HOH4011 4.5 12.3 1.0
CA C:HIS201 4.5 12.7 1.0
O C:CYS160 4.5 14.2 1.0
N C:MET202 4.5 12.4 1.0
CA C:MET202 4.6 13.1 1.0
O C:VAL157 4.7 14.1 1.0
CA C:ASP159 4.8 13.9 1.0
CB C:ASN100 4.8 11.6 1.0
O C:LEU168 4.8 14.7 1.0
CB C:ARG158 4.9 15.1 1.0
O C:HOH4024 4.9 14.1 1.0

Calcium binding site 4 out of 4 in 1kxq

Go back to Calcium Binding Sites List in 1kxq
Calcium binding site 4 out of 4 in the Camelid Vhh Domain 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 4 of Camelid Vhh Domain in Complex with Porcine Pancreatic Alpha-Amylase within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca4007

b:10.9
occ:1.00
 O D:ARG158 2.4 11.6 1.0
O D:HIS201 2.4 10.4 1.0
OD1 D:ASN100 2.4 9.3 1.0
OD1 D:ASP167 2.5 11.0 1.0
OD2 D:ASP167 2.5 10.7 1.0
O D:HOH4041 2.5 11.2 1.0
O D:HOH4016 2.5 10.2 1.0
O D:HOH4038 2.6 11.3 1.0
CG D:ASP167 2.8 11.1 1.0
C D:ARG158 3.4 12.0 1.0
CG D:ASN100 3.5 9.3 1.0
C D:HIS201 3.6 10.3 1.0
ND2 D:ASN100 4.0 9.3 1.0
CA D:ARG158 4.0 11.8 1.0
CB D:HIS201 4.2 10.9 1.0
O D:ASN100 4.3 9.8 1.0
CB D:ASP167 4.3 11.3 1.0
ND2 D:ASN137 4.4 12.7 1.0
CA D:HIS201 4.4 10.5 1.0
O D:HOH4042 4.5 10.5 1.0
N D:ASP159 4.5 12.3 1.0
CG D:MET202 4.5 10.7 1.0
N D:MET202 4.5 10.3 1.0
O D:CYS160 4.5 12.7 1.0
CA D:MET202 4.6 10.7 1.0
O D:VAL157 4.7 11.7 1.0
CA D:ASP159 4.8 12.7 1.0
CB D:ASN100 4.8 9.4 1.0
O D:LEU168 4.8 11.8 1.0
CB D:ARG158 4.9 12.1 1.0
O D:HOH4023 4.9 11.2 1.0

Reference:

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
Page generated: Sat Dec 12 03:04:31 2020

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