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Calcium in PDB 1ob0: Kinetic Stabilization of Bacillus Licheniformis Alpha-Amylase Through Introduction of Hydrophobic Residues at the Surface

Enzymatic activity of Kinetic Stabilization of Bacillus Licheniformis Alpha-Amylase Through Introduction of Hydrophobic Residues at the Surface

All present enzymatic activity of Kinetic Stabilization of Bacillus Licheniformis Alpha-Amylase Through Introduction of Hydrophobic Residues at the Surface:
3.2.1.1;

Protein crystallography data

The structure of Kinetic Stabilization of Bacillus Licheniformis Alpha-Amylase Through Introduction of Hydrophobic Residues at the Surface, PDB code: 1ob0 was solved by M.Machius, N.Declerck, R.Huber, G.Wiegand, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.89 / 1.83
Space group P 61
Cell size a, b, c (Å), α, β, γ (°) 91.292, 91.292, 137.466, 90.00, 90.00, 120.00
R / Rfree (%) 14.7 / 15.4

Other elements in 1ob0:

The structure of Kinetic Stabilization of Bacillus Licheniformis Alpha-Amylase Through Introduction of Hydrophobic Residues at the Surface also contains other interesting chemical elements:

Sodium (Na) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the Kinetic Stabilization of Bacillus Licheniformis Alpha-Amylase Through Introduction of Hydrophobic Residues at the Surface (pdb code 1ob0). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Kinetic Stabilization of Bacillus Licheniformis Alpha-Amylase Through Introduction of Hydrophobic Residues at the Surface, PDB code: 1ob0:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in 1ob0

Go back to Calcium Binding Sites List in 1ob0
Calcium binding site 1 out of 3 in the Kinetic Stabilization of Bacillus Licheniformis Alpha-Amylase Through Introduction of Hydrophobic Residues at the Surface


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Kinetic Stabilization of Bacillus Licheniformis Alpha-Amylase Through Introduction of Hydrophobic Residues at the Surface within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca501

b:15.8
occ:1.00
 O A:HIS235 2.4 15.2 1.0
OD1 A:ASN104 2.4 14.8 1.0
OD1 A:ASP194 2.4 15.8 1.0
OD1 A:ASP200 2.4 17.9 1.0
O A:ASP194 2.4 13.6 1.0
O A:HOH2060 2.5 15.6 1.0
OD2 A:ASP200 3.0 18.7 1.0
CG A:ASP200 3.1 18.9 1.0
C A:ASP194 3.3 15.0 1.0
CG A:ASP194 3.5 17.9 1.0
CG A:ASN104 3.5 15.9 1.0
C A:HIS235 3.5 16.5 1.0
CA A:ASP194 3.8 14.8 1.0
O A:HOH2125 3.9 15.3 1.0
CB A:HIS235 4.0 14.5 1.0
O A:ASN104 4.0 15.2 1.0
NA A:NA504 4.1 19.1 1.0
ND2 A:ASN104 4.1 16.0 1.0
CB A:ASP194 4.2 15.1 1.0
CA A:HIS235 4.3 14.5 1.0
OD2 A:ASP194 4.4 16.6 1.0
O A:HOH2136 4.4 16.2 1.0
N A:TYR195 4.5 15.2 1.0
N A:ILE236 4.5 15.1 1.0
CB A:ASP200 4.5 14.4 1.0
CA A:ILE236 4.6 15.4 1.0
CB A:ASN104 4.6 14.7 1.0
O A:ILE201 4.7 15.2 1.0
C A:ASN104 4.8 15.3 1.0
CA A:TYR195 4.8 14.7 1.0
CA A:ASN104 4.8 14.6 1.0
CG1 A:ILE236 4.8 15.7 1.0

Calcium binding site 2 out of 3 in 1ob0

Go back to Calcium Binding Sites List in 1ob0
Calcium binding site 2 out of 3 in the Kinetic Stabilization of Bacillus Licheniformis Alpha-Amylase Through Introduction of Hydrophobic Residues at the Surface


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Kinetic Stabilization of Bacillus Licheniformis Alpha-Amylase Through Introduction of Hydrophobic Residues at the Surface within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca502

b:19.5
occ:1.00
 OD1 A:ASP183 2.4 17.8 1.0
O A:ALA181 2.4 18.0 1.0
OD2 A:ASP202 2.5 20.2 1.0
OD1 A:ASP204 2.5 21.7 1.0
OD1 A:ASP161 2.5 17.0 1.0
O A:HOH2122 2.6 15.8 1.0
OD2 A:ASP161 2.6 16.4 1.0
CG A:ASP161 2.9 19.3 1.0
CG A:ASP204 3.3 21.9 1.0
CG A:ASP202 3.3 21.2 1.0
CG A:ASP183 3.5 19.2 1.0
C A:ALA181 3.6 19.0 1.0
CB A:ASP204 3.7 20.7 1.0
N A:ASP183 3.9 18.7 1.0
OD1 A:ASP202 4.0 20.5 1.0
C A:TRP182 4.1 20.0 1.0
OD2 A:ASP183 4.2 17.6 1.0
N A:ALA181 4.2 19.4 1.0
CB A:ASP202 4.2 18.3 1.0
CA A:ASP183 4.3 18.0 1.0
CA A:ASP202 4.3 17.2 1.0
OD2 A:ASP204 4.3 24.1 1.0
N A:ASP204 4.3 20.2 1.0
CB A:ASP161 4.4 15.8 1.0
O A:HOH2140 4.4 31.2 1.0
NA A:NA504 4.5 19.1 1.0
CA A:TRP182 4.5 19.3 1.0
CB A:ASP183 4.5 17.6 1.0
CA A:ALA181 4.5 18.9 1.0
N A:TRP182 4.5 18.7 1.0
N A:TYR203 4.6 17.2 1.0
O A:TRP182 4.6 18.7 1.0
O A:HOH2141 4.7 38.1 1.0
CA A:ASP204 4.7 21.5 1.0
C A:ASP202 4.7 17.8 1.0
OD2 A:ASP194 4.9 16.6 1.0

Calcium binding site 3 out of 3 in 1ob0

Go back to Calcium Binding Sites List in 1ob0
Calcium binding site 3 out of 3 in the Kinetic Stabilization of Bacillus Licheniformis Alpha-Amylase Through Introduction of Hydrophobic Residues at the Surface


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Kinetic Stabilization of Bacillus Licheniformis Alpha-Amylase Through Introduction of Hydrophobic Residues at the Surface within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca503

b:26.7
occ:1.00
 O A:TYR302 2.3 20.8 1.0
OD2 A:ASP407 2.4 25.2 1.0
O A:HIS406 2.6 22.4 1.0
O A:GLY300 2.6 25.8 1.0
OD1 A:ASP430 2.6 21.8 1.0
OD2 A:ASP430 2.6 21.5 1.0
O A:HOH2204 2.7 30.2 1.0
CG A:ASP430 3.0 22.9 1.0
C A:HIS406 3.5 22.1 1.0
C A:GLY300 3.5 25.6 1.0
CG A:ASP407 3.5 26.3 1.0
C A:TYR302 3.5 22.1 1.0
CA A:ASP407 3.7 21.9 1.0
N A:TYR302 3.9 22.7 1.0
N A:ASP407 3.9 21.3 1.0
CB A:ASP407 4.1 23.1 1.0
C A:GLY301 4.2 24.5 1.0
CG A:MET304 4.2 17.3 1.0
CA A:GLY300 4.2 24.9 1.0
CA A:TYR302 4.2 21.9 1.0
N A:GLY301 4.4 24.5 1.0
O A:HOH2200 4.4 41.1 1.0
CB A:ASP430 4.5 22.1 1.0
N A:MET304 4.5 17.5 1.0
OD1 A:ASP407 4.5 28.2 1.0
N A:ASP303 4.5 20.8 1.0
CA A:GLY301 4.5 23.7 1.0
ND1 A:HIS406 4.5 34.7 1.0
CA A:ASP303 4.6 20.6 1.0
CB A:HIS406 4.6 27.7 1.0
CA A:HIS406 4.6 24.1 1.0
O A:GLY301 4.7 24.6 1.0
O A:HOH2203 4.7 36.4 1.0
CB A:TYR302 4.8 22.7 1.0
O A:HOH2201 4.9 22.5 1.0
C A:ASP407 4.9 21.1 1.0

Reference:

M.Machius, N.Declerck, R.Huber, G.Wiegand. Kinetic Stabilization of Bacillus Licheniformis Alpha-Amylase Through Introduction of Hydrophobic Residues at the Surface J.Biol.Chem. V. 278 11546 2003.
ISSN: ISSN 0021-9258
PubMed: 12540849
DOI: 10.1074/JBC.M212618200
Page generated: Sat Dec 12 03:11:30 2020

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