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Calcium in PDB 8ibl: Mes Bound Form of Pet-Degrading Cutinase CUT190 with Thermostability- Improving Mutations of S226P/R228S/Q138A/D250C-E296C/Q123H/N202H and S176A Inactivation

Enzymatic activity of Mes Bound Form of Pet-Degrading Cutinase CUT190 with Thermostability- Improving Mutations of S226P/R228S/Q138A/D250C-E296C/Q123H/N202H and S176A Inactivation

All present enzymatic activity of Mes Bound Form of Pet-Degrading Cutinase CUT190 with Thermostability- Improving Mutations of S226P/R228S/Q138A/D250C-E296C/Q123H/N202H and S176A Inactivation:
3.1.1.74;

Protein crystallography data

The structure of Mes Bound Form of Pet-Degrading Cutinase CUT190 with Thermostability- Improving Mutations of S226P/R228S/Q138A/D250C-E296C/Q123H/N202H and S176A Inactivation, PDB code: 8ibl was solved by M.Emori, N.Numoto, N.Kamiya, M.Oda, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 32.36 / 2.60
Space group P 3
Cell size a, b, c (Å), α, β, γ (°) 83.869, 83.869, 64.723, 90, 90, 120
R / Rfree (%) 21.1 / 26.3

Other elements in 8ibl:

The structure of Mes Bound Form of Pet-Degrading Cutinase CUT190 with Thermostability- Improving Mutations of S226P/R228S/Q138A/D250C-E296C/Q123H/N202H and S176A Inactivation also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Mes Bound Form of Pet-Degrading Cutinase CUT190 with Thermostability- Improving Mutations of S226P/R228S/Q138A/D250C-E296C/Q123H/N202H and S176A Inactivation (pdb code 8ibl). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Mes Bound Form of Pet-Degrading Cutinase CUT190 with Thermostability- Improving Mutations of S226P/R228S/Q138A/D250C-E296C/Q123H/N202H and S176A Inactivation, PDB code: 8ibl:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 8ibl

Go back to Calcium Binding Sites List in 8ibl
Calcium binding site 1 out of 2 in the Mes Bound Form of Pet-Degrading Cutinase CUT190 with Thermostability- Improving Mutations of S226P/R228S/Q138A/D250C-E296C/Q123H/N202H and S176A Inactivation


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Mes Bound Form of Pet-Degrading Cutinase CUT190 with Thermostability- Improving Mutations of S226P/R228S/Q138A/D250C-E296C/Q123H/N202H and S176A Inactivation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca401

b:56.8
occ:1.00
 O A:ALA78 2.3 40.7 1.0
O A:PHE81 2.4 30.9 1.0
O A:SER76 2.4 45.1 1.0
C A:ALA78 3.5 36.6 1.0
C A:PHE81 3.5 26.9 1.0
C A:SER76 3.6 38.9 1.0
OD1 A:ASN133 3.7 28.5 1.0
C A:PHE77 3.8 33.3 1.0
N A:ALA78 4.0 29.8 1.0
CA A:PHE77 4.0 30.0 1.0
N A:PHE81 4.1 35.8 1.0
O A:PHE77 4.2 33.2 1.0
N A:PHE77 4.3 33.6 1.0
CA A:ALA78 4.3 32.5 1.0
N A:SER79 4.4 40.0 1.0
N A:GLY80 4.4 28.4 1.0
CA A:GLY82 4.4 23.3 1.0
CA A:SER79 4.4 33.4 1.0
N A:GLY82 4.4 28.3 1.0
CA A:PHE81 4.5 30.7 1.0
C A:SER79 4.6 33.5 1.0
CA A:SER76 4.7 38.8 1.0
O A:HOH527 4.8 36.2 1.0
CG A:ASN133 4.9 31.4 1.0

Calcium binding site 2 out of 2 in 8ibl

Go back to Calcium Binding Sites List in 8ibl
Calcium binding site 2 out of 2 in the Mes Bound Form of Pet-Degrading Cutinase CUT190 with Thermostability- Improving Mutations of S226P/R228S/Q138A/D250C-E296C/Q123H/N202H and S176A Inactivation


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Mes Bound Form of Pet-Degrading Cutinase CUT190 with Thermostability- Improving Mutations of S226P/R228S/Q138A/D250C-E296C/Q123H/N202H and S176A Inactivation within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca401

b:50.6
occ:1.00
 O B:ALA78 2.4 36.6 1.0
O B:SER76 2.4 40.8 1.0
O B:PHE81 2.5 31.2 1.0
C B:SER76 3.4 37.7 1.0
C B:ALA78 3.4 34.3 1.0
C B:PHE77 3.6 35.1 1.0
C B:PHE81 3.7 27.6 1.0
N B:ALA78 3.7 32.7 1.0
CA B:PHE77 3.7 34.3 1.0
N B:PHE77 3.9 36.6 1.0
O B:PHE77 4.0 36.2 1.0
OD1 B:ASN133 4.0 29.6 1.0
CA B:ALA78 4.2 31.6 1.0
CA B:GLY82 4.3 25.2 1.0
N B:SER79 4.4 40.7 1.0
N B:PHE81 4.4 31.9 1.0
N B:GLY82 4.5 28.6 1.0
CA B:SER76 4.5 32.7 1.0
CA B:SER79 4.5 31.9 1.0
CA B:PHE81 4.7 31.1 1.0
N B:GLY80 4.8 29.5 1.0
C B:SER79 4.9 31.4 1.0
C B:GLY82 4.9 24.8 1.0
N B:GLY83 5.0 22.1 1.0
CB B:ALA78 5.0 27.2 1.0

Reference:

N.Numoto, N.Kamiya, M.Oda. Improvement of Thermostability and Activity of Pet-Degrading Enzyme CUT190 Towards A Detailed Understanding and Application of the Enzymatic Reaction Mechanism. Biorxiv 2023.
ISSN: ISSN 2692-8205
DOI: 10.1101/2023.02.26.529345
Page generated: Fri Jul 19 09:37:37 2024

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