Calcium in PDB 8ibm: Sulfate 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 Sulfate 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 Sulfate 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 Sulfate Bound Form of Pet-Degrading Cutinase CUT190 with Thermostability-Improving Mutations of S226P/R228S/Q138A/D250C- E296C/Q123H/N202H and S176A Inactivation, PDB code: 8ibm 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) 36.27 / 2.20
Space group P 3
Cell size a, b, c (Å), α, β, γ (°) 83.755, 83.755, 64.752, 90, 90, 120
R / Rfree (%) 23.4 / 26.7

Calcium Binding Sites:

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

Calcium binding site 1 out of 2 in 8ibm

Go back to Calcium Binding Sites List in 8ibm
Calcium binding site 1 out of 2 in the Sulfate 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 Sulfate 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:63.5
occ:1.00
 O A:ALA78 2.3 49.0 1.0
O A:PHE81 2.4 48.8 1.0
O A:SER76 2.4 47.9 1.0
C A:ALA78 3.5 49.8 1.0
C A:PHE81 3.5 39.5 1.0
C A:SER76 3.5 44.6 1.0
C A:PHE77 3.8 47.0 1.0
N A:ALA78 3.8 42.8 1.0
CA A:PHE77 3.9 44.0 1.0
CA A:GLY82 4.2 37.2 1.0
N A:PHE77 4.2 42.1 1.0
O A:PHE77 4.2 45.8 1.0
OD1 A:ASN133 4.3 43.0 1.0
CA A:ALA78 4.3 46.5 1.0
N A:PHE81 4.3 42.2 1.0
N A:GLY82 4.3 43.8 1.0
N A:SER79 4.5 49.9 1.0
CA A:PHE81 4.5 42.1 1.0
CA A:SER76 4.6 42.5 1.0
CA A:SER79 4.7 51.0 1.0
N A:GLY80 4.7 42.4 1.0
C A:GLY82 4.9 40.6 1.0
C A:SER79 4.9 43.5 1.0
CB A:ALA78 5.0 41.5 1.0

Calcium binding site 2 out of 2 in 8ibm

Go back to Calcium Binding Sites List in 8ibm
Calcium binding site 2 out of 2 in the Sulfate 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 Sulfate 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:60.1
occ:1.00
 O B:ALA78 2.3 51.9 1.0
O B:SER76 2.4 49.9 1.0
O B:PHE81 2.5 47.7 1.0
C B:ALA78 3.5 50.0 1.0
C B:SER76 3.6 44.9 1.0
C B:PHE81 3.6 40.4 1.0
C B:PHE77 3.8 48.1 1.0
N B:ALA78 3.8 45.2 1.0
OD1 B:ASN133 3.9 45.4 1.0
CA B:PHE77 4.0 45.3 1.0
N B:PHE81 4.2 43.5 1.0
N B:PHE77 4.2 42.2 1.0
O B:PHE77 4.2 45.5 1.0
CA B:ALA78 4.3 45.4 1.0
CA B:GLY82 4.3 37.8 1.0
N B:GLY82 4.4 44.2 1.0
N B:SER79 4.4 48.4 1.0
CA B:PHE81 4.5 43.3 1.0
CA B:SER79 4.6 48.7 1.0
N B:GLY80 4.6 47.3 1.0
CA B:SER76 4.7 41.4 1.0
O B:HOH526 4.7 48.6 1.0
C B:SER79 4.8 44.0 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: Tue Apr 4 19:48:53 2023

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