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Calcium in PDB 5zno: Crystal Structure of Pet-Degrading Cutinase CUT190 S176A/S226P/R228S/ Mutant in Ca(2+)-Bound State

Enzymatic activity of Crystal Structure of Pet-Degrading Cutinase CUT190 S176A/S226P/R228S/ Mutant in Ca(2+)-Bound State

All present enzymatic activity of Crystal Structure of Pet-Degrading Cutinase CUT190 S176A/S226P/R228S/ Mutant in Ca(2+)-Bound State:
3.1.1.74;

Protein crystallography data

The structure of Crystal Structure of Pet-Degrading Cutinase CUT190 S176A/S226P/R228S/ Mutant in Ca(2+)-Bound State, PDB code: 5zno was solved by N.Numoto, S.Inaba, Y.Yamagami, N.Kamiya, G.J.Bekker, K.Ishii, S.Uchiyama, F.Kawai, N.Ito, M.Oda, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.72 / 1.60
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 123.705, 49.732, 95.655, 90.00, 99.59, 90.00
R / Rfree (%) 17.9 / 22.2

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Pet-Degrading Cutinase CUT190 S176A/S226P/R228S/ Mutant in Ca(2+)-Bound State (pdb code 5zno). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 7 binding sites of Calcium where determined in the Crystal Structure of Pet-Degrading Cutinase CUT190 S176A/S226P/R228S/ Mutant in Ca(2+)-Bound State, PDB code: 5zno:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7;

Calcium binding site 1 out of 7 in 5zno

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Calcium binding site 1 out of 7 in the Crystal Structure of Pet-Degrading Cutinase CUT190 S176A/S226P/R228S/ Mutant in Ca(2+)-Bound State


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Pet-Degrading Cutinase CUT190 S176A/S226P/R228S/ Mutant in Ca(2+)-Bound State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca401

b:13.9
occ:1.00
 OD1 A:ASP250 2.4 16.4 1.0
O A:HOH783 2.4 22.1 1.0
OE1 A:GLU220 2.4 15.9 1.0
O A:HOH757 2.4 13.2 1.0
OE1 A:GLU296 2.5 13.2 1.0
OE2 A:GLU220 2.5 13.7 1.0
CD A:GLU220 2.8 11.9 1.0
CD A:GLU296 3.5 10.8 1.0
CG A:ASP250 3.6 19.8 1.0
OE2 A:GLU296 4.2 11.1 1.0
O A:HOH608 4.2 23.2 1.0
O A:HOH575 4.3 29.9 1.0
CG A:GLU296 4.3 12.0 1.0
CG A:GLU220 4.3 10.9 1.0
OD2 A:ASP250 4.4 18.0 1.0
O A:HOH863 4.4 33.6 1.0
N A:GLY251 4.4 10.6 1.0
CB A:GLU296 4.5 9.7 1.0
CB A:ASP250 4.5 12.7 1.0
CA A:ASP250 4.6 10.4 1.0
C A:ASP250 5.0 13.9 1.0

Calcium binding site 2 out of 7 in 5zno

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Calcium binding site 2 out of 7 in the Crystal Structure of Pet-Degrading Cutinase CUT190 S176A/S226P/R228S/ Mutant in Ca(2+)-Bound State


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Pet-Degrading Cutinase CUT190 S176A/S226P/R228S/ Mutant in Ca(2+)-Bound State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca402

b:13.7
occ:1.00
 O A:HOH728 2.4 20.4 1.0
O A:THR206 2.4 10.2 1.0
O A:HOH793 2.5 19.8 1.0
OG1 A:THR206 2.5 11.1 1.0
OD2 A:ASP204 2.5 12.6 1.0
OD1 A:ASP204 2.5 13.9 1.0
O A:HOH676 2.5 13.1 1.0
O A:HOH754 2.6 15.6 1.0
CG A:ASP204 2.9 12.7 1.0
C A:THR206 3.4 11.0 1.0
CB A:THR206 3.6 15.3 1.0
CA A:THR206 3.9 12.2 1.0
N A:THR206 4.1 13.5 1.0
O A:HOH711 4.4 32.7 1.0
O A:HOH790 4.4 39.3 1.0
CB A:ASP204 4.4 15.0 1.0
O A:HOH808 4.6 18.9 1.0
O A:HOH746 4.6 29.4 1.0
NE2 A:GLN209 4.6 16.1 1.0
N A:TRP207 4.6 10.8 1.0
O A:HOH814 4.6 39.2 1.0
O A:HOH803 4.7 23.4 1.0
O A:HOH514 4.7 14.8 1.0
CG2 A:THR206 4.9 15.6 1.0
O A:HOH767 4.9 27.4 1.0

Calcium binding site 3 out of 7 in 5zno

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Calcium binding site 3 out of 7 in the Crystal Structure of Pet-Degrading Cutinase CUT190 S176A/S226P/R228S/ Mutant in Ca(2+)-Bound State


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Pet-Degrading Cutinase CUT190 S176A/S226P/R228S/ Mutant in Ca(2+)-Bound State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca403

b:41.3
occ:1.00
 O A:PHE81 2.3 18.8 1.0
O A:HOH786 2.4 31.6 1.0
O A:ALA78 2.4 23.2 1.0
O A:SER76 2.4 29.0 1.0
O A:HOH627 2.5 26.6 1.0
O A:HOH657 2.6 26.1 1.0
C A:PHE81 3.5 17.8 1.0
C A:SER76 3.5 28.6 1.0
C A:ALA78 3.5 27.0 1.0
N A:ALA78 4.0 27.2 1.0
OD1 A:ASN133 4.0 16.7 1.0
N A:PHE81 4.0 17.6 1.0
C A:PHE77 4.1 26.0 1.0
CA A:GLY82 4.2 15.6 1.0
N A:GLY82 4.3 14.4 1.0
CA A:ALA78 4.3 25.7 1.0
N A:GLY80 4.4 19.0 1.0
CA A:PHE81 4.4 19.7 1.0
CA A:PHE77 4.4 29.9 1.0
N A:PHE77 4.4 24.6 1.0
CA A:SER76 4.4 21.8 1.0
N A:SER79 4.6 22.4 1.0
O A:PHE77 4.6 34.0 1.0
CA A:SER79 4.7 29.8 1.0
O A:HOH766 4.8 41.0 1.0
C A:SER79 4.8 24.8 1.0
CB A:SER76 4.9 30.5 1.0
CB A:ALA78 4.9 22.5 1.0
C A:GLY82 4.9 14.1 1.0

Calcium binding site 4 out of 7 in 5zno

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Calcium binding site 4 out of 7 in the Crystal Structure of Pet-Degrading Cutinase CUT190 S176A/S226P/R228S/ Mutant in Ca(2+)-Bound State


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of Pet-Degrading Cutinase CUT190 S176A/S226P/R228S/ Mutant in Ca(2+)-Bound State within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca401

b:16.0
occ:1.00
 O B:HOH634 2.4 20.8 1.0
O B:THR206 2.4 12.2 1.0
O B:HOH639 2.5 18.7 1.0
O B:HOH757 2.5 22.4 1.0
O B:HOH719 2.5 21.3 1.0
OG1 B:THR206 2.5 16.6 1.0
OD1 B:ASP204 2.5 16.2 1.0
OD2 B:ASP204 2.6 16.8 1.0
CG B:ASP204 2.9 15.1 1.0
C B:THR206 3.4 12.0 1.0
CB B:THR206 3.6 15.5 1.0
CA B:THR206 3.9 13.7 1.0
N B:THR206 4.0 16.3 1.0
NE2 B:GLN209 4.3 21.2 0.5
OE1 B:GLN209 4.4 18.2 0.5
CB B:ASP204 4.4 13.9 1.0
N B:TRP207 4.6 14.1 1.0
O B:HOH782 4.7 21.4 1.0
CG2 B:THR206 4.8 17.8 1.0
CD B:GLN209 4.9 21.2 0.5

Calcium binding site 5 out of 7 in 5zno

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Calcium binding site 5 out of 7 in the Crystal Structure of Pet-Degrading Cutinase CUT190 S176A/S226P/R228S/ Mutant in Ca(2+)-Bound State


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of Pet-Degrading Cutinase CUT190 S176A/S226P/R228S/ Mutant in Ca(2+)-Bound State within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca402

b:22.2
occ:1.00
 O B:HOH553 2.3 31.3 1.0
OE1 B:GLU296 2.3 21.3 1.0
O B:HOH755 2.4 27.9 1.0
OD1 B:ASP250 2.4 21.0 1.0
OE1 B:GLU220 2.5 21.6 1.0
OE2 B:GLU220 2.5 23.2 1.0
O B:HOH749 2.6 34.8 1.0
O B:HOH737 2.8 39.5 1.0
CD B:GLU220 2.9 23.5 1.0
CD B:GLU296 3.3 21.8 1.0
CG B:ASP250 3.6 18.4 1.0
OE2 B:GLU296 3.9 29.9 1.0
O B:HOH761 4.1 27.2 1.0
CG B:GLU296 4.2 17.7 1.0
CG B:GLU220 4.4 16.6 1.0
CB B:ASP250 4.4 14.6 1.0
OD2 B:ASP250 4.5 21.0 1.0
N B:GLY251 4.5 14.6 1.0
O B:HOH684 4.5 38.7 1.0
CB B:GLU296 4.5 14.0 1.0
O B:HOH623 4.5 27.2 1.0
CA B:ASP250 4.5 15.1 1.0
O B:HOH687 5.0 33.1 1.0
C B:ASP250 5.0 14.2 1.0

Calcium binding site 6 out of 7 in 5zno

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Calcium binding site 6 out of 7 in the Crystal Structure of Pet-Degrading Cutinase CUT190 S176A/S226P/R228S/ Mutant in Ca(2+)-Bound State


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of Pet-Degrading Cutinase CUT190 S176A/S226P/R228S/ Mutant in Ca(2+)-Bound State within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca403

b:61.0
occ:1.00
 O B:ALA78 2.4 38.8 1.0
O B:PHE81 2.5 43.9 1.0
O B:SER76 2.6 47.6 1.0
O B:HOH766 2.7 43.9 1.0
C B:ALA78 3.5 44.1 1.0
C B:PHE81 3.6 42.8 1.0
C B:SER76 3.7 47.3 1.0
OD1 B:ASN133 3.8 32.8 1.0
N B:ALA78 3.9 47.5 1.0
C B:PHE77 3.9 46.9 1.0
N B:PHE81 4.1 34.0 1.0
CA B:PHE77 4.1 51.0 1.0
N B:GLY80 4.2 47.5 1.0
CA B:ALA78 4.3 41.0 1.0
O B:PHE77 4.4 43.8 1.0
N B:PHE77 4.4 45.1 1.0
CA B:PHE81 4.5 35.2 1.0
N B:SER79 4.5 45.5 1.0
N B:GLY82 4.5 29.3 1.0
CA B:GLY82 4.6 37.0 1.0
CA B:SER79 4.6 43.1 1.0
O B:HOH573 4.7 41.8 1.0
C B:SER79 4.8 44.8 1.0
CA B:SER76 4.8 42.4 1.0
C B:GLY80 4.9 41.0 1.0
CG B:ASN133 5.0 38.0 1.0

Calcium binding site 7 out of 7 in 5zno

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Calcium binding site 7 out of 7 in the Crystal Structure of Pet-Degrading Cutinase CUT190 S176A/S226P/R228S/ Mutant in Ca(2+)-Bound State


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Crystal Structure of Pet-Degrading Cutinase CUT190 S176A/S226P/R228S/ Mutant in Ca(2+)-Bound State within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca404

b:20.6
occ:1.00
 O B:HOH853 2.3 32.0 1.0
O A:HOH765 2.4 25.1 1.0
O A:HOH531 2.5 22.5 1.0
O B:HOH571 2.5 37.3 1.0
O B:HOH739 2.5 28.8 1.0
O B:HOH529 2.5 21.2 1.0
O A:HOH713 2.6 25.4 1.0
O B:HOH679 3.8 34.5 1.0
O A:HOH742 4.2 33.4 1.0
O B:HOH590 4.4 39.5 1.0
OE1 A:GLU61 4.4 16.8 1.0
CD B:ARG281 4.6 11.1 1.0
OE1 B:GLU50 4.6 18.7 1.0
OE2 A:GLU61 4.7 15.2 1.0
OE2 B:GLU50 4.7 24.1 1.0
CG B:ARG281 4.8 13.8 1.0
OD1 B:ASP54 4.8 15.2 1.0
OE1 A:GLU57 4.9 28.0 1.0
O B:HOH609 4.9 29.6 1.0

Reference:

N.Numoto, N.Kamiya, G.J.Bekker, Y.Yamagami, S.Inaba, K.Ishii, S.Uchiyama, F.Kawai, N.Ito, M.Oda. Structural Dynamics of the Pet-Degrading Cutinase-Like Enzyme From Saccharomonospora Viridis AHK190 in Substrate-Bound States Elucidates the CA2+-Driven Catalytic Cycle. Biochemistry V. 57 5289 2018.
ISSN: ISSN 1520-4995
PubMed: 30110540
DOI: 10.1021/ACS.BIOCHEM.8B00624
Page generated: Mon Jul 15 15:52:57 2024

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