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Zinc in PDB 7cef: Crystal Structure of Pet-Degrading Cutinase CUT190 /S226P/R228S/ Mutant with the C-Terminal Three Residues Deletion

Enzymatic activity of Crystal Structure of Pet-Degrading Cutinase CUT190 /S226P/R228S/ Mutant with the C-Terminal Three Residues Deletion

All present enzymatic activity of Crystal Structure of Pet-Degrading Cutinase CUT190 /S226P/R228S/ Mutant with the C-Terminal Three Residues Deletion:
3.1.1.74;

Protein crystallography data

The structure of Crystal Structure of Pet-Degrading Cutinase CUT190 /S226P/R228S/ Mutant with the C-Terminal Three Residues Deletion, PDB code: 7cef was solved by A.Senga, N.Numoto, N.Ito, F.Kawai, M.Oda, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.72 / 1.60
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 60.512, 49.100, 82.948, 90.00, 107.45, 90.00
R / Rfree (%) 17.7 / 22

Other elements in 7cef:

The structure of Crystal Structure of Pet-Degrading Cutinase CUT190 /S226P/R228S/ Mutant with the C-Terminal Three Residues Deletion also contains other interesting chemical elements:

Calcium (Ca) 1 atom

Zinc Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 17;

Binding sites:

The binding sites of Zinc atom in the Crystal Structure of Pet-Degrading Cutinase CUT190 /S226P/R228S/ Mutant with the C-Terminal Three Residues Deletion (pdb code 7cef). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 17 binding sites of Zinc where determined in the Crystal Structure of Pet-Degrading Cutinase CUT190 /S226P/R228S/ Mutant with the C-Terminal Three Residues Deletion, PDB code: 7cef:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 17 in 7cef

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Zinc binding site 1 out of 17 in the Crystal Structure of Pet-Degrading Cutinase CUT190 /S226P/R228S/ Mutant with the C-Terminal Three Residues Deletion


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Pet-Degrading Cutinase CUT190 /S226P/R228S/ Mutant with the C-Terminal Three Residues Deletion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn402

b:35.6
occ:1.00
 OD1 A:ASP46 2.0 36.9 1.0
OE2 A:GLU50 2.0 26.9 1.0
OD2 A:ASP46 2.1 45.5 1.0
O A:HOH637 2.1 34.6 1.0
O A:GLY43 2.2 32.7 1.0
N A:GLY43 2.2 30.4 1.0
OE1 A:GLU50 2.3 28.9 1.0
CG A:ASP46 2.3 34.5 1.0
CD A:GLU50 2.5 21.1 1.0
C A:GLY43 2.8 34.2 1.0
CA A:GLY43 2.9 30.5 1.0
CB A:ASP46 3.8 38.8 1.0
O A:HOH511 4.0 24.1 1.0
CG A:GLU50 4.0 21.2 1.0
N A:PRO44 4.1 33.2 1.0
N A:ASP46 4.5 32.3 1.0
CB A:ASN47 4.5 23.4 1.0
N A:ASN47 4.5 19.7 1.0
CA A:ASP46 4.5 32.4 1.0
C A:ASP46 4.6 30.3 1.0
O A:HOH641 4.6 35.5 1.0
CG A:ARG281 4.7 20.0 1.0
CD A:ARG281 4.7 23.5 1.0
CA A:PRO44 4.8 32.2 1.0
CB A:GLU50 5.0 18.4 1.0

Zinc binding site 2 out of 17 in 7cef

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Zinc binding site 2 out of 17 in the Crystal Structure of Pet-Degrading Cutinase CUT190 /S226P/R228S/ Mutant with the C-Terminal Three Residues Deletion


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Pet-Degrading Cutinase CUT190 /S226P/R228S/ Mutant with the C-Terminal Three Residues Deletion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn403

b:15.7
occ:1.00
 OD1 A:ASP250 2.0 16.6 1.0
OE1 A:GLU296 2.0 15.3 1.0
OE1 A:GLU220 2.1 20.6 1.0
CG A:ASP250 2.9 15.4 1.0
CD A:GLU220 2.9 17.8 1.0
O A:HOH558 2.9 15.2 1.0
CD A:GLU296 3.0 17.8 1.0
OE2 A:GLU220 3.1 19.0 1.0
OE2 A:GLU296 3.4 16.4 1.0
OD2 A:ASP250 3.4 16.1 1.0
N A:GLY251 3.8 18.3 1.0
CB A:ASP250 4.0 14.7 1.0
CA A:ASP250 4.0 15.3 1.0
C A:ASP250 4.2 16.7 1.0
CG A:GLU296 4.3 20.9 1.0
CG A:GLU220 4.3 15.2 1.0
CA A:GLY251 4.6 18.0 1.0
CB A:GLU296 4.7 15.9 1.0
O A:HOH615 4.8 22.9 1.0
CB A:GLU220 4.8 14.7 1.0

Zinc binding site 3 out of 17 in 7cef

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Zinc binding site 3 out of 17 in the Crystal Structure of Pet-Degrading Cutinase CUT190 /S226P/R228S/ Mutant with the C-Terminal Three Residues Deletion


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Pet-Degrading Cutinase CUT190 /S226P/R228S/ Mutant with the C-Terminal Three Residues Deletion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn404

b:30.4
occ:1.00
 O A:HOH501 1.9 25.4 1.0
OD2 A:ASP204 2.0 23.1 1.0
CG A:ASP204 2.9 23.3 1.0
OD1 A:ASP204 3.2 18.9 1.0
O A:HOH577 3.9 26.6 1.0
O A:THR206 3.9 22.4 1.0
NE2 A:GLN209 3.9 24.9 1.0
CH2 A:TRP207 4.1 15.6 1.0
CZ3 A:TRP207 4.2 16.6 1.0
CB A:ASP204 4.2 15.9 1.0
CZ2 A:TRP207 4.5 13.6 1.0
CE3 A:TRP207 4.6 16.4 1.0
OG1 A:THR206 4.9 17.9 1.0
CE2 A:TRP207 4.9 17.6 1.0
CD A:GLN209 4.9 23.5 1.0
CD2 A:TRP207 5.0 16.8 1.0
OE1 A:GLN209 5.0 21.5 1.0

Zinc binding site 4 out of 17 in 7cef

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Zinc binding site 4 out of 17 in the Crystal Structure of Pet-Degrading Cutinase CUT190 /S226P/R228S/ Mutant with the C-Terminal Three Residues Deletion


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Pet-Degrading Cutinase CUT190 /S226P/R228S/ Mutant with the C-Terminal Three Residues Deletion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn405

b:39.5
occ:1.00
 OE2 A:GLU248 2.1 17.7 1.0
O A:HOH535 2.2 27.6 1.0
CD A:GLU248 2.8 15.0 1.0
OE1 A:GLU248 2.8 17.7 1.0
NZ A:LYS232 2.9 27.2 1.0
O A:HOH580 3.4 23.9 1.0
OE1 A:GLU297 3.6 21.1 1.0
CG A:GLU248 4.3 12.8 1.0
O A:HOH718 4.3 29.1 1.0
CG A:GLU296 4.4 20.9 1.0
OE2 A:GLU220 4.4 19.0 1.0
CE A:LYS232 4.4 29.4 1.0
O A:HOH631 4.5 29.5 1.0
CG A:GLU220 4.6 15.2 1.0
CD A:GLU297 4.8 28.7 1.0
CD A:GLU220 4.9 17.8 1.0
CG2 A:VAL227 4.9 18.1 1.0
CB A:GLU297 4.9 19.2 1.0
CB A:GLU248 5.0 13.7 1.0

Zinc binding site 5 out of 17 in 7cef

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Zinc binding site 5 out of 17 in the Crystal Structure of Pet-Degrading Cutinase CUT190 /S226P/R228S/ Mutant with the C-Terminal Three Residues Deletion


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of Pet-Degrading Cutinase CUT190 /S226P/R228S/ Mutant with the C-Terminal Three Residues Deletion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn406

b:36.8
occ:0.50
 OD2 A:ASP93 2.0 44.8 1.0
O A:HOH551 2.1 44.8 1.0
CG A:ASP93 3.0 38.8 1.0
OD1 A:ASP93 3.2 40.5 1.0
OE2 A:GLU94 4.0 31.1 1.0
O A:HOH728 4.2 48.7 1.0
CB A:ASP93 4.3 32.5 1.0
O A:HOH508 4.6 37.7 1.0
CG A:GLU94 4.7 30.3 1.0
CD A:GLU94 4.8 37.9 1.0

Zinc binding site 6 out of 17 in 7cef

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Zinc binding site 6 out of 17 in the Crystal Structure of Pet-Degrading Cutinase CUT190 /S226P/R228S/ Mutant with the C-Terminal Three Residues Deletion


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of Pet-Degrading Cutinase CUT190 /S226P/R228S/ Mutant with the C-Terminal Three Residues Deletion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn407

b:40.6
occ:0.50
 OE2 A:GLU184 2.0 22.8 1.0
O A:HOH577 2.1 26.6 1.0
O A:HOH519 2.1 31.6 1.0
CD A:GLU184 2.6 26.4 1.0
OE1 A:GLU184 2.8 28.5 1.0
O A:HOH649 3.1 30.8 1.0
N A:GLY140 3.6 24.6 1.0
CA A:GLY140 3.7 25.7 1.0
O A:HOH720 3.7 28.8 1.0
CG A:GLU184 3.9 22.5 1.0
OD2 A:ASP204 4.6 23.1 1.0
OD1 A:ASN202 4.6 16.7 1.0
C A:PRO139 4.6 21.1 1.0
ND2 A:ASN202 4.7 15.5 1.0
CB A:PRO139 4.8 16.7 1.0
CB A:ASP204 4.9 15.9 1.0
CB A:GLU184 5.0 19.1 1.0

Zinc binding site 7 out of 17 in 7cef

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Zinc binding site 7 out of 17 in the Crystal Structure of Pet-Degrading Cutinase CUT190 /S226P/R228S/ Mutant with the C-Terminal Three Residues Deletion


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of Pet-Degrading Cutinase CUT190 /S226P/R228S/ Mutant with the C-Terminal Three Residues Deletion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn408

b:42.4
occ:1.00
 OE2 B:GLU278 2.0 32.6 1.0
OE2 A:GLU118 2.0 43.4 1.0
OE1 A:GLU118 2.1 43.7 1.0
O A:HOH523 2.1 42.0 1.0
OE1 B:GLU278 2.2 28.5 1.0
CD A:GLU118 2.3 39.7 1.0
CD B:GLU278 2.4 25.0 1.0
O A:HOH512 3.6 37.0 1.0
CG A:GLU118 3.8 30.8 1.0
CG B:GLU278 3.9 19.9 1.0
O B:HOH512 4.0 28.3 1.0
O B:HOH810 4.0 28.0 1.0
O B:HOH518 4.2 30.6 1.0
CE2 B:TYR49 4.7 21.5 1.0
CB A:GLU118 4.8 21.5 1.0
O B:HOH793 4.8 36.4 1.0
CB B:GLU278 4.9 17.9 1.0
O A:HOH573 4.9 23.6 1.0
CE2 A:TYR87 5.0 18.1 1.0

Zinc binding site 8 out of 17 in 7cef

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Zinc binding site 8 out of 17 in the Crystal Structure of Pet-Degrading Cutinase CUT190 /S226P/R228S/ Mutant with the C-Terminal Three Residues Deletion


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of Pet-Degrading Cutinase CUT190 /S226P/R228S/ Mutant with the C-Terminal Three Residues Deletion within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn401

b:35.3
occ:0.50
 OD1 B:ASP46 2.0 42.7 1.0
OE2 B:GLU50 2.0 24.3 1.0
OD2 B:ASP46 2.0 52.9 1.0
N B:GLY43 2.1 34.2 1.0
O B:HOH625 2.1 33.7 1.0
CG B:ASP46 2.3 43.3 1.0
OE1 B:GLU50 2.3 27.5 1.0
O B:GLY43 2.4 44.8 1.0
CD B:GLU50 2.4 22.2 1.0
CA B:GLY43 2.8 44.8 1.0
C B:GLY43 2.9 43.9 1.0
CB B:ASP46 3.8 47.4 1.0
CG B:GLU50 3.9 16.5 1.0
O B:HOH534 4.1 19.0 1.0
N B:PRO44 4.2 47.9 1.0
O B:HOH506 4.4 22.8 1.0
CB B:ASN47 4.4 23.2 1.0
N B:ASN47 4.4 29.7 1.0
N B:ASP46 4.5 40.5 1.0
O B:HOH747 4.5 38.2 1.0
CA B:ASP46 4.5 43.7 1.0
C B:ASP46 4.6 39.5 1.0
O B:HOH618 4.6 32.8 1.0
O B:HOH685 4.9 24.1 1.0
CB B:GLU50 4.9 16.2 1.0

Zinc binding site 9 out of 17 in 7cef

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Zinc binding site 9 out of 17 in the Crystal Structure of Pet-Degrading Cutinase CUT190 /S226P/R228S/ Mutant with the C-Terminal Three Residues Deletion


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Crystal Structure of Pet-Degrading Cutinase CUT190 /S226P/R228S/ Mutant with the C-Terminal Three Residues Deletion within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn402

b:38.0
occ:1.00
 O B:HOH501 2.1 16.6 1.0
O B:THR206 2.1 20.2 1.0
OD1 B:ASP204 2.2 21.3 1.0
O B:HOH549 2.2 20.1 1.0
OG1 B:THR206 2.3 26.4 1.0
OD2 B:ASP204 2.3 28.1 1.0
CG B:ASP204 2.6 16.9 1.0
C B:THR206 3.1 17.6 1.0
CB B:THR206 3.4 18.1 1.0
CA B:THR206 3.6 18.6 1.0
N B:THR206 3.7 21.6 1.0
CB B:ASP204 4.1 22.5 1.0
N B:TRP207 4.3 16.7 1.0
O B:HOH784 4.3 30.8 1.0
NE2 B:GLN209 4.6 18.5 1.0
CG2 B:THR206 4.6 24.0 1.0
CE2 B:TRP207 4.7 18.2 1.0
CD2 B:TRP207 4.8 17.1 1.0
CA B:TRP207 4.8 16.9 1.0
OE1 B:GLN209 4.9 25.5 1.0
C B:ASP204 4.9 20.8 1.0
CA B:ASP204 4.9 22.0 1.0
CZ2 B:TRP207 5.0 17.6 1.0
N B:LYS205 5.0 18.8 1.0

Zinc binding site 10 out of 17 in 7cef

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Zinc binding site 10 out of 17 in the Crystal Structure of Pet-Degrading Cutinase CUT190 /S226P/R228S/ Mutant with the C-Terminal Three Residues Deletion


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Crystal Structure of Pet-Degrading Cutinase CUT190 /S226P/R228S/ Mutant with the C-Terminal Three Residues Deletion within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn403

b:16.7
occ:1.00
 O B:HOH698 1.9 19.4 1.0
O B:HOH504 2.0 16.1 1.0
OD1 B:ASP250 2.1 14.2 1.0
CG B:ASP250 3.1 19.1 1.0
ZN B:ZN405 3.2 19.1 1.0
OD2 B:ASP250 3.4 17.4 1.0
ZN B:ZN407 3.4 24.8 1.0
ZN B:ZN406 3.5 22.2 1.0
ZN B:ZN404 3.6 17.6 1.0
OE1 B:GLU296 3.8 23.0 1.0
OE1 B:GLU220 4.1 17.2 1.0
O B:HOH817 4.2 34.5 1.0
O B:HOH777 4.5 27.4 1.0
CB B:ASP250 4.5 16.5 1.0
OE2 B:GLU220 4.5 16.9 1.0
CD B:GLU220 4.7 20.8 1.0
N B:GLY251 4.7 13.9 1.0
CD B:GLU296 4.8 20.0 1.0
O B:HOH697 4.8 24.1 1.0
CA B:ASP250 5.0 14.6 1.0

Reference:

A.Senga, N.Numoto, M.Yamashita, A.Iida, N.Ito, F.Kawai, M.Oda. Multiple Structural States of CA2+ Regulated Pet Hydrolase, CUT190, and Its Correlation with Activity and Stability. J.Biochem. 2020.
ISSN: ISSN 0021-924X
PubMed: 32882044
DOI: 10.1093/JB/MVAA102
Page generated: Tue Oct 29 18:10:50 2024

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