Zinc in PDB 5zrq: Crystal Structure of Pet-Degrading Cutinase CUT190 S176A/S226P/R228S Mutant in Zn(2+)-Bound State

Protein crystallography data

The structure of Crystal Structure of Pet-Degrading Cutinase CUT190 S176A/S226P/R228S Mutant in Zn(2+)-Bound State, PDB code: 5zrq was solved by N.Numoto, N.Kamiya, G.J.Bekker, Y.Yamagami, S.Inaba, 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) 42.32 / 1.12
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 50.196, 63.243, 78.675, 90.00, 90.00, 90.00
R / Rfree (%) 12.1 / 14.2

Other elements in 5zrq:

The structure of Crystal Structure of Pet-Degrading Cutinase CUT190 S176A/S226P/R228S Mutant in Zn(2+)-Bound State also contains other interesting chemical elements:

Calcium (Ca) 1 atom

Zinc Binding Sites:

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

Zinc binding site 1 out of 5 in 5zrq

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Zinc binding site 1 out of 5 in the Crystal Structure of Pet-Degrading Cutinase CUT190 S176A/S226P/R228S Mutant in Zn(2+)-Bound State


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 S176A/S226P/R228S Mutant in Zn(2+)-Bound State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:6.6
occ:1.00
 OE1 A:GLU296 2.0 8.0 1.0
OE1 A:GLU220 2.0 6.7 1.0
OD1 A:ASP250 2.0 7.5 1.0
CD A:GLU220 2.6 6.9 1.0
OE2 A:GLU220 2.6 7.6 1.0
CD A:GLU296 2.9 7.7 1.0
CG A:ASP250 3.0 8.9 1.0
OE2 A:GLU296 3.5 8.9 1.0
CB A:ASP250 3.5 6.8 1.0
CA A:ASP250 3.7 5.9 1.0
CG A:GLU296 3.9 7.3 1.0
N A:GLY251 4.0 6.5 1.0
CG A:GLU220 4.1 7.2 1.0
OD2 A:ASP250 4.1 12.8 1.0
O A:HOH744 4.3 16.2 1.0
O A:HOH664 4.3 12.8 1.0
C A:ASP250 4.3 5.9 1.0
CB A:GLU296 4.4 6.3 1.0
O A:HOH777 4.4 31.2 1.0
CB A:GLU220 4.7 6.5 1.0
O A:HOH859 4.8 33.9 1.0
N A:ASP250 5.0 5.6 1.0
CA A:GLY251 5.0 8.0 1.0

Zinc binding site 2 out of 5 in 5zrq

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


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 S176A/S226P/R228S Mutant in Zn(2+)-Bound State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn402

b:11.0
occ:0.76
 O A:THR206 2.3 7.2 1.0
O A:HOH624 2.4 7.8 1.0
OD1 A:ASP204 2.4 8.0 1.0
O A:HOH708 2.4 16.8 1.0
OG1 A:THR206 2.4 9.5 1.0
O A:HOH702 2.5 15.2 1.0
O A:HOH783 2.5 15.8 1.0
OD2 A:ASP204 2.6 9.4 1.0
CG A:ASP204 2.9 7.8 1.0
C A:THR206 3.3 6.3 1.0
CB A:THR206 3.6 9.0 1.0
CA A:THR206 3.8 7.5 1.0
N A:THR206 3.9 6.8 1.0
O A:HOH606 4.3 23.8 1.0
NE2 A:GLN209 4.3 7.3 1.0
O A:HOH787 4.4 31.5 1.0
CB A:ASP204 4.4 7.3 1.0
N A:TRP207 4.5 6.7 1.0
O A:HOH806 4.5 16.6 1.0
CG2 A:THR206 4.8 10.4 1.0
OE1 A:GLN209 4.8 10.2 1.0
O A:HOH877 4.9 35.6 1.0
O A:HOH686 4.9 16.6 1.0
CE2 A:TRP207 4.9 6.0 1.0
O A:HOH525 5.0 13.4 1.0
CD2 A:TRP207 5.0 5.8 1.0

Zinc binding site 3 out of 5 in 5zrq

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Zinc binding site 3 out of 5 in the Crystal Structure of Pet-Degrading Cutinase CUT190 S176A/S226P/R228S Mutant in Zn(2+)-Bound State


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 S176A/S226P/R228S Mutant in Zn(2+)-Bound State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn403

b:14.1
occ:0.83
 OD1 A:ASP46 1.9 19.9 1.0
OE2 A:GLU50 2.0 12.1 1.0
N A:GLY43 2.0 17.7 1.0
O A:HOH725 2.1 20.0 1.0
O A:GLY43 2.2 17.8 1.0
CG A:ASP46 2.7 20.2 1.0
CD A:GLU50 2.7 10.8 1.0
OE1 A:GLU50 2.8 12.1 1.0
OD2 A:ASP46 2.8 21.1 1.0
C A:GLY43 2.9 18.4 1.0
CA A:GLY43 2.9 18.1 1.0
O A:HOH602 4.0 26.0 1.0
O A:HOH776 4.1 27.7 1.0
CB A:ASP46 4.1 19.0 1.0
CG A:GLU50 4.1 10.1 1.0
N A:PRO44 4.2 20.1 1.0
O A:HOH690 4.3 13.2 1.0
N A:ASN47 4.5 13.0 1.0
N A:ASP46 4.5 19.5 1.0
O A:HOH565 4.5 24.9 1.0
CB A:ASN47 4.6 11.2 1.0
O A:HOH528 4.6 19.9 1.0
CA A:ASP46 4.6 17.9 1.0
C A:ASP46 4.6 15.9 1.0
CA A:PRO44 4.9 21.6 1.0
CD A:ARG281 4.9 8.2 1.0

Zinc binding site 4 out of 5 in 5zrq

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Zinc binding site 4 out of 5 in the Crystal Structure of Pet-Degrading Cutinase CUT190 S176A/S226P/R228S Mutant in Zn(2+)-Bound State


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 S176A/S226P/R228S Mutant in Zn(2+)-Bound State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn404

b:9.4
occ:0.55
 OE1 A:GLU57 1.9 9.2 0.5
O A:HOH700 2.0 17.1 1.0
O A:HOH551 2.1 17.5 1.0
O A:HOH634 2.1 16.5 1.0
CD A:GLU57 2.9 9.7 0.5
OE2 A:GLU57 3.1 10.4 0.5
OE1 A:GLU57 3.2 13.5 0.5
CD A:GLU57 3.4 12.7 0.5
OE2 A:GLU57 3.5 13.2 0.5
O A:HOH501 4.0 29.1 1.0
NZ A:LYS266 4.0 7.2 1.0
O3 A:SO4407 4.1 48.2 1.0
O A:HOH748 4.1 17.0 1.0
O A:HOH579 4.2 17.5 1.0
CG A:GLU57 4.2 9.3 0.5
CG A:GLU57 4.3 12.0 0.5
O A:HOH503 4.3 12.5 1.0
O A:HOH786 4.4 40.5 1.0
OD1 A:ASP292 4.5 7.5 1.0
O A:HOH652 4.6 19.8 1.0
CG A:ASP292 4.8 7.2 1.0
OD2 A:ASP292 4.8 8.1 1.0
OH A:TYR267 5.0 7.0 1.0

Zinc binding site 5 out of 5 in 5zrq

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


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 S176A/S226P/R228S Mutant in Zn(2+)-Bound State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn405

b:19.9
occ:0.50
 O A:HOH503 2.0 12.5 1.0
O A:HOH582 2.2 25.2 1.0
O A:HOH908 2.3 37.5 1.0
O A:HOH754 2.3 30.7 1.0
O3 A:SO4407 4.1 48.2 1.0
O A:HOH758 4.2 24.0 1.0
OE2 A:GLU61 4.2 9.1 1.0
OE1 A:GLU61 4.2 10.0 1.0
OE2 A:GLU57 4.3 10.4 0.5
O A:HOH551 4.3 17.5 1.0
O2 A:SO4407 4.6 47.6 1.0
CD A:GLU61 4.7 8.3 1.0
S A:SO4407 4.8 47.8 1.0
O4 A:SO4407 4.9 48.6 1.0
CD A:GLU57 4.9 9.7 0.5

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: Wed Dec 16 11:27:46 2020

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