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

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

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

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 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 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 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 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 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

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