Zinc in PDB 5zrs: Crystal Structure of Pet-Degrading Cutinase CUT190 S176A/S226P/R228S Mutant in Monoethyl Adipate Bound State

The structure of Crystal Structure of Pet-Degrading Cutinase CUT190 S176A/S226P/R228S Mutant in Monoethyl Adipate Bound State, PDB code: 5zrs 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)	49.61 / 1.40
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	50.457, 63.856, 78.785, 90.00, 90.00, 90.00
R / Rfree (%)	16.1 / 19.2

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

Zinc binding site 1 out of 3 in the Crystal Structure of Pet-Degrading Cutinase CUT190 S176A/S226P/R228S Mutant in Monoethyl Adipate 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 Monoethyl Adipate Bound State within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:10.8 occ:1.00 OE1 A:GLU296 1.9 11.7 1.0 OD1 A:ASP250 2.0 10.7 1.0 OE1 A:GLU220 2.0 8.4 1.0 OE2 A:GLU220 2.6 12.9 1.0 CD A:GLU220 2.6 10.0 1.0 CD A:GLU296 2.8 12.9 1.0 CG A:ASP250 3.1 14.7 1.0 OE2 A:GLU296 3.4 13.6 1.0 CB A:ASP250 3.6 7.3 1.0 CA A:ASP250 3.8 8.1 1.0 CG A:GLU296 3.9 12.1 1.0 N A:GLY251 4.0 9.4 1.0 CG A:GLU220 4.1 10.7 1.0 OD2 A:ASP250 4.1 20.9 1.0 O A:HOH586 4.3 15.0 1.0 CB A:GLU296 4.3 9.1 1.0 C A:ASP250 4.4 6.7 1.0 O A:HOH777 4.6 32.5 1.0 CB A:GLU220 4.7 8.8 1.0 O A:HOH846 4.8 34.0 1.0

Zinc binding site 2 out of 3 in the Crystal Structure of Pet-Degrading Cutinase CUT190 S176A/S226P/R228S Mutant in Monoethyl Adipate 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 Monoethyl Adipate Bound State within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn403 b:23.6 occ:1.00 O A:THR206 2.1 10.7 1.0 O A:HOH652 2.2 16.1 1.0 OD1 A:ASP204 2.2 14.4 1.0 OG1 A:THR206 2.3 16.9 1.0 O A:HOH663 2.3 30.8 1.0 O A:HOH662 2.4 21.2 1.0 OD2 A:ASP204 2.9 22.4 1.0 CG A:ASP204 2.9 14.1 1.0 C A:THR206 3.1 9.4 1.0 CB A:THR206 3.4 15.9 1.0 CA A:THR206 3.6 16.8 1.0 N A:THR206 3.7 10.7 1.0 O A:HOH720 4.3 34.4 1.0 N A:TRP207 4.3 9.9 1.0 NE2 A:GLN209 4.4 12.6 1.0 CB A:ASP204 4.4 9.7 1.0 O A:HOH756 4.5 28.3 1.0 OE1 A:GLN209 4.5 14.0 1.0 CG2 A:THR206 4.7 15.6 1.0 CE2 A:TRP207 4.7 8.7 1.0 CD2 A:TRP207 4.8 8.3 1.0 CA A:TRP207 4.8 9.3 1.0 CD A:GLN209 5.0 12.4 1.0 CZ2 A:TRP207 5.0 10.0 1.0 C A:ASP204 5.0 9.4 1.0 N A:LYS205 5.0 9.3 1.0 CE3 A:TRP207 5.0 9.7 1.0

Zinc binding site 3 out of 3 in the Crystal Structure of Pet-Degrading Cutinase CUT190 S176A/S226P/R228S Mutant in Monoethyl Adipate 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 Monoethyl Adipate Bound State within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn404 b:28.9 occ:1.00 OD1 A:ASP46 2.0 33.2 1.0 OE2 A:GLU50 2.0 15.7 1.0 N A:GLY43 2.2 33.0 1.0 O A:HOH653 2.2 25.3 1.0 O A:GLY43 2.2 29.7 1.0 CG A:ASP46 2.6 44.0 1.0 OD2 A:ASP46 2.7 47.6 1.0 CD A:GLU50 2.7 13.5 1.0 OE1 A:GLU50 2.8 17.5 1.0 C A:GLY43 2.9 33.4 1.0 CA A:GLY43 3.0 35.3 1.0 CB A:ASP46 4.1 35.6 1.0 CG A:GLU50 4.1 15.0 1.0 O A:HOH774 4.1 38.5 1.0 N A:PRO44 4.2 28.0 1.0 O A:HOH569 4.2 17.7 1.0 O A:HOH710 4.3 35.9 1.0 O A:HOH602 4.4 32.3 1.0 N A:ASN47 4.5 18.2 1.0 N A:ASP46 4.5 29.5 1.0 CB A:ASN47 4.6 17.6 1.0 CA A:ASP46 4.6 32.0 1.0 O A:HOH563 4.6 30.8 1.0 C A:ASP46 4.6 29.1 1.0 CA A:PRO44 4.9 33.0 1.0 CD A:ARG281 5.0 10.4 1.0 O A:HOH558 5.0 21.7 1.0

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