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

The structure of Crystal Structure of Pet-Degrading Cutinase CUT190 S176A/S226P/R228S Mutant in Monoethyl Succinate Bound State, PDB code: 5zrr 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)	41.61 / 1.34
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	49.507, 61.397, 76.783, 90.00, 90.00, 90.00
R / Rfree (%)	16.2 / 18.5

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

Zinc binding site 1 out of 4 in the Crystal Structure of Pet-Degrading Cutinase CUT190 S176A/S226P/R228S Mutant in Monoethyl Succinate 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 Succinate Bound State within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:9.9 occ:1.00 OE1 A:GLU296 1.9 10.7 1.0 OD1 A:ASP250 1.9 11.2 1.0 OE1 A:GLU220 2.0 7.7 1.0 OE2 A:GLU220 2.6 22.6 1.0 CD A:GLU220 2.6 13.7 1.0 CD A:GLU296 2.8 22.2 1.0 CG A:ASP250 3.0 10.1 1.0 OE2 A:GLU296 3.1 20.3 1.0 CB A:ASP250 3.6 7.3 1.0 CA A:ASP250 3.8 7.0 1.0 CG A:GLU296 4.0 12.8 1.0 N A:GLY251 4.1 5.9 1.0 CG A:GLU220 4.1 10.7 1.0 OD2 A:ASP250 4.1 18.0 1.0 C A:ASP250 4.4 7.1 1.0 CB A:GLU296 4.5 10.2 1.0 CB A:GLU220 4.7 9.3 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of Pet-Degrading Cutinase CUT190 S176A/S226P/R228S Mutant in Monoethyl Succinate 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 Succinate Bound State within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn403 b:10.0 occ:1.00 O A:HOH603 2.0 13.7 1.0 OE2 A:GLU57 2.0 6.7 1.0 CD A:GLU57 2.7 7.6 1.0 OE1 A:GLU57 2.7 10.0 1.0 O A:HOH549 3.9 10.3 1.0 O A:HOH571 4.0 8.8 1.0 CG A:GLU57 4.1 7.6 1.0 OH A:TYR267 4.4 4.8 1.0 CD1 A:PHE285 4.4 7.2 1.0 CB A:GLU57 4.8 7.3 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of Pet-Degrading Cutinase CUT190 S176A/S226P/R228S Mutant in Monoethyl Succinate 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 Succinate Bound State within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn404 b:17.2 occ:1.00 O A:HOH672 2.2 21.6 1.0 O A:THR206 2.2 8.7 1.0 OD1 A:ASP204 2.3 11.7 1.0 OG1 A:THR206 2.3 14.2 1.0 O A:HOH550 2.3 24.0 1.0 O A:HOH574 2.3 14.1 1.0 O A:HOH729 2.7 35.3 1.0 OD2 A:ASP204 2.8 13.0 1.0 CG A:ASP204 2.9 10.6 1.0 C A:THR206 3.2 8.2 1.0 CB A:THR206 3.4 13.7 1.0 CA A:THR206 3.6 8.3 1.0 N A:THR206 3.8 6.7 1.0 NE2 A:GLN209 4.2 22.1 1.0 CB A:ASP204 4.4 8.5 1.0 N A:TRP207 4.4 7.4 1.0 OE1 A:GLN209 4.4 20.2 1.0 O A:HOH735 4.6 34.8 1.0 CG2 A:THR206 4.6 16.6 1.0 CD A:GLN209 4.8 23.7 1.0 CE2 A:TRP207 4.9 5.0 1.0 CD2 A:TRP207 4.9 4.8 1.0 CA A:TRP207 4.9 6.2 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of Pet-Degrading Cutinase CUT190 S176A/S226P/R228S Mutant in Monoethyl Succinate 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 Monoethyl Succinate Bound State within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn405 b:23.1 occ:1.00 OD1 A:ASP46 2.0 29.8 1.0 OE2 A:GLU50 2.0 11.8 1.0 N A:GLY43 2.2 27.9 1.0 O A:GLY43 2.3 23.4 1.0 O A:HOH710 2.3 31.5 1.0 CG A:ASP46 2.7 42.1 1.0 CD A:GLU50 2.8 14.0 1.0 OD2 A:ASP46 2.8 45.0 1.0 OE1 A:GLU50 2.9 14.9 1.0 C A:GLY43 3.0 25.1 1.0 CA A:GLY43 3.1 24.8 1.0 O A:HOH639 4.2 12.3 1.0 CG A:GLU50 4.2 10.7 1.0 CB A:ASP46 4.2 31.5 1.0 N A:PRO44 4.3 25.5 1.0 N A:ASN47 4.4 13.5 1.0 CB A:ASN47 4.5 10.7 1.0 N A:ASP46 4.5 24.4 1.0 CA A:ASP46 4.7 27.6 1.0 C A:ASP46 4.7 25.0 1.0 O A:HOH602 4.7 36.5 1.0 O A:HOH712 4.7 33.6 1.0 O A:HOH508 4.9 19.3 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