Zinc in PDB 8ytz: The P185V Variant of Kubu-Petase From Kutzneria Buriramensis

The structure of The P185V Variant of Kubu-Petase From Kutzneria Buriramensis, PDB code: 8ytz was solved by J.Park, H.Seo, H.Hong, K.-J.Kim, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.34 / 1.70
Space group	I 41 3 2
Cell size a, b, c (Å), α, β, γ (°)	157.219, 157.219, 157.219, 90, 90, 90
R / Rfree (%)	16.1 / 19.5

The binding sites of Zinc atom in the The P185V Variant of Kubu-Petase From Kutzneria Buriramensis (pdb code 8ytz). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 9 binding sites of Zinc where determined in the The P185V Variant of Kubu-Petase From Kutzneria Buriramensis, PDB code: 8ytz:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Zinc binding site 1 out of 9 in the The P185V Variant of Kubu-Petase From Kutzneria Buriramensis


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of The P185V Variant of Kubu-Petase From Kutzneria Buriramensis within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:33.2 occ:1.00 OXT A:ACT313 1.7 49.0 1.0 O A:ACT312 1.9 47.4 1.0 OD1 A:ASP266 2.0 28.4 1.0 O A:ACT314 2.1 60.0 1.0 C A:ACT313 2.5 53.5 1.0 OD2 A:ASP266 2.6 31.6 1.0 CG A:ASP266 2.6 31.8 1.0 O A:ACT313 2.7 45.6 1.0 C A:ACT312 2.9 55.8 1.0 CH3 A:ACT312 3.1 58.8 1.0 C A:ACT314 3.2 84.7 1.0 NE2 A:GLN40 3.5 30.1 1.0 OXT A:ACT314 3.7 102.1 1.0 O A:HOH457 4.0 26.9 1.0 CH3 A:ACT313 4.0 48.1 1.0 OXT A:ACT312 4.1 49.7 1.0 CB A:ASP266 4.1 28.6 1.0 CH3 A:ACT314 4.5 79.4 1.0 C A:ASP266 4.7 25.3 1.0 N A:ARG267 4.7 23.1 1.0 CA A:ASP266 4.8 23.5 1.0 CD A:GLN40 4.8 28.6 1.0 N A:ASP266 4.9 23.1 1.0

Zinc binding site 2 out of 9 in the The P185V Variant of Kubu-Petase From Kutzneria Buriramensis


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of The P185V Variant of Kubu-Petase From Kutzneria Buriramensis within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:44.7 occ:1.00 OXT A:ACT316 1.8 57.6 1.0 OXT A:ACT315 1.9 59.0 1.0 OD2 A:ASP239 2.0 36.4 1.0 O A:HOH535 2.3 48.5 1.0 C A:ACT316 2.5 45.6 1.0 O A:ACT316 2.5 47.5 1.0 CG A:ASP239 2.7 33.3 1.0 OD1 A:ASP239 2.7 29.9 1.0 C A:ACT315 3.0 50.2 1.0 O A:ACT315 3.5 46.3 1.0 CH3 A:ACT316 3.9 47.2 1.0 O A:HOH412 4.0 30.2 1.0 CB A:ASP239 4.1 30.1 1.0 CH3 A:ACT315 4.3 49.9 1.0 CB A:PHE241 4.4 27.9 1.0

Zinc binding site 3 out of 9 in the The P185V Variant of Kubu-Petase From Kutzneria Buriramensis


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of The P185V Variant of Kubu-Petase From Kutzneria Buriramensis within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn303 b:27.1 occ:1.00 OG A:SER162 2.0 25.3 1.0 NE2 A:HIS240 2.1 26.6 1.0 O A:ACT317 2.2 36.6 1.0 O A:HOH540 2.3 23.4 1.0 CB A:SER162 2.8 24.7 1.0 C A:ACT317 2.9 44.0 1.0 OXT A:ACT317 2.9 46.5 1.0 CE1 A:HIS240 3.0 26.0 1.0 CD2 A:HIS240 3.1 27.2 1.0 CA A:SER162 3.9 23.0 1.0 CG2 A:ILE212 4.1 28.5 1.0 N A:PHE92 4.2 27.0 1.0 ND1 A:HIS240 4.2 25.4 1.0 CG A:HIS240 4.2 25.2 1.0 N A:MET163 4.2 21.7 1.0 CB A:PHE92 4.3 31.0 1.0 CH3 A:ACT317 4.3 35.9 1.0 C A:SER162 4.5 21.3 1.0 CA A:PHE92 4.8 28.3 1.0 CA A:GLY91 4.9 27.8 1.0 CB A:TRP189 5.0 26.0 1.0

Zinc binding site 4 out of 9 in the The P185V Variant of Kubu-Petase From Kutzneria Buriramensis


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of The P185V Variant of Kubu-Petase From Kutzneria Buriramensis within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn304 b:55.1 occ:1.00 O A:HOH544 2.6 55.8 1.0

Zinc binding site 5 out of 9 in the The P185V Variant of Kubu-Petase From Kutzneria Buriramensis


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of The P185V Variant of Kubu-Petase From Kutzneria Buriramensis within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn305 b:67.0 occ:1.00 OD2 A:ASP53 2.1 36.7 1.0 OD1 A:ASP53 2.6 26.2 1.0 CG A:ASP53 2.6 31.6 1.0 O A:HOH486 3.3 57.8 1.0 O A:HOH454 4.1 39.5 1.0 CB A:ASP53 4.1 30.7 1.0 O A:HOH421 4.2 43.8 1.0 CB A:PRO104 4.3 26.4 1.0 O A:PRO104 4.4 23.9 1.0 C A:PRO104 4.4 22.9 1.0 N A:ARG105 4.5 22.1 1.0 CA A:ARG105 4.6 21.8 1.0 NE A:ARG105 4.8 30.6 1.0 NH2 A:ARG105 4.9 41.9 1.0 OG A:SER108 4.9 23.2 1.0

Zinc binding site 6 out of 9 in the The P185V Variant of Kubu-Petase From Kutzneria Buriramensis


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of The P185V Variant of Kubu-Petase From Kutzneria Buriramensis within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn306 b:75.5 occ:1.00 O A:HOH505 2.2 62.0 1.0 OE2 A:GLU234 2.3 35.5 1.0 O A:HOH566 2.3 57.9 1.0 O A:HOH572 2.7 59.9 1.0 OE1 A:GLU234 2.9 39.5 1.0 CD A:GLU234 2.9 36.6 1.0 CG A:GLU234 4.4 33.0 1.0 OH A:TYR232 4.5 29.5 1.0 CB A:GLU234 4.9 29.7 1.0

Zinc binding site 7 out of 9 in the The P185V Variant of Kubu-Petase From Kutzneria Buriramensis


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of The P185V Variant of Kubu-Petase From Kutzneria Buriramensis within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn307 b:65.9 occ:1.00 OD2 A:ASP117 2.0 29.8 1.0 O A:HOH462 2.2 34.1 1.0 O A:HOH424 3.0 42.3 1.0 CG A:ASP117 3.0 27.6 1.0 O A:HOH583 3.1 62.4 1.0 OD1 A:ASP117 3.5 26.9 1.0 CB A:ASP117 4.2 24.1 1.0 CA A:GLY72 4.2 22.4 1.0 N A:GLY72 4.6 21.9 1.0 O A:HOH494 4.7 39.4 1.0 CB A:TRP96 4.8 23.4 1.0 N A:SER97 4.9 25.3 1.0 N A:TRP96 5.0 23.5 1.0 C A:GLY72 5.0 21.1 1.0

Zinc binding site 8 out of 9 in the The P185V Variant of Kubu-Petase From Kutzneria Buriramensis


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of The P185V Variant of Kubu-Petase From Kutzneria Buriramensis within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn308 b:81.5 occ:1.00 OD2 A:ASP130 2.1 40.6 1.0 O A:HOH404 2.7 47.3 1.0 CG A:ASP130 2.9 32.5 1.0 OD1 A:ASP130 3.1 34.3 1.0 O A:HOH562 3.1 58.7 1.0 NZ A:LYS174 3.6 55.2 1.0 O A:HOH475 4.2 52.5 1.0 CB A:ASP130 4.4 26.6 1.0 CE A:LYS174 4.6 56.5 1.0 O A:SER126 4.8 27.1 1.0

Zinc binding site 9 out of 9 in the The P185V Variant of Kubu-Petase From Kutzneria Buriramensis


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of The P185V Variant of Kubu-Petase From Kutzneria Buriramensis within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn309 b:74.5 occ:1.00 O A:HOH406 2.1 52.4 1.0 O A:HOH513 2.1 31.9 1.0 O A:HOH525 2.3 40.7 1.0 O A:HOH402 2.3 26.9 1.0 O A:THR82 2.5 24.8 1.0 O A:HOH425 2.6 39.6 1.0 O A:HOH527 2.7 31.3 1.0 C A:THR82 3.7 25.6 1.0 OD1 A:ASP39 3.8 76.1 1.0 NH2 A:ARG155 4.0 36.9 1.0 CG A:ASP39 4.2 72.6 1.0 O A:HOH515 4.3 26.6 1.0 CG1 A:VAL41 4.3 31.2 1.0 OG1 A:THR82 4.3 27.4 1.0 N A:THR82 4.4 23.8 1.0 OD2 A:ASP39 4.5 80.5 1.0 CA A:THR82 4.6 25.6 1.0 N A:TYR83 4.6 22.4 1.0 CA A:TYR83 4.7 20.6 1.0 CD1 A:TYR83 4.8 23.6 1.0

H.Seo, H.Hong, J.Park, S.H.Lee, D.Ki, A.Ryu, H.Y.Sagong, K.J.Kim. Landscape Profiling of Pet Depolymerases Using A Natural Sequence Cluster Framework. Science V. 387 P5637 2025.
ISSN: ESSN 1095-9203
PubMed: 39745946
DOI: 10.1126/SCIENCE.ADP5637