Zinc in PDB 1wy2: Crystal Structure of the Prolidase From Pyrococcus Horikoshii OT3

All present enzymatic activity of Crystal Structure of the Prolidase From Pyrococcus Horikoshii OT3:
3.4.13.9;

The structure of Crystal Structure of the Prolidase From Pyrococcus Horikoshii OT3, PDB code: 1wy2 was solved by H.Mizutani, N.Kunishima, Riken Structural Genomics/Proteomicsinitiative (Rsgi), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 1.70
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	66.697, 105.876, 106.291, 90.00, 90.00, 90.00
R / Rfree (%)	18.7 / 21

The structure of Crystal Structure of the Prolidase From Pyrococcus Horikoshii OT3 also contains other interesting chemical elements:

Magnesium	(Mg)	1 atom
Arsenic	(As)	2 atoms

The binding sites of Zinc atom in the Crystal Structure of the Prolidase From Pyrococcus Horikoshii OT3 (pdb code 1wy2). 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 the Prolidase From Pyrococcus Horikoshii OT3, PDB code: 1wy2:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of the Prolidase From Pyrococcus Horikoshii OT3


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 the Prolidase From Pyrococcus Horikoshii OT3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn405 b:17.2 occ:1.00 OE1 A:GLU330 2.0 16.7 1.0 OD1 A:ASP212 2.0 15.2 1.0 OD1 A:ASP223 2.0 15.6 1.0 O1 A:CAC403 2.1 23.3 1.0 CG A:ASP212 2.7 15.6 1.0 OD2 A:ASP212 2.7 17.9 1.0 CD A:GLU330 2.9 18.0 1.0 CG A:ASP223 2.9 16.2 1.0 OE2 A:GLU330 3.1 18.7 1.0 OD2 A:ASP223 3.1 16.0 1.0 ZN A:ZN406 3.2 18.1 1.0 AS A:CAC403 3.3 30.5 1.0 OG1 A:THR225 3.5 16.2 1.0 CZ A:PHE181 3.8 19.6 1.0 OE1 A:GLU316 3.9 23.5 1.0 C1 A:CAC403 3.9 29.4 1.0 C2 A:CAC403 4.0 27.1 1.0 CB A:ASP212 4.1 15.5 1.0 O A:ILE224 4.2 15.1 1.0 CB A:ASP223 4.3 14.2 1.0 CG A:GLU330 4.3 15.8 1.0 N A:ILE224 4.3 14.5 1.0 CE2 A:PHE181 4.4 20.6 1.0 C A:ILE224 4.5 13.6 1.0 CE1 A:PHE181 4.5 20.5 1.0 O A:HOH1512 4.6 33.3 1.0 CD A:GLU316 4.6 22.4 1.0 O2 A:CAC403 4.6 28.3 1.0 C A:ASP223 4.6 14.7 1.0 OE2 A:GLU316 4.6 22.7 1.0 CA A:ASP223 4.7 14.9 1.0 CA A:ASP212 4.7 15.2 1.0 CB A:GLU330 4.8 15.7 1.0 CB A:THR225 4.9 15.3 1.0 CA A:ILE224 4.9 14.2 1.0 O A:LEU213 4.9 14.2 1.0 N A:LEU213 4.9 13.9 1.0 C A:ASP212 5.0 15.5 1.0 N A:THR225 5.0 13.4 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of the Prolidase From Pyrococcus Horikoshii OT3


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 the Prolidase From Pyrococcus Horikoshii OT3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn406 b:18.1 occ:1.00 O1 A:CAC403 2.1 23.3 1.0 OE2 A:GLU330 2.1 18.7 1.0 NE2 A:HIS287 2.1 14.8 1.0 OD2 A:ASP223 2.1 16.0 1.0 OE2 A:GLU316 2.2 22.7 1.0 CD A:GLU316 3.0 22.4 1.0 CG A:ASP223 3.0 16.2 1.0 CE1 A:HIS287 3.1 15.1 1.0 CD2 A:HIS287 3.1 15.2 1.0 CD A:GLU330 3.1 18.0 1.0 ZN A:ZN405 3.2 17.2 1.0 OE1 A:GLU316 3.2 23.5 1.0 AS A:CAC403 3.2 30.5 1.0 OE1 A:GLU330 3.5 16.7 1.0 OD1 A:ASP223 3.5 15.6 1.0 O2 A:CAC403 3.5 28.3 1.0 C2 A:CAC403 3.8 27.1 1.0 OG1 A:THR314 3.9 16.6 1.0 CG2 A:THR314 4.0 14.7 1.0 ND1 A:HIS287 4.2 14.3 1.0 CB A:ASP223 4.2 14.2 1.0 CG A:HIS287 4.2 15.0 1.0 CB A:THR314 4.2 14.8 1.0 O A:HOH1512 4.3 33.3 1.0 CG A:GLU330 4.4 15.8 1.0 CG A:GLU316 4.4 21.2 1.0 O A:HOH1743 4.5 47.5 1.0 NE2 A:HIS294 4.9 28.8 1.0 C1 A:CAC403 4.9 29.4 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of the Prolidase From Pyrococcus Horikoshii OT3


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 the Prolidase From Pyrococcus Horikoshii OT3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn407 b:16.9 occ:1.00 OD1 B:ASP223 2.0 14.4 1.0 OE1 B:GLU330 2.0 16.2 1.0 OD1 B:ASP212 2.0 15.0 1.0 O1 B:CAC404 2.1 23.6 1.0 CG B:ASP212 2.7 12.7 1.0 OD2 B:ASP212 2.7 15.2 1.0 CD B:GLU330 2.8 19.2 1.0 CG B:ASP223 2.9 16.7 1.0 OE2 B:GLU330 3.0 18.4 1.0 OD2 B:ASP223 3.1 16.0 1.0 ZN B:ZN408 3.2 17.6 1.0 AS B:CAC404 3.3 30.4 1.0 OG1 B:THR225 3.5 14.9 1.0 CZ B:PHE181 3.8 19.1 1.0 C2 B:CAC404 3.9 27.9 1.0 OE1 B:GLU316 3.9 23.6 1.0 C1 B:CAC404 4.0 29.4 1.0 CB B:ASP212 4.2 13.4 1.0 N B:ILE224 4.2 14.7 1.0 CB B:ASP223 4.2 13.9 1.0 O B:ILE224 4.2 13.9 1.0 CG B:GLU330 4.2 16.9 1.0 CE2 B:PHE181 4.4 18.8 1.0 C B:ILE224 4.5 15.3 1.0 CE1 B:PHE181 4.5 18.9 1.0 OE2 B:GLU316 4.5 19.3 1.0 CD B:GLU316 4.6 22.3 1.0 C B:ASP223 4.6 15.7 1.0 O2 B:CAC404 4.7 27.2 1.0 CA B:ASP223 4.7 14.3 1.0 O B:HOH538 4.7 35.4 1.0 CA B:ASP212 4.8 13.5 1.0 CB B:GLU330 4.8 15.1 1.0 CA B:ILE224 4.8 15.7 1.0 CB B:THR225 4.9 14.6 1.0 O B:LEU213 4.9 14.7 1.0 N B:LEU213 4.9 13.9 1.0 N B:THR225 4.9 13.5 1.0 C B:ASP212 5.0 14.9 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of the Prolidase From Pyrococcus Horikoshii OT3


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 the Prolidase From Pyrococcus Horikoshii OT3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn408 b:17.6 occ:1.00 OE2 B:GLU330 2.1 18.4 1.0 OE2 B:GLU316 2.1 19.3 1.0 O1 B:CAC404 2.1 23.6 1.0 OD2 B:ASP223 2.1 16.0 1.0 NE2 B:HIS287 2.1 14.2 1.0 CD B:GLU316 3.0 22.3 1.0 CG B:ASP223 3.0 16.7 1.0 CD2 B:HIS287 3.1 17.2 1.0 CD B:GLU330 3.1 19.2 1.0 CE1 B:HIS287 3.1 15.4 1.0 ZN B:ZN407 3.2 16.9 1.0 OE1 B:GLU316 3.2 23.6 1.0 AS B:CAC404 3.3 30.4 1.0 OD1 B:ASP223 3.5 14.4 1.0 O2 B:CAC404 3.5 27.2 1.0 OE1 B:GLU330 3.5 16.2 1.0 OG1 B:THR314 3.8 16.8 1.0 C2 B:CAC404 3.9 27.9 1.0 CG2 B:THR314 4.0 13.9 1.0 CB B:THR314 4.2 14.4 1.0 CB B:ASP223 4.2 13.9 1.0 ND1 B:HIS287 4.2 16.8 1.0 CG B:HIS287 4.2 15.1 1.0 CG B:GLU316 4.3 19.9 1.0 CG B:GLU330 4.4 16.9 1.0 O B:HOH538 4.5 35.4 1.0 O B:HOH548 4.7 37.8 1.0 NE2 B:HIS294 4.8 30.3 1.0 C1 B:CAC404 4.9 29.4 1.0

H.Mizutani, N.Kunishima. Crystal Structure of the Prolidase From Pyrococcus Horikoshii OT3 To Be Published.