Zinc in PDB 1pv9: Prolidase From Pyrococcus Furiosus

All present enzymatic activity of Prolidase From Pyrococcus Furiosus:
3.4.13.9;

The structure of Prolidase From Pyrococcus Furiosus, PDB code: 1pv9 was solved by M.J.Maher, M.Ghosh, A.M.Grunden, A.L.Menon, M.W.Adams, H.C.Freeman, J.M.Guss, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 2.00
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	56.476, 97.227, 69.882, 90.00, 97.09, 90.00
R / Rfree (%)	24.5 / 27.7

The binding sites of Zinc atom in the Prolidase From Pyrococcus Furiosus (pdb code 1pv9). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Prolidase From Pyrococcus Furiosus, PDB code: 1pv9:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Prolidase From Pyrococcus Furiosus


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Prolidase From Pyrococcus Furiosus within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:37.2 occ:1.00 O A:HOH502 2.0 31.9 1.0 OE2 A:GLU327 2.1 20.8 1.0 NE2 A:HIS284 2.1 18.8 1.0 OD2 A:ASP220 2.2 22.5 1.0 OE2 A:GLU313 2.3 27.5 1.0 CG A:ASP220 3.0 20.3 1.0 CE1 A:HIS284 3.1 17.4 1.0 CD A:GLU327 3.1 21.2 1.0 ZN A:ZN402 3.1 38.1 1.0 CD A:GLU313 3.1 25.4 1.0 CD2 A:HIS284 3.1 16.8 1.0 OE1 A:GLU313 3.3 27.3 1.0 OD1 A:ASP220 3.4 18.2 1.0 OE1 A:GLU327 3.4 21.0 1.0 OG1 A:THR311 3.8 19.6 1.0 CG2 A:THR311 4.0 19.0 1.0 CB A:ASP220 4.1 19.1 1.0 ND1 A:HIS284 4.2 16.1 1.0 CB A:THR311 4.2 18.0 1.0 CG A:HIS284 4.3 18.4 1.0 CG A:GLU327 4.4 20.1 1.0 CG A:GLU313 4.5 22.9 1.0 NE2 A:HIS291 4.7 33.9 1.0

Zinc binding site 2 out of 4 in the Prolidase From Pyrococcus Furiosus


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Prolidase From Pyrococcus Furiosus within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:38.1 occ:1.00 OE1 A:GLU327 2.0 21.0 1.0 OD1 A:ASP220 2.1 18.2 1.0 OD1 A:ASP209 2.1 16.7 1.0 O A:HOH502 2.1 31.9 1.0 OD2 A:ASP209 2.8 19.9 1.0 CG A:ASP209 2.8 19.9 1.0 CD A:GLU327 2.9 21.2 1.0 CG A:ASP220 2.9 20.3 1.0 ZN A:ZN401 3.1 37.2 1.0 OE2 A:GLU327 3.1 20.8 1.0 OD2 A:ASP220 3.2 22.5 1.0 OG1 A:THR222 3.4 19.6 1.0 CZ A:PHE178 3.8 22.9 1.0 OE1 A:GLU313 3.9 27.3 1.0 O A:ILE221 4.2 20.1 1.0 CB A:ASP220 4.3 19.1 1.0 CG A:GLU327 4.3 20.1 1.0 CB A:ASP209 4.3 18.8 1.0 N A:ILE221 4.3 19.8 1.0 CE2 A:PHE178 4.4 21.3 1.0 C A:ILE221 4.5 19.2 1.0 CE1 A:PHE178 4.5 23.2 1.0 OE2 A:GLU313 4.6 27.5 1.0 CD A:GLU313 4.6 25.4 1.0 C A:ASP220 4.7 20.0 1.0 CA A:ASP220 4.7 19.5 1.0 CB A:THR222 4.8 18.9 1.0 CB A:GLU327 4.8 19.1 1.0 CA A:ASP209 4.8 18.3 1.0 O A:LEU210 4.9 17.6 1.0 CA A:ILE221 4.9 19.4 1.0 N A:THR222 4.9 18.8 1.0 N A:LEU210 4.9 17.2 1.0

Zinc binding site 3 out of 4 in the Prolidase From Pyrococcus Furiosus


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Prolidase From Pyrococcus Furiosus within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:55.2 occ:1.00 NE2 B:HIS284 2.0 14.2 1.0 OD2 B:ASP220 2.2 20.6 1.0 OE2 B:GLU327 2.3 18.8 1.0 OE2 B:GLU313 2.6 24.8 1.0 CE1 B:HIS284 2.9 15.9 1.0 CD2 B:HIS284 3.0 16.3 1.0 CG B:ASP220 3.1 18.4 1.0 CD B:GLU313 3.3 23.6 1.0 OE1 B:GLU313 3.5 24.1 1.0 CD B:GLU327 3.5 16.7 1.0 CG2 B:THR311 3.5 20.1 1.0 ZN B:ZN402 3.6 53.8 1.0 OD1 B:ASP220 3.7 17.8 1.0 OG1 B:THR311 3.9 21.7 1.0 OE1 B:GLU327 4.0 17.8 1.0 ND1 B:HIS284 4.0 16.0 1.0 CG B:HIS284 4.1 17.2 1.0 CB B:THR311 4.2 20.0 1.0 CB B:ASP220 4.2 18.5 1.0 CG B:GLU313 4.5 21.8 1.0 CE1 B:HIS291 4.5 29.8 1.0 NE2 B:HIS291 4.6 30.0 1.0 CG B:GLU327 4.7 17.8 1.0

Zinc binding site 4 out of 4 in the Prolidase From Pyrococcus Furiosus


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Prolidase From Pyrococcus Furiosus within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn402 b:53.8 occ:1.00 OD1 B:ASP209 1.9 19.4 1.0 OD1 B:ASP220 2.2 17.8 1.0 OE1 B:GLU327 2.3 17.8 1.0 OD2 B:ASP209 2.6 18.9 1.0 CG B:ASP209 2.6 18.3 1.0 CG B:ASP220 3.1 18.4 1.0 CD B:GLU327 3.1 16.7 1.0 OE2 B:GLU327 3.3 18.8 1.0 OG1 B:THR222 3.3 17.4 1.0 OD2 B:ASP220 3.3 20.6 1.0 CZ B:PHE178 3.5 21.4 1.0 ZN B:ZN401 3.6 55.2 1.0 OE1 B:GLU313 4.0 24.1 1.0 O B:ILE221 4.1 18.8 1.0 CB B:ASP209 4.1 18.0 1.0 CE2 B:PHE178 4.2 22.5 1.0 CE1 B:PHE178 4.3 22.0 1.0 N B:ILE221 4.3 18.3 1.0 C B:ILE221 4.4 18.2 1.0 CB B:ASP220 4.4 18.5 1.0 CG B:GLU327 4.6 17.8 1.0 CB B:THR222 4.7 18.6 1.0 CA B:ASP209 4.7 17.5 1.0 N B:LEU210 4.7 16.7 1.0 O B:LEU210 4.7 16.0 1.0 C B:ASP220 4.8 18.2 1.0 CA B:ASP220 4.8 18.2 1.0 N B:THR222 4.8 18.3 1.0 CD B:GLU313 4.8 23.6 1.0 C B:ASP209 4.9 17.1 1.0 CA B:ILE221 4.9 18.1 1.0

M.J.Maher, M.Ghosh, A.M.Grunden, A.L.Menon, M.W.Adams, H.C.Freeman, J.M.Guss. Structure of the Prolidase From Pyrococcus Furiosus. Biochemistry V. 43 2771 2004.
ISSN: ISSN 0006-2960
PubMed: 15005612
DOI: 10.1021/BI0356451