Zinc in PDB 6r4y: Crystal Structure of Holo Ppep-1(E143A/Y178F) in Complex with Product Peptide Ac-Evnp-CO2 (Substrate Peptide: Ac-Evnpavp-CONH2)

All present enzymatic activity of Crystal Structure of Holo Ppep-1(E143A/Y178F) in Complex with Product Peptide Ac-Evnp-CO2 (Substrate Peptide: Ac-Evnpavp-CONH2):
3.4.24.89;

The structure of Crystal Structure of Holo Ppep-1(E143A/Y178F) in Complex with Product Peptide Ac-Evnp-CO2 (Substrate Peptide: Ac-Evnpavp-CONH2), PDB code: 6r4y was solved by C.Pichlo, U.Baumann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.24 / 1.45
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	37.036, 42.800, 118.274, 90.00, 92.78, 90.00
R / Rfree (%)	14.5 / 16.5

The binding sites of Zinc atom in the Crystal Structure of Holo Ppep-1(E143A/Y178F) in Complex with Product Peptide Ac-Evnp-CO2 (Substrate Peptide: Ac-Evnpavp-CONH2) (pdb code 6r4y). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of Holo Ppep-1(E143A/Y178F) in Complex with Product Peptide Ac-Evnp-CO2 (Substrate Peptide: Ac-Evnpavp-CONH2), PDB code: 6r4y:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of Holo Ppep-1(E143A/Y178F) in Complex with Product Peptide Ac-Evnp-CO2 (Substrate Peptide: Ac-Evnpavp-CONH2)


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 Holo Ppep-1(E143A/Y178F) in Complex with Product Peptide Ac-Evnp-CO2 (Substrate Peptide: Ac-Evnpavp-CONH2) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn300 b:13.7 occ:1.00 OE1 A:GLU185 1.9 13.1 1.0 OXT E:PRO4 1.9 16.4 1.0 NE2 A:HIS142 2.0 14.4 1.0 NE2 A:HIS146 2.0 13.2 1.0 CD A:GLU185 2.7 13.3 1.0 CD2 A:HIS142 2.9 14.1 1.0 OE2 A:GLU185 2.9 15.7 1.0 C E:PRO4 3.0 21.2 1.0 CE1 A:HIS142 3.0 12.0 1.0 CE1 A:HIS146 3.0 11.6 1.0 CD2 A:HIS146 3.0 13.3 1.0 HD2 A:HIS142 3.1 16.9 1.0 HD2 A:HIS146 3.2 16.0 1.0 HE1 A:HIS146 3.2 13.9 1.0 HE1 A:HIS142 3.2 14.4 1.0 O E:PRO4 3.3 20.2 1.0 HB3 E:ASN3 3.5 19.1 1.0 HZ A:PHE178 3.6 20.7 1.0 HA A:GLU185 3.7 14.9 1.0 HB3 A:ALA188 3.8 15.8 1.0 O E:HOH105 3.9 15.8 1.0 HE2 A:PHE178 4.0 19.3 1.0 HB2 E:ASN3 4.1 19.1 1.0 ND1 A:HIS142 4.1 12.0 1.0 CG A:HIS142 4.1 12.6 1.0 ND1 A:HIS146 4.1 13.8 1.0 CG A:HIS146 4.2 12.1 1.0 CG A:GLU185 4.2 12.9 1.0 CB E:ASN3 4.2 15.9 1.0 O E:HOH103 4.3 16.9 1.0 HB1 A:ALA188 4.3 15.8 1.0 CA E:PRO4 4.3 17.0 1.0 CZ A:PHE178 4.3 17.2 1.0 HB3 A:GLU185 4.4 16.0 1.0 CB A:ALA188 4.4 13.1 1.0 N E:PRO4 4.4 13.8 1.0 HB2 A:ALA188 4.5 15.8 1.0 HD2 E:PRO4 4.5 17.4 1.0 CE2 A:PHE178 4.5 16.1 1.0 C E:ASN3 4.6 14.6 1.0 CA A:GLU185 4.6 12.4 1.0 CB A:GLU185 4.6 13.3 1.0 HG3 A:GLU185 4.6 15.4 1.0 HG2 E:PRO4 4.7 18.0 1.0 HG2 A:GLU185 4.7 15.4 1.0 O E:ASN3 4.8 13.4 1.0 HZ2 A:LYS101 4.8 23.4 1.0 HA E:PRO4 4.9 20.4 1.0 HD1 A:HIS142 4.9 14.4 1.0 HD1 A:HIS146 4.9 16.5 1.0 CD E:PRO4 4.9 14.5 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Holo Ppep-1(E143A/Y178F) in Complex with Product Peptide Ac-Evnp-CO2 (Substrate Peptide: Ac-Evnpavp-CONH2)


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 Holo Ppep-1(E143A/Y178F) in Complex with Product Peptide Ac-Evnp-CO2 (Substrate Peptide: Ac-Evnpavp-CONH2) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn300 b:13.1 occ:1.00 OXT D:PRO4 1.9 15.8 1.0 OE1 B:GLU185 1.9 12.2 1.0 NE2 B:HIS142 2.0 11.2 1.0 NE2 B:HIS146 2.0 11.2 1.0 CD B:GLU185 2.7 12.4 1.0 OE2 B:GLU185 2.9 12.6 1.0 CD2 B:HIS142 2.9 10.9 1.0 C D:PRO4 3.0 15.5 1.0 CE1 B:HIS146 3.0 11.4 1.0 CE1 B:HIS142 3.0 13.8 1.0 CD2 B:HIS146 3.0 11.3 1.0 HD2 B:HIS142 3.1 13.1 1.0 HD2 B:HIS146 3.2 13.5 1.0 HE1 B:HIS146 3.2 13.7 1.0 HE1 B:HIS142 3.3 16.6 1.0 O D:PRO4 3.3 24.1 1.0 HB3 D:ASN3 3.4 23.6 1.0 HA B:GLU185 3.8 15.3 1.0 HZ B:PHE178 3.8 22.7 1.0 HB3 B:ALA188 3.9 13.6 1.0 O D:HOH107 3.9 15.4 1.0 HB2 D:ASN3 4.0 23.6 1.0 HE2 B:PHE178 4.0 20.8 1.0 CG B:HIS142 4.1 11.1 1.0 ND1 B:HIS142 4.1 12.4 1.0 ND1 B:HIS146 4.1 13.1 1.0 CG B:HIS146 4.2 11.2 1.0 CG B:GLU185 4.2 13.0 1.0 CB D:ASN3 4.2 19.6 1.0 O D:HOH104 4.2 15.8 1.0 CA D:PRO4 4.3 14.7 1.0 N D:PRO4 4.3 16.4 1.0 HB1 B:ALA188 4.4 13.6 1.0 HD2 D:PRO4 4.4 22.6 1.0 HB3 B:GLU185 4.4 15.8 1.0 CZ B:PHE178 4.5 18.9 1.0 C D:ASN3 4.5 17.4 1.0 CB B:ALA188 4.5 11.3 1.0 CE2 B:PHE178 4.6 17.4 1.0 HB2 B:ALA188 4.6 13.6 1.0 CA B:GLU185 4.6 12.8 1.0 HG3 B:GLU185 4.6 15.6 1.0 CB B:GLU185 4.6 13.2 1.0 O D:ASN3 4.7 16.9 1.0 HG2 B:GLU185 4.7 15.6 1.0 HG2 D:PRO4 4.7 21.9 1.0 HZ1 B:LYS101 4.8 26.9 1.0 HA D:PRO4 4.8 17.6 1.0 CD D:PRO4 4.9 18.8 1.0 HD1 B:HIS142 4.9 14.9 1.0 HD1 B:HIS146 4.9 15.7 1.0

C.Pichlo, L.Juetten, F.Wojtalla, M.Schacherl, D.Diaz, U.Baumann. Molecular Determinants of the Mechanism and Substrate Specificity Ofclostridium Difficileproline-Proline Endopeptidase-1. J.Biol.Chem. V. 294 11525 2019.
ISSN: ESSN 1083-351X
PubMed: 31182482
DOI: 10.1074/JBC.RA119.009029