Zinc in PDB 6r50: Crystal Structure of Holo Ppep-1(E143A/Y178F) in Complex with Substrate Peptide Ac-Evnapvp-CONH2

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

The structure of Crystal Structure of Holo Ppep-1(E143A/Y178F) in Complex with Substrate Peptide Ac-Evnapvp-CONH2, PDB code: 6r50 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)	40.93 / 1.81
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	37.540, 42.927, 123.450, 90.00, 95.98, 90.00
R / Rfree (%)	14.5 / 17.6

The binding sites of Zinc atom in the Crystal Structure of Holo Ppep-1(E143A/Y178F) in Complex with Substrate Peptide Ac-Evnapvp-CONH2 (pdb code 6r50). 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 Substrate Peptide Ac-Evnapvp-CONH2, PDB code: 6r50:
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 Substrate Peptide Ac-Evnapvp-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 Substrate Peptide Ac-Evnapvp-CONH2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:11.3 occ:0.94 OE1 A:GLU185 1.9 12.4 1.0 NE2 A:HIS146 2.0 10.3 1.0 O D:ALA4 2.0 12.8 1.0 NE2 A:HIS142 2.0 9.6 1.0 CD A:GLU185 2.7 13.5 1.0 OE2 A:GLU185 2.9 11.8 1.0 CE1 A:HIS146 2.9 12.9 1.0 CD2 A:HIS142 3.0 10.2 1.0 CE1 A:HIS142 3.1 13.6 1.0 CD2 A:HIS146 3.1 10.7 1.0 HE1 A:HIS146 3.1 15.5 1.0 HD2 A:HIS142 3.1 12.2 1.0 HA D:PRO5 3.1 14.2 1.0 C D:ALA4 3.2 14.5 1.0 HD2 A:HIS146 3.3 12.8 1.0 HE1 A:HIS142 3.3 16.3 1.0 HB3 D:ASN3 3.6 15.4 1.0 HZ A:PHE178 3.7 13.8 1.0 HA A:GLU185 3.8 14.7 1.0 CA D:PRO5 3.8 11.8 1.0 HE2 A:PHE178 3.8 17.3 1.0 HB3 A:ALA188 3.8 11.6 1.0 N D:PRO5 3.9 11.9 1.0 O D:HOH104 3.9 13.3 1.0 ND1 A:HIS146 4.1 10.0 1.0 CG A:HIS142 4.1 9.4 1.0 N D:ALA4 4.1 11.6 1.0 ND1 A:HIS142 4.2 9.7 1.0 CG A:HIS146 4.2 11.0 1.0 CG A:GLU185 4.2 12.3 1.0 HB2 D:ASN3 4.2 15.4 1.0 CA D:ALA4 4.3 10.8 1.0 H D:ALA4 4.3 13.8 1.0 CB D:ASN3 4.3 12.8 1.0 C D:PRO5 4.3 11.8 1.0 HB1 A:ALA188 4.4 11.6 1.0 CZ A:PHE178 4.4 11.5 1.0 C D:ASN3 4.4 12.3 1.0 CB A:ALA188 4.4 9.7 1.0 HB3 A:GLU185 4.5 14.1 1.0 CE2 A:PHE178 4.5 14.4 1.0 HB2 A:ALA188 4.5 11.6 1.0 O D:ASN3 4.6 11.8 1.0 HG3 A:GLU185 4.6 14.8 1.0 CA A:GLU185 4.6 12.3 1.0 CB A:GLU185 4.7 11.7 1.0 O D:PRO5 4.7 14.2 1.0 HG2 A:GLU185 4.7 14.8 1.0 HA D:ALA4 4.8 13.0 1.0 O D:HOH102 4.8 26.7 1.0 HZ3 A:LYS101 4.8 34.1 1.0 HD1 A:HIS146 4.8 12.0 1.0 N D:VAL6 4.9 10.9 1.0 H D:VAL6 4.9 13.1 1.0 HD1 A:HIS142 4.9 11.6 1.0 CA D:ASN3 5.0 12.8 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Holo Ppep-1(E143A/Y178F) in Complex with Substrate Peptide Ac-Evnapvp-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 Substrate Peptide Ac-Evnapvp-CONH2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:12.3 occ:0.91 OE1 B:GLU185 2.0 12.7 1.0 O C:ALA4 2.0 16.9 1.0 NE2 B:HIS142 2.0 12.7 1.0 NE2 B:HIS146 2.1 11.7 1.0 CD B:GLU185 2.7 13.4 1.0 OE2 B:GLU185 2.8 15.3 1.0 CD2 B:HIS142 3.0 11.0 1.0 CE1 B:HIS146 3.0 12.0 1.0 CE1 B:HIS142 3.0 13.2 1.0 CD2 B:HIS146 3.1 11.3 1.0 HA C:PRO5 3.1 24.6 1.0 HD2 B:HIS142 3.1 13.2 1.0 C C:ALA4 3.2 20.2 1.0 HE1 B:HIS146 3.2 14.3 1.0 HD2 B:HIS146 3.2 13.6 1.0 HE1 B:HIS142 3.3 15.9 1.0 HB3 C:ASN3 3.6 24.9 1.0 CA C:PRO5 3.8 20.5 1.0 HA B:GLU185 3.8 15.6 1.0 HB3 B:ALA188 3.8 13.6 1.0 N C:PRO5 3.9 16.5 1.0 HZ B:PHE178 3.9 22.0 1.0 HE2 B:PHE178 3.9 18.2 1.0 O C:HOH102 4.0 16.9 1.0 CG B:HIS142 4.1 10.8 1.0 N C:ALA4 4.1 19.1 1.0 ND1 B:HIS142 4.1 11.8 1.0 ND1 B:HIS146 4.1 11.8 1.0 CG B:GLU185 4.2 18.1 1.0 HB2 C:ASN3 4.2 24.9 1.0 CG B:HIS146 4.2 11.7 1.0 H C:ALA4 4.2 23.0 1.0 C C:PRO5 4.3 16.5 1.0 CA C:ALA4 4.3 17.6 1.0 HB1 B:ALA188 4.3 13.6 1.0 CB C:ASN3 4.3 20.8 1.0 C C:ASN3 4.4 19.5 1.0 CB B:ALA188 4.4 11.3 1.0 HB3 B:GLU185 4.5 19.9 1.0 HB2 B:ALA188 4.5 13.6 1.0 CZ B:PHE178 4.6 18.3 1.0 CE2 B:PHE178 4.6 15.2 1.0 HG3 B:GLU185 4.6 21.8 1.0 CA B:GLU185 4.6 13.0 1.0 O C:PRO5 4.6 17.8 1.0 CB B:GLU185 4.7 16.6 1.0 HG2 B:GLU185 4.7 21.8 1.0 O C:ASN3 4.7 19.3 1.0 HZ3 B:LYS101 4.8 41.7 1.0 O C:HOH101 4.8 32.4 1.0 N C:VAL6 4.8 13.5 1.0 HA C:ALA4 4.8 21.1 1.0 H C:VAL6 4.8 16.2 1.0 HD1 B:HIS142 4.9 14.2 1.0 HD1 B:HIS146 4.9 14.2 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