Zinc in PDB 6r5c: Crystal Structure of Ppep-1(W103F/E143A/Y178F) in Complex with Substrate Peptide Ac-Evnppvp-CONH2

All present enzymatic activity of Crystal Structure of Ppep-1(W103F/E143A/Y178F) in Complex with Substrate Peptide Ac-Evnppvp-CONH2:
3.4.24.89;

The structure of Crystal Structure of Ppep-1(W103F/E143A/Y178F) in Complex with Substrate Peptide Ac-Evnppvp-CONH2, PDB code: 6r5c 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)	40.85 / 1.88
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	37.358, 43.008, 123.214, 90.00, 95.99, 90.00
R / Rfree (%)	17.7 / 21.3

The binding sites of Zinc atom in the Crystal Structure of Ppep-1(W103F/E143A/Y178F) in Complex with Substrate Peptide Ac-Evnppvp-CONH2 (pdb code 6r5c). 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 Ppep-1(W103F/E143A/Y178F) in Complex with Substrate Peptide Ac-Evnppvp-CONH2, PDB code: 6r5c:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of Ppep-1(W103F/E143A/Y178F) in Complex with Substrate Peptide Ac-Evnppvp-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 Ppep-1(W103F/E143A/Y178F) in Complex with Substrate Peptide Ac-Evnppvp-CONH2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:10.2 occ:0.20 OE1 A:GLU185 1.8 21.7 1.0 O C:PRO4 2.0 18.9 1.0 NE2 A:HIS142 2.2 16.1 1.0 NE2 A:HIS146 2.2 17.3 1.0 CD A:GLU185 2.4 20.9 1.0 OE2 A:GLU185 2.5 26.2 1.0 CD2 A:HIS142 3.1 14.0 1.0 CE1 A:HIS146 3.1 17.3 1.0 CE1 A:HIS142 3.2 16.0 1.0 CD2 A:HIS146 3.2 16.2 1.0 C C:PRO4 3.2 16.6 1.0 HA C:PRO5 3.2 22.3 1.0 HD2 A:HIS142 3.3 16.8 1.0 HE1 A:HIS146 3.3 20.8 1.0 HD2 A:HIS146 3.3 19.5 1.0 HE1 A:HIS142 3.3 19.2 1.0 HB3 C:ASN3 3.5 23.0 1.0 HZ A:PHE178 3.7 26.2 1.0 HA A:GLU185 3.8 17.7 1.0 HE2 A:PHE178 3.8 25.5 1.0 CA C:PRO5 3.9 18.5 1.0 CG A:GLU185 3.9 16.6 1.0 N C:PRO5 4.0 17.0 1.0 HB3 A:ALA188 4.0 15.9 1.0 N C:PRO4 4.1 15.6 1.0 HD2 C:PRO4 4.1 21.4 1.0 O C:HOH104 4.2 23.2 1.0 HB2 C:ASN3 4.2 23.0 1.0 C C:PRO5 4.2 18.1 1.0 HB3 A:GLU185 4.2 17.3 1.0 ND1 A:HIS146 4.2 15.9 1.0 ND1 A:HIS142 4.3 15.1 1.0 CA C:PRO4 4.3 16.5 1.0 CG A:HIS142 4.3 14.0 1.0 CB C:ASN3 4.3 19.2 1.0 CG A:HIS146 4.3 15.1 1.0 HG2 A:GLU185 4.4 20.0 1.0 HG3 A:GLU185 4.4 20.0 1.0 CZ A:PHE178 4.4 21.8 1.0 C C:ASN3 4.4 14.0 1.0 CB A:GLU185 4.5 14.4 1.0 CE2 A:PHE178 4.5 21.2 1.0 HG2 C:PRO4 4.5 22.0 1.0 HB1 A:ALA188 4.5 15.9 1.0 O C:PRO5 4.6 22.4 1.0 CA A:GLU185 4.6 14.7 1.0 CB A:ALA188 4.6 13.2 1.0 CD C:PRO4 4.6 17.8 1.0 HB2 A:ALA188 4.6 15.9 1.0 O C:ASN3 4.7 13.6 1.0 HZ1 A:LYS101 4.7 45.1 1.0 N C:VAL6 4.7 17.2 1.0 H C:VAL6 4.8 20.7 1.0 HA C:PRO4 4.9 19.9 1.0 CA C:ASN3 4.9 16.9 1.0 CG C:PRO4 5.0 18.3 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Ppep-1(W103F/E143A/Y178F) in Complex with Substrate Peptide Ac-Evnppvp-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 Ppep-1(W103F/E143A/Y178F) in Complex with Substrate Peptide Ac-Evnppvp-CONH2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:14.2 occ:0.34 O D:PRO4 1.8 26.2 1.0 OE1 B:GLU185 1.9 29.4 1.0 NE2 B:HIS142 2.1 23.2 1.0 NE2 B:HIS146 2.1 26.8 1.0 CD B:GLU185 2.7 28.3 1.0 OE2 B:GLU185 2.8 29.4 1.0 HA D:PRO5 3.0 43.2 1.0 C D:PRO4 3.0 29.4 1.0 CD2 B:HIS142 3.0 19.3 1.0 CD2 B:HIS146 3.1 23.5 1.0 CE1 B:HIS142 3.1 21.9 1.0 CE1 B:HIS146 3.1 25.5 1.0 HD2 B:HIS142 3.2 23.2 1.0 HD2 B:HIS146 3.2 28.2 1.0 HE1 B:HIS142 3.3 26.3 1.0 HE1 B:HIS146 3.3 30.6 1.0 HB3 D:ASN3 3.6 34.5 1.0 CA D:PRO5 3.6 36.0 1.0 N D:PRO5 3.7 32.7 1.0 HZ B:PHE178 3.8 33.6 1.0 HA B:GLU185 4.0 27.9 1.0 C D:PRO5 4.0 34.0 1.0 HE2 B:PHE178 4.0 29.8 1.0 N D:PRO4 4.1 30.7 1.0 HD2 D:PRO4 4.1 42.8 1.0 CG B:GLU185 4.1 27.1 1.0 O D:HOH102 4.1 34.7 1.0 CA D:PRO4 4.1 29.7 1.0 ND1 B:HIS142 4.2 21.3 1.0 CG B:HIS142 4.2 19.1 1.0 HB3 B:ALA188 4.2 29.2 1.0 CG B:HIS146 4.2 22.9 1.0 ND1 B:HIS146 4.2 25.5 1.0 C D:ASN3 4.3 26.4 1.0 HB2 D:ASN3 4.3 34.5 1.0 HG2 D:PRO4 4.4 44.9 1.0 O D:PRO5 4.4 31.1 1.0 CB D:ASN3 4.4 28.8 1.0 HB3 B:GLU185 4.4 28.3 1.0 N D:VAL6 4.5 32.2 1.0 CD D:PRO4 4.5 35.7 1.0 H D:VAL6 4.5 38.7 1.0 HG3 B:GLU185 4.5 32.5 1.0 CZ B:PHE178 4.6 28.0 1.0 O D:ASN3 4.6 20.4 1.0 CE2 B:PHE178 4.6 24.8 1.0 HG2 B:GLU185 4.6 32.5 1.0 CB B:GLU185 4.6 23.6 1.0 HB1 B:ALA188 4.7 29.2 1.0 CA B:GLU185 4.8 23.2 1.0 HA D:PRO4 4.8 35.6 1.0 CB B:ALA188 4.8 24.3 1.0 CG D:PRO4 4.8 37.3 1.0 HB2 B:ALA188 4.9 29.2 1.0 HD1 B:HIS142 5.0 25.6 1.0 CA D:ASN3 5.0 27.9 1.0 CB D:PRO5 5.0 36.5 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