Zinc in PDB 6r4w: Crystal Structure of Apo Ppep-1(E143A/Y178F) in Complex with Substrate Peptide Ac-Evnapvp-CONH2

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

The structure of Crystal Structure of Apo Ppep-1(E143A/Y178F) in Complex with Substrate Peptide Ac-Evnapvp-CONH2, PDB code: 6r4w 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)	40.87 / 1.39
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	37.364, 42.923, 123.354, 90.00, 96.28, 90.00
R / Rfree (%)	16.7 / 18.8

The binding sites of Zinc atom in the Crystal Structure of Apo Ppep-1(E143A/Y178F) in Complex with Substrate Peptide Ac-Evnapvp-CONH2 (pdb code 6r4w). 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 Apo Ppep-1(E143A/Y178F) in Complex with Substrate Peptide Ac-Evnapvp-CONH2, PDB code: 6r4w:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of Apo 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 Apo 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:12.7 occ:0.07 OE1 A:GLU185 1.9 15.2 1.0 NE2 A:HIS142 2.0 17.9 1.0 O D:ALA122 2.4 14.9 1.0 NE2 A:HIS146 2.4 15.7 1.0 CD A:GLU185 2.7 17.0 1.0 OE2 A:GLU185 3.0 23.8 1.0 CD2 A:HIS142 3.0 12.0 1.0 CE1 A:HIS142 3.0 14.1 1.0 CD2 A:HIS146 3.1 14.3 1.0 HD2 A:HIS146 3.1 17.1 1.0 HD2 A:HIS142 3.2 14.3 1.0 HB3 D:ASN121 3.2 19.1 1.0 HE1 A:HIS142 3.2 16.8 1.0 O A:HOH417 3.3 29.5 1.0 HA D:PRO123 3.3 16.3 1.0 HZ A:PHE178 3.4 20.2 1.0 C D:ALA122 3.4 14.5 1.0 CE1 A:HIS146 3.5 15.5 1.0 HE2 A:PHE178 3.7 16.3 1.0 HE1 A:HIS146 3.7 18.5 1.0 HA A:GLU185 4.0 14.6 1.0 CB D:ASN121 4.0 16.0 1.0 HB2 D:ASN121 4.0 19.1 1.0 CA D:PRO123 4.0 13.6 1.0 O D:HOH206 4.1 18.4 1.0 ND1 A:HIS142 4.1 19.3 1.0 CG A:HIS142 4.1 14.0 1.0 HB3 A:ALA188 4.1 13.2 1.0 CG A:GLU185 4.1 13.2 1.0 CZ A:PHE178 4.2 16.9 1.0 N D:PRO123 4.2 13.8 1.0 N D:ALA122 4.3 15.4 1.0 CE2 A:PHE178 4.3 13.6 1.0 CG A:HIS146 4.3 10.8 1.0 C D:ASN121 4.3 15.2 1.0 HB3 A:GLU185 4.4 14.6 1.0 ND1 A:HIS146 4.4 12.7 1.0 C D:PRO123 4.5 14.1 1.0 HG3 A:GLU185 4.5 15.8 1.0 H D:ALA122 4.5 18.4 1.0 CA D:ALA122 4.5 14.8 1.0 O D:ASN121 4.5 14.6 1.0 HB1 A:ALA188 4.6 13.2 1.0 HZ3 A:LYS101 4.7 25.0 1.0 CB A:GLU185 4.7 12.2 1.0 CB A:ALA188 4.7 11.1 1.0 CA D:ASN121 4.7 16.0 1.0 HB2 A:ALA188 4.8 13.2 1.0 HG2 A:GLU185 4.8 15.8 1.0 CA A:GLU185 4.8 12.2 1.0 H D:VAL124 4.9 16.7 1.0 N D:VAL124 4.9 14.0 1.0 HD1 A:HIS142 4.9 23.1 1.0 O D:PRO123 4.9 14.6 1.0 HA D:ASN121 5.0 19.1 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Apo 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 Apo 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:16.5 occ:0.17 OE1 B:GLU185 1.9 18.3 1.0 NE2 B:HIS142 2.0 20.6 1.0 NE2 B:HIS146 2.2 21.5 1.0 O C:ALA4 2.4 23.3 1.0 CD B:GLU185 2.8 22.7 1.0 CE1 B:HIS142 3.0 13.2 1.0 CD2 B:HIS142 3.0 15.1 1.0 OE2 B:GLU185 3.0 32.1 1.0 HA C:PRO5 3.1 30.2 1.0 CD2 B:HIS146 3.1 22.3 1.0 HD2 B:HIS142 3.1 18.1 1.0 HE1 B:HIS142 3.2 15.7 1.0 HD2 B:HIS146 3.2 26.7 1.0 CE1 B:HIS146 3.2 19.2 1.0 O B:HOH403 3.4 36.4 1.0 HE1 B:HIS146 3.5 22.9 1.0 HB3 C:ASN3 3.5 28.8 1.0 C C:ALA4 3.5 23.6 1.0 CA C:PRO5 3.8 25.2 1.0 HE2 B:PHE178 3.9 21.7 1.0 HZ B:PHE178 3.9 20.1 1.0 HA B:GLU185 4.0 18.4 1.0 O C:HOH103 4.0 22.9 1.0 ND1 B:HIS142 4.1 14.9 1.0 CG B:HIS142 4.1 13.3 1.0 HB3 B:ALA188 4.1 15.2 1.0 N C:PRO5 4.1 22.2 1.0 CG B:GLU185 4.2 15.2 1.0 HB2 C:ASN3 4.2 28.8 1.0 C C:PRO5 4.2 17.8 1.0 CG B:HIS146 4.3 14.6 1.0 CB C:ASN3 4.3 24.1 1.0 ND1 B:HIS146 4.3 20.3 1.0 HB3 B:GLU185 4.4 18.4 1.0 H C:VAL6 4.5 22.6 1.0 CE2 B:PHE178 4.5 18.1 1.0 CZ B:PHE178 4.5 16.8 1.0 N C:ALA4 4.6 21.9 1.0 HG3 B:GLU185 4.6 18.2 1.0 HB1 B:ALA188 4.6 15.2 1.0 N C:VAL6 4.6 18.9 1.0 C C:ASN3 4.6 22.7 1.0 CB B:GLU185 4.7 15.4 1.0 CA C:ALA4 4.7 20.7 1.0 CB B:ALA188 4.7 12.7 1.0 O C:PRO5 4.8 19.6 1.0 HG2 B:GLU185 4.8 18.2 1.0 O C:ASN3 4.8 22.5 1.0 CA B:GLU185 4.8 15.4 1.0 HB2 B:ALA188 4.8 15.2 1.0 H C:ALA4 4.8 26.2 1.0 HD1 B:HIS142 4.8 17.8 1.0 HG23 C:VAL6 4.9 24.1 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