Zinc in PDB 6r4x: Crystal Structure of Ppep-1(E143A/Y178F) in Complex with Substrate Peptide Ac-Evnpavp-CONH2

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

The structure of Crystal Structure of Ppep-1(E143A/Y178F) in Complex with Substrate Peptide Ac-Evnpavp-CONH2, PDB code: 6r4x 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)	60.21 / 1.83
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	37.237, 42.933, 121.227, 90.00, 96.64, 90.00
R / Rfree (%)	17.7 / 21.2

The binding sites of Zinc atom in the Crystal Structure of Ppep-1(E143A/Y178F) in Complex with Substrate Peptide Ac-Evnpavp-CONH2 (pdb code 6r4x). 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(E143A/Y178F) in Complex with Substrate Peptide Ac-Evnpavp-CONH2, PDB code: 6r4x:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of Ppep-1(E143A/Y178F) in Complex with 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 Ppep-1(E143A/Y178F) in Complex with Substrate Peptide Ac-Evnpavp-CONH2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:11.1 occ:0.09 OE1 A:GLU185 2.0 22.8 1.0 NE2 A:HIS142 2.1 21.6 1.0 NE2 A:HIS146 2.2 22.5 1.0 O D:PRO122 2.4 20.4 1.0 CD A:GLU185 2.7 21.2 1.0 OE2 A:GLU185 2.8 22.7 1.0 CE1 A:HIS142 2.9 21.5 1.0 CD2 A:HIS146 2.9 21.7 1.0 HD2 A:HIS146 3.0 26.0 1.0 HE1 A:HIS142 3.0 25.8 1.0 CD2 A:HIS142 3.1 20.8 1.0 HB3 D:ASN121 3.2 27.3 1.0 CE1 A:HIS146 3.3 22.4 1.0 HD2 A:HIS142 3.4 24.9 1.0 HZ A:PHE178 3.5 25.6 1.0 C D:PRO122 3.6 20.4 1.0 HE1 A:HIS146 3.6 26.9 1.0 HE2 A:PHE178 3.7 25.0 1.0 HB2 D:ASN121 4.0 27.3 1.0 CB D:ASN121 4.0 22.8 1.0 HA A:GLU185 4.0 18.2 1.0 HA D:ALA123 4.0 26.1 1.0 ND1 A:HIS142 4.0 21.4 1.0 CG A:HIS146 4.1 21.1 1.0 CG A:GLU185 4.2 18.2 1.0 N D:PRO122 4.2 20.9 1.0 CZ A:PHE178 4.2 21.4 1.0 CG A:HIS142 4.2 20.4 1.0 HB3 A:ALA188 4.2 18.4 1.0 C D:ASN121 4.3 21.3 1.0 CE2 A:PHE178 4.3 20.9 1.0 ND1 A:HIS146 4.3 22.1 1.0 CD D:PRO122 4.4 21.1 1.0 HB3 A:GLU185 4.5 19.4 1.0 N D:ALA123 4.5 20.8 1.0 CA D:PRO122 4.5 20.7 1.0 HG3 A:GLU185 4.5 21.8 1.0 O D:ASN121 4.5 21.8 1.0 CA D:ALA123 4.6 21.8 1.0 HZ3 A:LYS101 4.6 28.3 1.0 C D:ALA123 4.7 21.7 1.0 HG2 A:GLU185 4.7 21.8 1.0 CB A:GLU185 4.7 16.2 1.0 HB1 A:ALA188 4.7 18.4 1.0 HG22 D:VAL124 4.7 27.3 1.0 CA D:ASN121 4.7 22.0 1.0 HD1 A:HIS142 4.8 25.6 1.0 CB A:ALA188 4.8 15.3 1.0 HB2 A:ALA188 4.8 18.4 1.0 CA A:GLU185 4.8 15.2 1.0 HG23 D:VAL124 4.9 27.3 1.0 N D:VAL124 4.9 20.5 1.0 H D:VAL124 5.0 24.6 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Ppep-1(E143A/Y178F) in Complex with 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 Ppep-1(E143A/Y178F) in Complex with Substrate Peptide Ac-Evnpavp-CONH2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:18.7 occ:0.17 OE1 B:GLU185 2.0 26.4 1.0 NE2 B:HIS142 2.1 23.9 1.0 NE2 B:HIS146 2.4 30.0 1.0 O C:PRO122 2.4 25.7 1.0 CD B:GLU185 2.8 23.3 1.0 OE2 B:GLU185 2.9 25.5 1.0 CD2 B:HIS142 3.0 22.1 1.0 HD2 B:HIS146 3.0 35.7 1.0 CD2 B:HIS146 3.0 29.8 1.0 HD2 B:HIS142 3.1 26.6 1.0 CE1 B:HIS142 3.2 23.6 1.0 HE1 B:HIS142 3.4 28.3 1.0 HB3 C:ASN121 3.4 28.3 1.0 CE1 B:HIS146 3.5 31.0 1.0 C C:PRO122 3.6 24.1 1.0 HE2 B:PHE178 3.6 23.9 1.0 HZ B:PHE178 3.8 25.5 1.0 HE1 B:HIS146 3.8 37.2 1.0 HA C:ALA123 3.8 23.0 1.0 O C:HOH202 4.0 30.6 1.0 HA B:GLU185 4.1 19.1 1.0 CG B:HIS142 4.2 21.3 1.0 CG B:GLU185 4.2 19.9 1.0 HB2 C:ASN121 4.2 28.3 1.0 ND1 B:HIS142 4.2 22.9 1.0 CB C:ASN121 4.2 23.6 1.0 CG B:HIS146 4.3 28.2 1.0 HG22 C:VAL124 4.3 24.2 1.0 N C:PRO122 4.3 22.3 1.0 HB3 B:ALA188 4.3 18.6 1.0 CE2 B:PHE178 4.3 20.0 1.0 HG23 C:VAL124 4.4 24.2 1.0 CA C:ALA123 4.4 19.2 1.0 CZ B:PHE178 4.4 21.2 1.0 C C:ASN121 4.4 21.8 1.0 N C:ALA123 4.4 21.2 1.0 HB3 B:GLU185 4.5 20.2 1.0 ND1 B:HIS146 4.5 30.3 1.0 C C:ALA123 4.5 19.0 1.0 HG3 B:GLU185 4.5 23.9 1.0 CD C:PRO122 4.6 24.1 1.0 CA C:PRO122 4.6 23.7 1.0 N C:VAL124 4.6 19.1 1.0 H C:VAL124 4.6 22.9 1.0 O C:ASN121 4.7 22.1 1.0 CB B:GLU185 4.7 16.9 1.0 HZ3 B:LYS101 4.7 27.6 1.0 HG2 B:GLU185 4.8 23.9 1.0 HB1 B:ALA188 4.8 18.6 1.0 CG2 C:VAL124 4.8 20.2 1.0 CA B:GLU185 4.9 15.9 1.0 HA C:VAL124 4.9 24.2 1.0 O C:ALA123 4.9 19.2 1.0 CB B:ALA188 4.9 15.5 1.0 CA C:ASN121 5.0 23.0 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