Zinc in PDB 6r59: Crystal Structure of Ppep-1(E143A/Y178F) in Complex with Substrate Peptide Ac-Evappvp-NH2

All present enzymatic activity of Crystal Structure of Ppep-1(E143A/Y178F) in Complex with Substrate Peptide Ac-Evappvp-NH2:
3.4.24.89;

The structure of Crystal Structure of Ppep-1(E143A/Y178F) in Complex with Substrate Peptide Ac-Evappvp-NH2, PDB code: 6r59 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)	40.49 / 1.65
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	37.110, 42.950, 122.240, 90.00, 96.60, 90.00
R / Rfree (%)	19.1 / 22

The binding sites of Zinc atom in the Crystal Structure of Ppep-1(E143A/Y178F) in Complex with Substrate Peptide Ac-Evappvp-NH2 (pdb code 6r59). 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-Evappvp-NH2, PDB code: 6r59:
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-Evappvp-NH2


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-Evappvp-NH2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:16.4 occ:0.17 OE1 A:GLU185 1.9 30.2 1.0 NE2 A:HIS142 2.0 27.5 1.0 NE2 A:HIS146 2.1 29.3 0.4 O E:PRO122 2.2 27.3 1.0 CD A:GLU185 2.7 28.3 1.0 CD2 A:HIS142 2.7 24.1 1.0 HD2 A:HIS142 2.8 28.9 1.0 OE2 A:GLU185 2.9 31.7 1.0 CD2 A:HIS146 2.9 27.7 0.4 HD2 A:HIS146 3.0 33.2 0.4 CE1 A:HIS142 3.1 25.6 1.0 CE1 A:HIS146 3.2 29.0 0.4 HA E:PRO123 3.3 33.8 1.0 C E:PRO122 3.3 27.7 1.0 HE1 A:HIS142 3.5 30.8 1.0 HB1 E:ALA121 3.5 39.5 1.0 HE1 A:HIS146 3.5 34.8 0.4 HZ A:PHE178 3.6 31.1 1.0 HE2 A:PHE178 3.7 29.3 1.0 HA A:GLU185 4.0 27.6 1.0 CG A:HIS142 4.0 23.5 1.0 CA E:PRO123 4.0 28.2 1.0 HB3 A:ALA188 4.1 24.6 1.0 N E:PRO123 4.1 28.1 1.0 CG A:HIS146 4.1 28.0 0.4 ND1 A:HIS142 4.1 25.5 1.0 HB3 E:ALA121 4.1 39.5 1.0 CG A:GLU185 4.2 25.3 1.0 ND1 A:HIS146 4.2 29.5 0.4 HD2 E:PRO122 4.2 32.4 1.0 CB E:ALA121 4.2 32.9 1.0 N E:PRO122 4.2 27.1 1.0 CZ A:PHE178 4.3 25.9 1.0 C E:PRO123 4.3 28.2 1.0 CE2 A:PHE178 4.3 24.4 1.0 CA E:PRO122 4.4 27.6 1.0 O E:HOH203 4.4 31.9 1.0 HB3 A:GLU185 4.4 29.3 1.0 C E:ALA121 4.5 26.9 1.0 HG3 A:GLU185 4.5 30.4 1.0 HB2 A:HIS146 4.6 32.0 0.6 HB1 A:ALA188 4.6 24.6 1.0 HZ1 A:LYS101 4.7 43.0 1.0 CB A:GLU185 4.7 24.4 1.0 CB A:ALA188 4.7 20.5 1.0 O E:ALA121 4.7 27.0 1.0 CD E:PRO122 4.7 27.0 1.0 O E:PRO123 4.7 28.2 1.0 HG2 A:GLU185 4.7 30.4 1.0 N E:VAL124 4.8 28.2 1.0 CA A:GLU185 4.8 23.0 1.0 H E:VAL124 4.8 33.9 1.0 HG2 E:PRO122 4.8 33.0 1.0 HB2 A:ALA188 4.8 24.6 1.0 HD1 A:HIS142 4.9 30.6 1.0 HB2 E:ALA121 5.0 39.5 1.0 HA E:PRO122 5.0 33.2 1.0 HD1 A:HIS146 5.0 35.4 0.4

Zinc binding site 2 out of 2 in the Crystal Structure of Ppep-1(E143A/Y178F) in Complex with Substrate Peptide Ac-Evappvp-NH2


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-Evappvp-NH2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:20.7 occ:0.21 OE1 B:GLU185 2.2 40.4 1.0 NE2 B:HIS142 2.2 29.4 1.0 NE2 B:HIS146 2.2 35.8 0.4 O C:PRO122 2.4 24.4 1.0 HD2 B:HIS146 2.7 36.8 0.4 CD2 B:HIS146 2.7 30.7 0.4 CD B:GLU185 2.9 38.2 1.0 OE2 B:GLU185 2.9 39.4 1.0 CD2 B:HIS142 2.9 27.9 1.0 HD2 B:HIS142 2.9 33.5 1.0 CE1 B:HIS142 3.3 30.4 1.0 CE1 B:HIS146 3.3 33.5 0.4 O C:HOH202 3.4 32.0 1.0 HA C:PRO123 3.5 34.7 1.0 C C:PRO122 3.6 24.8 1.0 HB1 C:ALA121 3.6 35.1 1.0 HE1 B:HIS142 3.6 36.4 1.0 HE1 B:HIS146 3.7 40.1 0.4 HB3 C:ALA121 3.9 35.1 1.0 CG B:HIS146 3.9 30.5 0.4 HE2 B:PHE178 4.0 40.0 1.0 O C:HOH204 4.1 38.0 1.0 HA B:GLU185 4.1 42.0 1.0 HZ B:PHE178 4.1 43.0 1.0 CG B:HIS142 4.2 27.7 1.0 CA C:PRO123 4.2 28.9 1.0 ND1 B:HIS146 4.2 33.1 0.4 CB C:ALA121 4.2 29.3 1.0 HB3 B:ALA188 4.2 38.5 1.0 HD2 C:PRO122 4.3 34.5 1.0 ND1 B:HIS142 4.3 28.2 1.0 N C:PRO123 4.3 28.4 1.0 CG B:GLU185 4.3 38.2 1.0 HB2 B:HIS146 4.4 34.4 0.6 N C:PRO122 4.4 24.5 1.0 C C:PRO123 4.5 24.7 1.0 C C:ALA121 4.5 23.5 1.0 CA C:PRO122 4.6 22.7 1.0 HB1 B:ALA188 4.6 38.5 1.0 CE2 B:PHE178 4.7 33.3 1.0 HB3 B:GLU185 4.7 43.1 1.0 H C:VAL124 4.7 27.9 1.0 HG3 B:GLU185 4.7 45.9 1.0 CZ B:PHE178 4.7 35.8 1.0 O C:ALA121 4.7 21.2 1.0 N C:VAL124 4.8 23.2 1.0 CB B:ALA188 4.8 32.1 1.0 CD C:PRO122 4.8 28.8 1.0 HB2 B:ALA188 4.9 38.5 1.0 HG2 B:GLU185 4.9 45.9 1.0 CB B:GLU185 4.9 35.9 1.0 HZ1 B:LYS101 4.9 64.5 1.0 HG2 C:PRO122 4.9 33.2 1.0 CA B:GLU185 4.9 35.0 1.0 HB2 C:ALA121 4.9 35.1 1.0 O C:PRO123 4.9 23.1 1.0 HD1 B:HIS146 5.0 39.7 0.4

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