Zinc in PDB 6r5a: Crystal Structure of Ppep-1(W103F)

All present enzymatic activity of Crystal Structure of Ppep-1(W103F):
3.4.24.89;

The structure of Crystal Structure of Ppep-1(W103F), PDB code: 6r5a 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)	44.12 / 1.48
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	42.579, 66.161, 118.399, 90.00, 90.00, 90.00
R / Rfree (%)	16.5 / 19.9

The binding sites of Zinc atom in the Crystal Structure of Ppep-1(W103F) (pdb code 6r5a). 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), PDB code: 6r5a:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of Ppep-1(W103F)


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) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:14.9 occ:1.00 NE2 A:HIS146 2.1 12.8 1.0 NE2 A:HIS142 2.1 11.2 1.0 OE1 A:GLU185 2.1 12.6 1.0 N A:TRS302 2.1 13.6 1.0 O2 A:TRS302 2.1 15.6 1.0 O3 A:TRS302 2.2 16.4 1.0 HO3 A:TRS302 2.5 19.7 1.0 HN2 A:TRS302 2.6 16.4 1.0 HN1 A:TRS302 2.6 16.4 1.0 C A:TRS302 2.9 15.6 1.0 HO2 A:TRS302 2.9 18.7 1.0 CD A:GLU185 3.0 13.2 1.0 C2 A:TRS302 3.0 17.4 1.0 CD2 A:HIS146 3.0 10.1 1.0 CD2 A:HIS142 3.0 13.2 1.0 C3 A:TRS302 3.1 17.7 1.0 CE1 A:HIS146 3.1 12.7 1.0 CE1 A:HIS142 3.1 10.4 1.0 HD2 A:HIS146 3.1 12.1 1.0 OE2 A:GLU185 3.1 13.9 1.0 HD2 A:HIS142 3.2 15.8 1.0 HE1 A:HIS146 3.3 15.2 1.0 HE1 A:HIS142 3.3 12.5 1.0 H31 A:TRS302 3.6 21.3 1.0 H22 A:TRS302 3.7 20.8 1.0 H21 A:TRS302 3.8 20.8 1.0 H32 A:TRS302 4.0 21.3 1.0 OH A:TYR178 4.1 15.8 1.0 O A:HOH490 4.1 17.8 1.0 HA A:GLU185 4.1 11.5 1.0 CG A:HIS146 4.2 11.6 1.0 ND1 A:HIS146 4.2 12.2 1.0 CG A:HIS142 4.2 11.7 1.0 ND1 A:HIS142 4.2 12.0 1.0 OE2 A:GLU143 4.3 20.3 1.0 HE2 A:TYR178 4.3 16.1 1.0 C1 A:TRS302 4.3 16.6 1.0 O A:HOH547 4.3 14.3 1.0 HB3 A:ALA188 4.3 13.6 1.0 CG A:GLU185 4.4 11.7 1.0 HH A:TYR178 4.6 18.9 1.0 HB3 A:GLU185 4.6 12.2 1.0 H11 A:TRS302 4.6 19.9 1.0 OE1 A:GLU143 4.7 18.7 1.0 HG3 A:GLU185 4.8 14.1 1.0 HB1 A:ALA188 4.8 13.6 1.0 O1 A:TRS302 4.9 16.1 1.0 CB A:GLU185 4.9 10.1 1.0 O A:HOH474 4.9 17.8 1.0 CD A:GLU143 4.9 17.7 1.0 CB A:ALA188 4.9 11.3 1.0 CA A:GLU185 4.9 9.6 1.0 HB2 A:ALA188 5.0 13.6 1.0 HG2 A:GLU185 5.0 14.1 1.0 HD1 A:HIS146 5.0 14.6 1.0 CE2 A:TYR178 5.0 13.4 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Ppep-1(W103F)


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) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:13.3 occ:1.00 NE2 B:HIS142 2.1 8.7 1.0 NE2 B:HIS146 2.1 11.3 1.0 O3 B:TRS302 2.1 14.8 1.0 OE1 B:GLU185 2.1 10.4 1.0 O2 B:TRS302 2.1 13.5 1.0 N B:TRS302 2.2 13.7 1.0 HO3 B:TRS302 2.5 17.7 1.0 HN1 B:TRS302 2.6 16.5 1.0 HN2 B:TRS302 2.7 16.5 1.0 C B:TRS302 2.9 14.7 1.0 HO2 B:TRS302 2.9 16.2 1.0 C3 B:TRS302 3.0 15.7 1.0 C2 B:TRS302 3.0 14.5 1.0 CD2 B:HIS142 3.0 9.4 1.0 CD2 B:HIS146 3.1 11.7 1.0 CD B:GLU185 3.1 11.0 1.0 CE1 B:HIS142 3.1 10.5 1.0 CE1 B:HIS146 3.1 10.7 1.0 HD2 B:HIS142 3.2 11.2 1.0 HD2 B:HIS146 3.2 14.0 1.0 HE1 B:HIS142 3.3 12.6 1.0 OE2 B:GLU185 3.3 11.0 1.0 HE1 B:HIS146 3.3 12.9 1.0 H31 B:TRS302 3.5 18.9 1.0 H21 B:TRS302 3.7 17.4 1.0 H22 B:TRS302 3.8 17.4 1.0 H32 B:TRS302 3.9 18.9 1.0 OH B:TYR178 4.1 14.7 1.0 HA B:GLU185 4.1 11.7 1.0 ND1 B:HIS142 4.2 10.9 1.0 CG B:HIS142 4.2 9.6 1.0 O B:HOH518 4.2 18.2 1.0 ND1 B:HIS146 4.2 11.5 1.0 OE1 B:GLU143 4.2 13.5 1.0 CG B:HIS146 4.2 11.8 1.0 HE2 B:TYR178 4.3 16.8 1.0 C1 B:TRS302 4.3 15.4 1.0 O B:HOH564 4.3 13.5 1.0 HB3 B:ALA188 4.3 12.5 1.0 CG B:GLU185 4.5 10.5 1.0 HB3 B:GLU185 4.6 11.8 1.0 HH B:TYR178 4.6 17.6 1.0 O B:HOH538 4.7 37.0 1.0 H11 B:TRS302 4.7 18.4 1.0 OE2 B:GLU143 4.8 17.5 1.0 HG3 B:GLU185 4.8 12.6 1.0 HB1 B:ALA188 4.8 12.5 1.0 O1 B:TRS302 4.9 15.3 1.0 CB B:GLU185 4.9 9.8 1.0 CD B:GLU143 4.9 14.7 1.0 CB B:ALA188 4.9 10.4 1.0 HD1 B:HIS142 4.9 13.1 1.0 CA B:GLU185 5.0 9.8 1.0 HD1 B:HIS146 5.0 13.8 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