Zinc in PDB 6r54: Crystal Structure of Ppep-1(E184A)

All present enzymatic activity of Crystal Structure of Ppep-1(E184A):
3.4.24.89;

The structure of Crystal Structure of Ppep-1(E184A), PDB code: 6r54 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)	61.44 / 1.42
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	43.210, 71.940, 118.080, 90.00, 90.00, 90.00
R / Rfree (%)	15.7 / 17.3

The structure of Crystal Structure of Ppep-1(E184A) also contains other interesting chemical elements:

Nickel

(Ni)

1 atom

The binding sites of Zinc atom in the Crystal Structure of Ppep-1(E184A) (pdb code 6r54). 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(E184A), PDB code: 6r54:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of Ppep-1(E184A)


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(E184A) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:13.2 occ:1.00 OE1 A:GLU185 2.1 10.5 1.0 NE2 A:HIS146 2.1 10.3 1.0 O3 A:TRS301 2.1 14.7 1.0 N A:TRS301 2.1 12.6 1.0 NE2 A:HIS142 2.1 11.3 1.0 O2 A:TRS301 2.1 15.0 1.0 HN2 A:TRS301 2.2 15.1 1.0 C A:TRS301 2.8 14.0 1.0 HN1 A:TRS301 2.8 15.1 1.0 C3 A:TRS301 2.9 14.1 1.0 C2 A:TRS301 3.0 15.0 1.0 CD A:GLU185 3.0 12.1 1.0 CD2 A:HIS146 3.0 9.3 1.0 CD2 A:HIS142 3.0 10.4 1.0 CE1 A:HIS146 3.1 10.4 1.0 CE1 A:HIS142 3.1 12.2 1.0 HD2 A:HIS142 3.2 12.6 1.0 HD2 A:HIS146 3.2 11.2 1.0 OE2 A:GLU185 3.2 14.9 1.0 HE1 A:HIS146 3.3 12.6 1.0 HE1 A:HIS142 3.4 14.7 1.0 H31 A:TRS301 3.4 17.0 1.0 H22 A:TRS301 3.6 18.0 1.0 H21 A:TRS301 3.8 18.0 1.0 H32 A:TRS301 3.8 17.0 1.0 HA A:GLU185 4.2 11.4 1.0 O A:HOH547 4.2 18.5 1.0 ND1 A:HIS146 4.2 11.8 1.0 CG A:HIS146 4.2 11.0 1.0 CG A:HIS142 4.2 9.2 1.0 ND1 A:HIS142 4.2 11.2 1.0 OH A:TYR178 4.2 13.9 1.0 C1 A:TRS301 4.2 16.2 1.0 OE1 A:GLU143 4.3 16.5 1.0 HB3 A:ALA188 4.4 14.4 1.0 O A:HOH601 4.4 14.2 1.0 CG A:GLU185 4.4 11.0 1.0 HE2 A:TYR178 4.5 17.9 1.0 H11 A:TRS301 4.6 19.4 1.0 HB3 A:GLU185 4.6 12.8 1.0 HH A:TYR178 4.7 16.8 1.0 HB1 A:ALA188 4.8 14.4 1.0 HG3 A:GLU185 4.8 13.2 1.0 O1 A:TRS301 4.8 16.9 1.0 OE2 A:GLU143 4.8 19.8 1.0 CB A:GLU185 4.9 10.6 1.0 H12 A:TRS301 4.9 19.4 1.0 CB A:ALA188 4.9 12.0 1.0 HB2 A:ALA188 5.0 14.4 1.0 HD1 A:HIS146 5.0 14.2 1.0 CD A:GLU143 5.0 17.4 1.0 CA A:GLU185 5.0 9.5 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Ppep-1(E184A)


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(E184A) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn302 b:13.6 occ:1.00 OE1 B:GLU185 2.1 12.4 1.0 NE2 B:HIS146 2.1 10.2 1.0 NE2 B:HIS142 2.1 10.0 1.0 O3 B:TRS301 2.1 18.2 1.0 N B:TRS301 2.2 16.3 1.0 O2 B:TRS301 2.2 15.9 1.0 HN2 B:TRS301 2.3 19.5 1.0 C B:TRS301 2.9 16.9 1.0 HN1 B:TRS301 2.9 19.5 1.0 C3 B:TRS301 3.0 17.0 1.0 CD B:GLU185 3.0 11.1 1.0 CD2 B:HIS142 3.0 10.1 1.0 CE1 B:HIS146 3.0 10.2 1.0 C2 B:TRS301 3.0 16.1 1.0 CD2 B:HIS146 3.1 10.9 1.0 HD2 B:HIS142 3.1 12.2 1.0 CE1 B:HIS142 3.2 11.5 1.0 HE1 B:HIS146 3.2 12.3 1.0 OE2 B:GLU185 3.2 14.9 1.0 HD2 B:HIS146 3.2 13.1 1.0 H31 B:TRS301 3.4 20.5 1.0 HE1 B:HIS142 3.4 13.9 1.0 H22 B:TRS301 3.7 19.4 1.0 H21 B:TRS301 3.9 19.4 1.0 H32 B:TRS301 3.9 20.5 1.0 HA B:GLU185 4.1 13.6 1.0 ND1 B:HIS146 4.2 12.7 1.0 CG B:HIS142 4.2 9.4 1.0 CG B:HIS146 4.2 10.9 1.0 ND1 B:HIS142 4.2 11.2 1.0 C1 B:TRS301 4.3 20.9 1.0 OH B:TYR178 4.3 16.8 1.0 HB3 B:ALA188 4.3 13.6 1.0 OE1 B:GLU143 4.3 17.2 1.0 CG B:GLU185 4.4 10.7 1.0 O B:HOH584 4.4 20.1 1.0 HE2 B:TYR178 4.5 18.9 1.0 HB3 B:GLU185 4.6 13.5 1.0 H12 B:TRS301 4.6 25.2 1.0 H11 B:TRS301 4.6 25.2 1.0 HH B:TYR178 4.8 20.2 1.0 HG3 B:GLU185 4.8 12.8 1.0 HB1 B:ALA188 4.8 13.6 1.0 CB B:GLU185 4.8 11.3 1.0 CB B:ALA188 4.9 11.3 1.0 CA B:GLU185 4.9 11.3 1.0 OE2 B:GLU143 4.9 21.6 1.0 HD1 B:HIS146 4.9 15.2 1.0 HB2 B:ALA188 5.0 13.6 1.0 HG2 B:GLU185 5.0 12.8 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