Zinc in PDB 6r53: Crystal Structure of Ppep-1(K101R)

All present enzymatic activity of Crystal Structure of Ppep-1(K101R):
3.4.24.89;

The structure of Crystal Structure of Ppep-1(K101R), PDB code: 6r53 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)	45.56 / 1.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	43.150, 71.830, 117.860, 90.00, 90.00, 90.00
R / Rfree (%)	18.3 / 21.8

The binding sites of Zinc atom in the Crystal Structure of Ppep-1(K101R) (pdb code 6r53). 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(K101R), PDB code: 6r53:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of Ppep-1(K101R)


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(K101R) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:15.6 occ:1.00 NE2 A:HIS146 2.1 15.9 1.0 O2 A:TRS302 2.1 20.5 1.0 O3 A:TRS302 2.1 17.9 1.0 OE1 A:GLU185 2.1 13.8 1.0 N A:TRS302 2.1 15.1 1.0 NE2 A:HIS142 2.2 13.2 1.0 HN1 A:TRS302 2.6 18.2 1.0 HN2 A:TRS302 2.7 18.2 1.0 C A:TRS302 2.8 21.4 1.0 HO2 A:TRS302 2.8 24.6 1.0 C3 A:TRS302 2.9 20.1 1.0 C2 A:TRS302 2.9 22.4 1.0 HO3 A:TRS302 2.9 21.5 1.0 CD2 A:HIS142 3.0 12.5 1.0 CD A:GLU185 3.0 16.2 1.0 CE1 A:HIS146 3.0 16.8 1.0 CD2 A:HIS146 3.1 17.4 1.0 HD2 A:HIS142 3.1 15.1 1.0 HE1 A:HIS146 3.2 20.2 1.0 HD2 A:HIS146 3.2 21.0 1.0 OE2 A:GLU185 3.2 16.4 1.0 CE1 A:HIS142 3.3 13.9 1.0 H31 A:TRS302 3.3 24.1 1.0 HE1 A:HIS142 3.6 16.7 1.0 H22 A:TRS302 3.6 26.9 1.0 H21 A:TRS302 3.7 26.9 1.0 H32 A:TRS302 3.8 24.1 1.0 HA A:GLU185 4.1 18.0 1.0 ND1 A:HIS146 4.2 16.1 1.0 CG A:HIS146 4.2 16.6 1.0 C1 A:TRS302 4.2 28.4 1.0 CG A:HIS142 4.2 12.0 1.0 OH A:TYR178 4.3 23.3 1.0 O A:HOH475 4.3 15.2 1.0 OE2 A:GLU143 4.3 20.8 1.0 HB3 A:ALA188 4.3 17.5 1.0 ND1 A:HIS142 4.3 13.4 1.0 O A:HOH558 4.4 14.0 1.0 CG A:GLU185 4.5 12.6 1.0 HE2 A:TYR178 4.5 25.1 1.0 H11 A:TRS302 4.6 34.1 1.0 H12 A:TRS302 4.6 34.1 1.0 HB3 A:GLU185 4.6 13.4 1.0 HH A:TYR178 4.7 28.0 1.0 HB1 A:ALA188 4.8 17.5 1.0 HG3 A:GLU185 4.8 15.1 1.0 CB A:ALA188 4.9 14.6 1.0 CB A:GLU185 4.9 11.3 1.0 HD1 A:HIS146 4.9 19.4 1.0 HB2 A:ALA188 4.9 17.5 1.0 CA A:GLU185 5.0 15.0 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Ppep-1(K101R)


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(K101R) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:19.4 occ:1.00 NE2 B:HIS146 2.1 16.6 1.0 OE2 B:GLU185 2.1 15.1 1.0 NE2 B:HIS142 2.2 12.5 1.0 O2 B:TRS302 2.2 21.4 1.0 O3 B:TRS302 2.2 19.9 1.0 N B:TRS302 2.2 17.8 1.0 HN1 B:TRS302 2.7 21.4 1.0 HN2 B:TRS302 2.7 21.4 1.0 C B:TRS302 2.8 21.0 1.0 HO2 B:TRS302 3.0 25.7 1.0 C3 B:TRS302 3.0 19.8 1.0 C2 B:TRS302 3.0 23.4 1.0 CD B:GLU185 3.0 14.3 1.0 HO3 B:TRS302 3.0 23.9 1.0 CD2 B:HIS142 3.0 12.4 1.0 CD2 B:HIS146 3.1 17.7 1.0 HD2 B:HIS142 3.1 14.9 1.0 CE1 B:HIS146 3.1 16.5 1.0 OE1 B:GLU185 3.2 13.8 1.0 HD2 B:HIS146 3.2 21.3 1.0 CE1 B:HIS142 3.2 13.2 1.0 HE1 B:HIS146 3.3 19.9 1.0 H31 B:TRS302 3.4 23.8 1.0 HE1 B:HIS142 3.5 15.9 1.0 H22 B:TRS302 3.6 28.1 1.0 H21 B:TRS302 3.8 28.1 1.0 H32 B:TRS302 3.9 23.8 1.0 HA B:GLU185 4.1 15.4 1.0 OE2 B:GLU143 4.2 17.6 1.0 ND1 B:HIS146 4.2 16.9 1.0 CG B:HIS142 4.2 11.0 1.0 CG B:HIS146 4.2 17.1 1.0 OH B:TYR178 4.2 15.7 1.0 O B:HOH546 4.2 20.5 1.0 C1 B:TRS302 4.3 26.8 1.0 ND1 B:HIS142 4.3 11.0 1.0 HB3 B:ALA188 4.3 13.1 1.0 O B:HOH568 4.3 11.4 1.0 CG B:GLU185 4.4 11.4 1.0 HE2 B:TYR178 4.5 20.2 1.0 HB3 B:GLU185 4.6 12.7 1.0 H11 B:TRS302 4.7 32.2 1.0 HH B:TYR178 4.7 18.9 1.0 HB1 B:ALA188 4.8 13.1 1.0 O B:HOH583 4.8 43.2 1.0 HG3 B:GLU185 4.8 13.6 1.0 OE1 B:GLU143 4.8 19.5 1.0 O1 B:TRS302 4.8 24.4 1.0 CB B:GLU185 4.9 10.7 1.0 CB B:ALA188 4.9 10.9 1.0 CD B:GLU143 4.9 20.9 1.0 HB2 B:ALA188 4.9 13.1 1.0 CA B:GLU185 5.0 12.8 1.0 H12 B:TRS302 5.0 32.2 1.0 HD1 B:HIS146 5.0 20.3 1.0 HG2 B:GLU185 5.0 13.6 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