Zinc in PDB 6r52: Crystal Structure of Ppep-1(K101A)

All present enzymatic activity of Crystal Structure of Ppep-1(K101A):
3.4.24.89;

The structure of Crystal Structure of Ppep-1(K101A), PDB code: 6r52 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)	44.83 / 2.02
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	42.920, 70.940, 115.670, 90.00, 90.00, 90.00
R / Rfree (%)	17.7 / 20.6

The binding sites of Zinc atom in the Crystal Structure of Ppep-1(K101A) (pdb code 6r52). 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(K101A), PDB code: 6r52:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of Ppep-1(K101A)


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(K101A) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:19.0 occ:1.00 O3 A:TRS301 2.0 27.9 1.0 OE1 A:GLU185 2.1 21.2 1.0 N A:TRS301 2.2 27.8 1.0 NE2 A:HIS146 2.2 14.1 1.0 NE2 A:HIS142 2.2 19.4 1.0 O2 A:TRS301 2.3 22.2 1.0 HN1 A:TRS301 2.6 33.3 1.0 HN2 A:TRS301 2.7 33.3 1.0 C A:TRS301 2.7 27.7 1.0 HO3 A:TRS301 2.8 33.5 1.0 C3 A:TRS301 2.8 27.2 1.0 CD A:GLU185 2.9 18.3 1.0 CD2 A:HIS146 3.0 14.9 1.0 CD2 A:HIS142 3.0 18.3 1.0 C2 A:TRS301 3.0 25.7 1.0 HD2 A:HIS146 3.1 17.9 1.0 HD2 A:HIS142 3.1 22.0 1.0 OE2 A:GLU185 3.1 17.1 1.0 HO2 A:TRS301 3.2 26.6 1.0 CE1 A:HIS146 3.3 15.8 1.0 CE1 A:HIS142 3.3 19.1 1.0 H31 A:TRS301 3.3 32.6 1.0 HE1 A:HIS146 3.6 18.9 1.0 HE1 A:HIS142 3.6 22.9 1.0 H22 A:TRS301 3.7 30.9 1.0 H32 A:TRS301 3.7 32.6 1.0 H21 A:TRS301 3.8 30.9 1.0 O A:HOH447 4.0 17.9 1.0 HA A:GLU185 4.1 16.2 1.0 C1 A:TRS301 4.2 29.8 1.0 OH A:TYR178 4.2 24.9 1.0 CG A:HIS146 4.2 14.8 1.0 CG A:HIS142 4.2 17.5 1.0 OE2 A:GLU143 4.3 23.2 1.0 ND1 A:HIS146 4.3 15.1 1.0 O A:HOH504 4.3 24.6 1.0 ND1 A:HIS142 4.3 18.2 1.0 CG A:GLU185 4.4 17.4 1.0 HB3 A:ALA188 4.4 16.7 1.0 HB3 A:GLU185 4.6 16.5 1.0 HE2 A:TYR178 4.6 30.8 1.0 HH A:TYR178 4.6 29.9 1.0 H11 A:TRS301 4.6 35.7 1.0 O1 A:TRS301 4.7 31.4 1.0 HG3 A:GLU185 4.7 20.9 1.0 HB1 A:ALA188 4.8 16.7 1.0 CB A:GLU185 4.8 13.8 1.0 OE1 A:GLU143 4.9 23.1 1.0 H12 A:TRS301 4.9 35.7 1.0 HB2 A:ALA188 4.9 16.7 1.0 CA A:GLU185 4.9 13.5 1.0 CB A:ALA188 4.9 13.9 1.0 HG2 A:GLU185 4.9 20.9 1.0 CD A:GLU143 5.0 21.2 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Ppep-1(K101A)


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(K101A) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn302 b:16.9 occ:1.00 O3 B:TRS301 2.1 16.0 1.0 NE2 B:HIS142 2.1 18.9 1.0 NE2 B:HIS146 2.1 19.3 1.0 OE2 B:GLU185 2.1 17.2 1.0 O2 B:TRS301 2.2 18.4 1.0 N B:TRS301 2.2 14.7 1.0 HN2 B:TRS301 2.6 17.6 1.0 HN1 B:TRS301 2.8 17.6 1.0 C B:TRS301 2.8 14.6 1.0 HO3 B:TRS301 2.9 19.2 1.0 C3 B:TRS301 2.9 12.0 1.0 HO2 B:TRS301 3.0 22.1 1.0 C2 B:TRS301 3.0 16.8 1.0 CD B:GLU185 3.0 14.8 1.0 CD2 B:HIS142 3.0 15.1 1.0 CD2 B:HIS146 3.1 17.1 1.0 CE1 B:HIS146 3.2 18.4 1.0 CE1 B:HIS142 3.2 15.6 1.0 HD2 B:HIS142 3.2 18.2 1.0 HD2 B:HIS146 3.2 20.5 1.0 OE1 B:GLU185 3.2 17.9 1.0 HE1 B:HIS146 3.4 22.0 1.0 HE1 B:HIS142 3.4 18.7 1.0 H31 B:TRS301 3.5 14.4 1.0 H22 B:TRS301 3.7 20.1 1.0 H21 B:TRS301 3.8 20.1 1.0 H32 B:TRS301 3.8 14.4 1.0 HA B:GLU185 4.1 15.0 1.0 O B:HOH498 4.1 12.2 1.0 OH B:TYR178 4.2 18.9 1.0 CG B:HIS142 4.2 14.5 1.0 O B:HOH504 4.2 14.5 1.0 CG B:HIS146 4.2 16.6 1.0 ND1 B:HIS146 4.2 18.1 1.0 ND1 B:HIS142 4.2 16.2 1.0 OE2 B:GLU143 4.3 22.7 1.0 C1 B:TRS301 4.3 16.4 1.0 O B:HOH499 4.3 43.6 1.0 HB3 B:ALA188 4.4 16.2 1.0 CG B:GLU185 4.4 15.1 1.0 HB3 B:GLU185 4.6 16.7 1.0 HE2 B:TYR178 4.6 21.2 1.0 HH B:TYR178 4.6 22.7 1.0 H11 B:TRS301 4.7 19.6 1.0 HB1 B:ALA188 4.7 16.2 1.0 OE1 B:GLU143 4.8 22.0 1.0 O1 B:TRS301 4.8 15.7 1.0 HG3 B:GLU185 4.8 18.1 1.0 HB2 B:ALA188 4.9 16.2 1.0 CB B:ALA188 4.9 13.5 1.0 CD B:GLU143 4.9 19.9 1.0 CB B:GLU185 4.9 13.9 1.0 CA B:GLU185 4.9 12.5 1.0 H12 B:TRS301 5.0 19.6 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