Zinc in PDB 5a0x: Substrate Peptide-Bound Structure of Metalloprotease ZMP1 Variant E143AY178F From Clostridium Difficile

The structure of Substrate Peptide-Bound Structure of Metalloprotease ZMP1 Variant E143AY178F From Clostridium Difficile, PDB code: 5a0x was solved by M.Schacherl, C.Pichlo, I.Neundorf, U.Baumann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.85 / 1.70
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	37.435, 42.941, 123.244, 90.00, 96.09, 90.00
R / Rfree (%)	18 / 20.8

The binding sites of Zinc atom in the Substrate Peptide-Bound Structure of Metalloprotease ZMP1 Variant E143AY178F From Clostridium Difficile (pdb code 5a0x). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Substrate Peptide-Bound Structure of Metalloprotease ZMP1 Variant E143AY178F From Clostridium Difficile, PDB code: 5a0x:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Substrate Peptide-Bound Structure of Metalloprotease ZMP1 Variant E143AY178F From Clostridium Difficile


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Substrate Peptide-Bound Structure of Metalloprotease ZMP1 Variant E143AY178F From Clostridium Difficile within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1221 b:66.1 occ:1.00 OE1 A:GLU185 2.0 10.2 1.0 NE2 A:HIS142 2.0 12.9 1.0 O C:PRO4 2.1 10.3 1.0 NE2 A:HIS146 2.2 10.3 1.0 CD A:GLU185 2.7 11.9 1.0 CD2 A:HIS142 2.9 13.2 1.0 OE2 A:GLU185 2.9 13.6 1.0 HD2 A:HIS142 2.9 15.8 1.0 CD2 A:HIS146 2.9 10.4 1.0 HD2 A:HIS146 3.0 12.5 1.0 CE1 A:HIS142 3.1 12.4 1.0 C C:PRO4 3.2 10.9 1.0 HB3 C:ASN3 3.4 13.9 1.0 CE1 A:HIS146 3.4 10.9 1.0 HA C:PRO5 3.4 15.4 1.0 HE1 A:HIS142 3.4 14.8 1.0 HZ A:PHE178 3.6 17.2 1.0 HE1 A:HIS146 3.7 13.1 1.0 O A:HOH2138 3.8 21.8 1.0 HE2 A:PHE178 3.8 16.9 1.0 HD2 C:PRO4 4.0 13.7 1.0 HB2 C:ASN3 4.0 13.9 1.0 HA A:GLU185 4.0 12.0 1.0 N C:PRO4 4.0 10.8 1.0 CA C:PRO5 4.0 12.9 1.0 N C:PRO5 4.0 12.5 1.0 CG A:HIS142 4.1 12.8 1.0 CB C:ASN3 4.1 11.6 1.0 HB1 A:ALA188 4.1 11.7 1.0 ND1 A:HIS142 4.2 13.7 1.0 CG A:HIS146 4.2 10.5 1.0 CG A:GLU185 4.2 11.1 1.0 C C:ASN3 4.2 11.5 1.0 CA C:PRO4 4.2 11.3 1.0 CZ A:PHE178 4.3 14.4 1.0 ND1 A:HIS146 4.3 10.7 1.0 CE2 A:PHE178 4.4 14.1 1.0 O C:ASN3 4.4 11.5 1.0 C C:PRO5 4.4 12.3 1.0 HB3 A:GLU185 4.5 12.0 1.0 CD C:PRO4 4.5 11.4 1.0 HG2 C:PRO4 4.5 14.4 1.0 HB2 A:ALA188 4.5 11.7 1.0 HG3 A:GLU185 4.5 13.3 1.0 CB A:ALA188 4.6 9.8 1.0 HB3 A:ALA188 4.7 11.7 1.0 HZ2 A:LYS101 4.7 17.2 1.0 CB A:GLU185 4.7 10.0 1.0 HG2 A:GLU185 4.8 13.3 1.0 O C:PRO5 4.8 12.9 1.0 CA C:ASN3 4.8 11.8 1.0 CA A:GLU185 4.8 10.0 1.0 HA C:PRO4 4.8 13.6 1.0 HD1 A:HIS142 5.0 16.4 1.0 CG C:PRO4 5.0 12.0 1.0 N C:VAL6 5.0 11.4 1.0

Zinc binding site 2 out of 2 in the Substrate Peptide-Bound Structure of Metalloprotease ZMP1 Variant E143AY178F From Clostridium Difficile


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Substrate Peptide-Bound Structure of Metalloprotease ZMP1 Variant E143AY178F From Clostridium Difficile within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1221 b:67.9 occ:1.00 OE1 B:GLU185 1.9 14.1 1.0 O D:PRO4 2.1 18.7 1.0 NE2 B:HIS142 2.2 12.8 1.0 NE2 B:HIS146 2.2 16.1 1.0 CD B:GLU185 2.7 18.7 1.0 OE2 B:GLU185 2.9 19.2 1.0 CD2 B:HIS142 3.0 12.3 1.0 CD2 B:HIS146 3.0 15.0 1.0 HD2 B:HIS142 3.1 14.8 1.0 HD2 B:HIS146 3.1 17.9 1.0 CE1 B:HIS146 3.2 16.4 1.0 CE1 B:HIS142 3.2 12.7 1.0 C D:PRO4 3.3 17.8 1.0 HA D:PRO5 3.3 22.9 1.0 HB3 D:ASN3 3.4 18.4 1.0 HE1 B:HIS146 3.5 19.7 1.0 HE1 B:HIS142 3.5 15.2 1.0 HE2 B:PHE178 3.8 19.4 1.0 HZ B:PHE178 3.8 19.2 1.0 HA B:GLU185 3.8 17.1 1.0 HB2 D:ASN3 3.9 18.4 1.0 CA D:PRO5 4.0 19.1 1.0 O B:HOH2120 4.0 22.3 1.0 N D:PRO5 4.1 18.5 1.0 HB1 B:ALA188 4.1 15.8 1.0 CB D:ASN3 4.1 15.4 1.0 N D:PRO4 4.1 18.1 1.0 HD2 D:PRO4 4.2 21.8 1.0 CG B:GLU185 4.2 18.0 1.0 CG B:HIS146 4.2 13.4 1.0 CG B:HIS142 4.2 11.1 1.0 ND1 B:HIS146 4.2 14.7 1.0 ND1 B:HIS142 4.3 13.2 1.0 CA D:PRO4 4.3 17.2 1.0 C D:ASN3 4.3 14.2 1.0 C D:PRO5 4.3 18.1 1.0 HB3 B:GLU185 4.4 18.5 1.0 CE2 B:PHE178 4.5 16.2 1.0 CZ B:PHE178 4.5 16.0 1.0 O D:ASN3 4.6 14.2 1.0 HB2 B:ALA188 4.6 15.8 1.0 HG2 D:PRO4 4.6 20.7 1.0 HG3 B:GLU185 4.6 21.6 1.0 O D:PRO5 4.6 16.4 1.0 CD D:PRO4 4.6 18.2 1.0 CB B:ALA188 4.6 13.2 1.0 HZ2 B:LYS101 4.7 26.9 1.0 CB B:GLU185 4.7 15.4 1.0 CA B:GLU185 4.7 14.3 1.0 HG2 B:GLU185 4.7 21.6 1.0 HB3 B:ALA188 4.7 15.8 1.0 CA D:ASN3 4.9 14.9 1.0 N D:VAL6 4.9 16.3 1.0 HA D:PRO4 4.9 20.6 1.0 H D:VAL6 4.9 19.5 1.0

M.Schacherl, C.Pichlo, I.Neundorf, U.Baumann. Structural Basis of Proline-Proline Peptide Bond Specificity of the Metalloprotease ZMP1 Implicated in Motility of Clostridium Difficile. Structure V. 23 1632 2015.
ISSN: ISSN 0969-2126
PubMed: 26211609
DOI: 10.1016/J.STR.2015.06.018