Zinc in PDB 5a0r: Product Peptide-Bound Structure of Metalloprotease ZMP1 Variant E143A From Clostridium Difficile

The structure of Product Peptide-Bound Structure of Metalloprotease ZMP1 Variant E143A From Clostridium Difficile, PDB code: 5a0r 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)	40.41 / 1.25
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	37.060, 42.960, 119.210, 90.00, 92.54, 90.00
R / Rfree (%)	14.2 / 16.2

The binding sites of Zinc atom in the Product Peptide-Bound Structure of Metalloprotease ZMP1 Variant E143A From Clostridium Difficile (pdb code 5a0r). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Product Peptide-Bound Structure of Metalloprotease ZMP1 Variant E143A From Clostridium Difficile, PDB code: 5a0r:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Product Peptide-Bound Structure of Metalloprotease ZMP1 Variant E143A 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 Product Peptide-Bound Structure of Metalloprotease ZMP1 Variant E143A From Clostridium Difficile within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1221 b:10.5 occ:1.00 O D:PRO4 1.9 12.3 1.0 OE1 A:GLU185 2.0 10.7 1.0 NE2 A:HIS142 2.0 8.8 1.0 NE2 A:HIS146 2.0 10.6 1.0 CD A:GLU185 2.8 10.7 1.0 C D:PRO4 2.9 14.2 1.0 OE2 A:GLU185 2.9 13.2 1.0 CD2 A:HIS142 3.0 9.0 1.0 CE1 A:HIS146 3.0 10.2 1.0 CE1 A:HIS142 3.0 9.2 1.0 CD2 A:HIS146 3.1 8.0 1.0 HD2 A:HIS142 3.2 10.8 1.0 HE1 A:HIS146 3.2 12.2 1.0 HE1 A:HIS142 3.2 11.0 1.0 OXT D:PRO4 3.3 20.2 1.0 HD2 A:HIS146 3.3 9.7 1.0 HH A:TYR178 3.4 26.3 1.0 HB3 D:ASN3 3.6 15.6 1.0 HA A:GLU185 3.8 11.0 1.0 HB1 A:ALA188 3.9 11.1 1.0 OH A:TYR178 4.0 21.9 1.0 O A:HOH2156 4.0 13.6 1.0 ND1 A:HIS142 4.1 8.7 1.0 ND1 A:HIS146 4.1 8.8 1.0 CG A:HIS142 4.1 8.6 1.0 HB2 D:ASN3 4.2 15.6 1.0 CG A:HIS146 4.2 8.2 1.0 CG A:GLU185 4.2 9.4 1.0 O A:HOH2185 4.2 23.9 1.0 CA D:PRO4 4.2 14.3 1.0 CB D:ASN3 4.3 13.0 1.0 N D:PRO4 4.4 14.3 1.0 HB2 A:ALA188 4.4 11.1 1.0 HD2 D:PRO4 4.4 18.2 1.0 HE2 A:TYR178 4.4 19.0 1.0 HB3 A:GLU185 4.4 11.8 1.0 CB A:ALA188 4.4 9.2 1.0 HB3 A:ALA188 4.5 11.1 1.0 C D:ASN3 4.5 13.7 1.0 HG2 D:PRO4 4.6 19.1 1.0 HG3 A:GLU185 4.6 11.3 1.0 CA A:GLU185 4.6 9.2 1.0 CB A:GLU185 4.6 9.8 1.0 O D:ASN3 4.7 13.3 1.0 HZ2 A:LYS101 4.7 23.4 1.0 HG2 A:GLU185 4.8 11.3 1.0 HA D:PRO4 4.8 17.2 1.0 CZ A:TYR178 4.8 15.1 1.0 CD D:PRO4 4.8 15.2 1.0 HD1 A:HIS146 4.9 10.6 1.0 HD1 A:HIS142 4.9 10.4 1.0 CE2 A:TYR178 4.9 15.8 1.0

Zinc binding site 2 out of 2 in the Product Peptide-Bound Structure of Metalloprotease ZMP1 Variant E143A 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 Product Peptide-Bound Structure of Metalloprotease ZMP1 Variant E143A From Clostridium Difficile within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1221 b:11.7 occ:1.00 OXT E:PRO4 1.8 24.3 1.0 OE1 B:GLU185 1.9 11.4 1.0 NE2 B:HIS146 2.0 11.4 1.0 NE2 B:HIS142 2.0 10.8 1.0 CD B:GLU185 2.8 11.2 1.0 C E:PRO4 2.8 23.1 1.0 OE2 B:GLU185 3.0 14.0 1.0 CE1 B:HIS146 3.0 10.0 1.0 CD2 B:HIS142 3.0 9.8 1.0 CD2 B:HIS146 3.0 10.1 1.0 CE1 B:HIS142 3.1 10.9 1.0 HD2 B:HIS142 3.1 11.8 1.0 HE1 B:HIS146 3.1 12.0 1.0 O E:PRO4 3.2 26.4 1.0 HD2 B:HIS146 3.2 12.1 1.0 HE1 B:HIS142 3.3 13.1 1.0 HH B:TYR178 3.4 27.5 1.0 HB3 E:ASN3 3.5 27.6 1.0 HA B:GLU185 3.8 12.7 1.0 O B:HOH2113 3.9 16.3 1.0 HB1 B:ALA188 4.0 13.2 1.0 HB2 E:ASN3 4.1 27.6 1.0 ND1 B:HIS146 4.1 10.6 1.0 OH B:TYR178 4.1 22.9 1.0 CG B:HIS142 4.1 8.9 1.0 CA E:PRO4 4.1 22.6 1.0 ND1 B:HIS142 4.2 11.0 1.0 CG B:HIS146 4.2 8.9 1.0 CG B:GLU185 4.2 11.6 1.0 CB E:ASN3 4.2 23.0 1.0 HE2 B:TYR178 4.3 23.4 1.0 N E:PRO4 4.3 22.0 1.0 O B:HOH2134 4.3 16.6 1.0 C E:ASN3 4.4 25.4 1.0 HB3 B:GLU185 4.4 14.0 1.0 HD2 E:PRO4 4.4 26.9 1.0 O E:ASN3 4.5 22.2 1.0 HB2 B:ALA188 4.5 13.2 1.0 CB B:ALA188 4.6 11.0 1.0 HG3 B:GLU185 4.6 13.9 1.0 CB B:GLU185 4.6 11.7 1.0 CA B:GLU185 4.6 10.5 1.0 HB3 B:ALA188 4.7 13.2 1.0 HA E:PRO4 4.7 27.1 1.0 HZ2 B:LYS101 4.7 28.7 1.0 HG2 B:GLU185 4.7 13.9 1.0 HG2 E:PRO4 4.8 35.3 1.0 CD E:PRO4 4.8 22.5 1.0 HD1 B:HIS146 4.9 12.7 1.0 HD1 B:HIS142 4.9 13.2 1.0 CE2 B:TYR178 4.9 19.5 1.0 CA E:ASN3 5.0 22.4 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