Zinc in PDB 5a0p: Apo-Structure of Metalloprotease ZMP1 From Clostridium Difficile

The structure of Apo-Structure of Metalloprotease ZMP1 From Clostridium Difficile, PDB code: 5a0p 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)	45.53 / 1.40
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	43.169, 71.769, 117.798, 90.00, 90.00, 90.00
R / Rfree (%)	15.6 / 18.2

The binding sites of Zinc atom in the Apo-Structure of Metalloprotease ZMP1 From Clostridium Difficile (pdb code 5a0p). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Apo-Structure of Metalloprotease ZMP1 From Clostridium Difficile, PDB code: 5a0p:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Apo-Structure of Metalloprotease ZMP1 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 Apo-Structure of Metalloprotease ZMP1 From Clostridium Difficile within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1221 b:11.3 occ:1.00 O A:HOH2191 1.9 25.2 1.0 OE1 A:GLU185 2.0 11.8 1.0 NE2 A:HIS146 2.0 9.5 1.0 NE2 A:HIS142 2.0 8.8 1.0 CD A:GLU185 2.8 11.7 1.0 CD2 A:HIS142 3.0 8.8 1.0 CE1 A:HIS146 3.0 10.1 1.0 OE2 A:GLU185 3.0 13.8 1.0 CD2 A:HIS146 3.1 9.0 1.0 HD2 A:HIS142 3.1 10.6 1.0 CE1 A:HIS142 3.1 8.9 1.0 O A:HOH2194 3.1 43.3 1.0 HE1 A:HIS146 3.2 12.1 1.0 HD2 A:HIS146 3.3 10.8 1.0 HE1 A:HIS142 3.3 10.7 1.0 HH A:TYR178 3.4 21.0 1.0 HA A:GLU185 3.8 10.9 1.0 HB1 A:ALA188 4.0 10.6 1.0 OH A:TYR178 4.1 17.5 1.0 ND1 A:HIS146 4.1 10.4 1.0 CG A:HIS142 4.1 8.5 1.0 ND1 A:HIS142 4.2 9.2 1.0 CG A:HIS146 4.2 9.0 1.0 HE2 A:TYR178 4.2 17.7 1.0 CG A:GLU185 4.3 10.4 1.0 O A:HOH2192 4.3 17.8 1.0 OE1 A:GLU143 4.3 15.1 1.0 HB3 A:GLU185 4.4 11.9 1.0 HB2 A:ALA188 4.4 10.6 1.0 CB A:ALA188 4.5 8.8 1.0 O A:HOH2152 4.5 20.1 1.0 HB3 A:ALA188 4.6 10.6 1.0 OE2 A:GLU143 4.6 20.9 1.0 CA A:GLU185 4.7 9.1 1.0 CB A:GLU185 4.7 9.9 1.0 HG3 A:GLU185 4.7 12.5 1.0 CD A:GLU143 4.8 17.2 1.0 HG2 A:GLU185 4.8 12.5 1.0 HD1 A:HIS146 4.9 12.5 1.0 CE2 A:TYR178 4.9 14.8 1.0 HD1 A:HIS142 4.9 11.0 1.0 CZ A:TYR178 5.0 15.1 1.0

Zinc binding site 2 out of 2 in the Apo-Structure of Metalloprotease ZMP1 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 Apo-Structure of Metalloprotease ZMP1 From Clostridium Difficile within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1221 b:9.0 occ:1.00 O B:HOH2182 1.9 30.4 1.0 OE1 B:GLU185 2.0 9.1 1.0 NE2 B:HIS142 2.0 8.4 1.0 NE2 B:HIS146 2.1 8.7 1.0 CD B:GLU185 2.8 10.1 1.0 CD2 B:HIS142 3.0 8.8 1.0 CE1 B:HIS146 3.0 9.7 1.0 OE2 B:GLU185 3.0 12.0 1.0 CE1 B:HIS142 3.1 8.5 1.0 CD2 B:HIS146 3.1 8.3 1.0 HD2 B:HIS142 3.1 10.6 1.0 HE1 B:HIS146 3.1 11.6 1.0 HE1 B:HIS142 3.3 10.2 1.0 HD2 B:HIS146 3.3 10.0 1.0 O B:HOH2223 3.8 40.1 1.0 HA B:GLU185 3.8 8.9 1.0 HB1 B:ALA188 4.0 10.9 1.0 O B:HOH2062 4.0 44.9 1.0 OH B:TYR178 4.0 13.1 1.0 ND1 B:HIS146 4.1 9.7 1.0 CG B:HIS142 4.1 8.9 1.0 ND1 B:HIS142 4.1 8.5 1.0 CG B:HIS146 4.2 8.8 1.0 OE1 B:GLU143 4.2 15.0 1.0 HE2 B:TYR178 4.2 13.0 1.0 CG B:GLU185 4.2 9.5 1.0 O B:HOH2181 4.3 15.3 1.0 OE2 B:GLU143 4.3 20.6 1.0 HB3 B:GLU185 4.4 10.3 1.0 HB2 B:ALA188 4.4 10.9 1.0 HH B:TYR178 4.5 15.8 1.0 CB B:ALA188 4.5 9.1 1.0 HB3 B:ALA188 4.6 10.9 1.0 CD B:GLU143 4.6 16.1 1.0 O B:HOH2147 4.6 20.6 1.0 HG3 B:GLU185 4.7 11.4 1.0 CB B:GLU185 4.7 8.6 1.0 CA B:GLU185 4.7 7.5 1.0 HG2 B:GLU185 4.8 11.4 1.0 HD1 B:HIS146 4.9 11.7 1.0 CE2 B:TYR178 4.9 10.8 1.0 HZ2 B:LYS101 4.9 24.9 1.0 HD1 B:HIS142 4.9 10.2 1.0 CZ B:TYR178 5.0 11.7 1.0 HA B:GLU143 5.0 10.0 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