Zinc in PDB 1dth: Metalloprotease

All present enzymatic activity of Metalloprotease:
3.4.24.42;

The structure of Metalloprotease, PDB code: 1dth was solved by I.Botos, L.Scapozza, D.Zhang, L.A.Liotta, E.F.Meyer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	8.00 / 2.00
Space group	P 65
Cell size a, b, c (Å), α, β, γ (°)	97.210, 97.210, 87.910, 90.00, 90.00, 120.00
R / Rfree (%)	16.8 / n/a

The structure of Metalloprotease also contains other interesting chemical elements:

Calcium

(Ca)

2 atoms

The binding sites of Zinc atom in the Metalloprotease (pdb code 1dth). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Metalloprotease, PDB code: 1dth:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Metalloprotease


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Metalloprotease within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn901 b:5.0 occ:1.00 O4 A:BAT972 1.9 29.7 0.9 NE2 A:HIS142 2.0 29.9 1.0 NE2 A:HIS152 2.0 16.7 1.0 NE2 A:HIS146 2.0 31.5 1.0 CD2 A:HIS142 2.9 5.8 1.0 CE1 A:HIS152 3.0 31.9 1.0 CE1 A:HIS142 3.0 5.0 1.0 C15 A:BAT972 3.0 28.1 0.9 CE1 A:HIS146 3.0 8.2 1.0 CD2 A:HIS146 3.1 28.6 1.0 CD2 A:HIS152 3.1 14.7 1.0 C16 A:BAT972 3.4 32.9 0.9 N3 A:BAT972 3.7 21.1 0.9 CG A:HIS142 4.1 5.0 1.0 ND1 A:HIS142 4.1 15.7 1.0 ND1 A:HIS152 4.1 20.0 1.0 OE2 A:GLU143 4.2 18.7 1.0 CG A:HIS152 4.2 7.8 1.0 ND1 A:HIS146 4.2 16.1 1.0 CG A:HIS146 4.2 6.1 1.0 C14 A:BAT972 4.3 33.8 0.9 N2 A:BAT972 4.3 30.7 0.9 C13 A:BAT972 4.4 18.3 0.9 OE1 A:GLU143 4.7 46.9 1.0 O3 A:BAT972 4.7 25.3 0.9 CE A:MET166 4.8 5.0 1.0 CD A:GLU143 4.8 15.4 1.0

Zinc binding site 2 out of 2 in the Metalloprotease


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Metalloprotease within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn902 b:7.9 occ:1.00 NE2 B:HIS142 2.0 24.7 1.0 O4 B:BAT973 2.0 36.2 0.9 NE2 B:HIS152 2.0 5.7 1.0 NE2 B:HIS146 2.1 31.0 1.0 CE1 B:HIS152 2.9 5.0 1.0 CD2 B:HIS142 2.9 5.0 1.0 CE1 B:HIS142 3.0 5.0 1.0 C15 B:BAT973 3.0 31.3 0.9 CD2 B:HIS146 3.1 8.4 1.0 CD2 B:HIS152 3.1 5.0 1.0 CE1 B:HIS146 3.1 22.3 1.0 C16 B:BAT973 3.2 31.4 0.9 N3 B:BAT973 3.5 29.4 0.9 ND1 B:HIS152 4.1 10.9 1.0 CG B:HIS142 4.1 5.0 1.0 ND1 B:HIS142 4.1 7.2 1.0 CG B:HIS152 4.2 6.5 1.0 CG B:HIS146 4.2 9.2 1.0 ND1 B:HIS146 4.2 11.1 1.0 C14 B:BAT973 4.3 27.1 0.9 N2 B:BAT973 4.3 36.4 0.9 OE2 B:GLU143 4.5 28.3 1.0 CE B:MET166 4.6 19.3 1.0 C13 B:BAT973 4.6 38.0 0.9 O B:ARG167 4.7 41.3 1.0 OE1 B:GLU143 4.9 30.8 1.0 O3 B:BAT973 4.9 25.5 0.9

I.Botos, L.Scapozza, D.Zhang, L.A.Liotta, E.F.Meyer. Batimastat, A Potent Matrix Mealloproteinase Inhibitor, Exhibits An Unexpected Mode of Binding. Proc.Natl.Acad.Sci.Usa V. 93 2749 1996.
ISSN: ISSN 0027-8424
PubMed: 8610113
DOI: 10.1073/PNAS.93.7.2749