Calcium 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:

Zinc

(Zn)

2 atoms

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

Calcium binding site 1 out of 2 in the Metalloprotease


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Metalloprotease within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca903 b:6.5 occ:1.00 O A:CYS197 2.2 11.0 1.0 OE1 A:GLU9 2.3 29.7 1.0 OD2 A:ASP93 2.5 27.7 1.0 OD1 A:ASP93 2.5 37.1 1.0 OD1 A:ASN200 2.5 45.2 1.0 CG A:ASP93 2.9 10.5 1.0 CD A:GLU9 3.4 13.4 1.0 CG A:ASN200 3.4 10.5 1.0 C A:CYS197 3.4 7.6 1.0 ND2 A:ASN200 3.7 8.4 1.0 CG A:GLU9 4.1 6.5 1.0 CA A:CYS197 4.2 15.2 1.0 O A:TYR7 4.2 38.8 1.0 OE2 A:GLU9 4.2 32.6 1.0 CB A:GLU9 4.3 5.0 1.0 CB A:ASP93 4.4 20.1 1.0 CB A:CYS197 4.4 5.9 1.0 N A:ILE198 4.5 6.8 1.0 O A:ASN200 4.5 29.3 1.0 CA A:ILE198 4.6 5.0 1.0 CB A:ASN200 4.8 9.8 1.0 N A:GLU9 4.9 6.5 1.0 N A:ASN200 4.9 5.0 1.0

Calcium binding site 2 out of 2 in the Metalloprotease


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Metalloprotease within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca904 b:5.7 occ:1.00 O B:CYS197 2.2 5.0 1.0 OE1 B:GLU9 2.2 27.6 1.0 OD1 B:ASP93 2.5 36.9 1.0 OD1 B:ASN200 2.5 43.7 1.0 OD2 B:ASP93 2.5 33.5 1.0 ND2 B:ASN200 2.8 31.9 1.0 CG B:ASP93 2.8 47.1 1.0 CG B:ASN200 3.0 10.2 1.0 CD B:GLU9 3.3 19.8 1.0 C B:CYS197 3.4 7.2 1.0 CG B:GLU9 4.0 6.3 1.0 CA B:CYS197 4.2 14.0 1.0 OE2 B:GLU9 4.3 13.0 1.0 CB B:ASP93 4.4 23.5 1.0 CB B:CYS197 4.4 14.6 1.0 N B:ILE198 4.4 8.2 1.0 CB B:ASN200 4.5 7.7 1.0 CA B:ILE198 4.5 5.0 1.0 O B:TYR7 4.5 12.1 1.0 O B:ASN200 4.6 30.5 1.0 N B:ASN200 4.7 17.0 1.0 CB B:GLU9 4.7 40.9 1.0 N B:LEU199 4.9 6.9 1.0 CA B:ASN200 5.0 5.0 1.0

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