Calcium in PDB 8k4z: Crystal Structure of Human Mmp-7 in Complex with Inhibitor

All present enzymatic activity of Crystal Structure of Human Mmp-7 in Complex with Inhibitor:
3.4.24.23;

The structure of Crystal Structure of Human Mmp-7 in Complex with Inhibitor, PDB code: 8k4z was solved by M.Kamitani, M.Mima, Y.Oka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	53.60 / 1.70
Space group	I 4
Cell size a, b, c (Å), α, β, γ (°)	75.799, 75.799, 60.53, 90, 90, 90
R / Rfree (%)	20.3 / 23.9

The structure of Crystal Structure of Human Mmp-7 in Complex with Inhibitor also contains other interesting chemical elements:

Chlorine	(Cl)	2 atoms
Iodine	(I)	1 atom
Fluorine	(F)	3 atoms
Zinc	(Zn)	2 atoms

The binding sites of Calcium atom in the Crystal Structure of Human Mmp-7 in Complex with Inhibitor (pdb code 8k4z). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Crystal Structure of Human Mmp-7 in Complex with Inhibitor, PDB code: 8k4z:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Crystal Structure of Human Mmp-7 in Complex with Inhibitor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Human Mmp-7 in Complex with Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca301 b:11.8 occ:1.00 O A:ASP153 2.2 15.9 1.0 O A:GLY187 2.2 11.3 1.0 O A:HOH403 2.3 17.0 1.0 O A:GLY185 2.3 14.3 1.0 O A:HOH422 2.4 9.1 1.0 OD1 A:ASP189 2.4 12.2 1.0 C A:ASP153 3.3 16.0 1.0 CG A:ASP189 3.4 12.0 1.0 C A:GLY187 3.4 11.7 1.0 C A:GLY185 3.6 14.4 1.0 OD2 A:ASP189 3.8 12.5 1.0 O A:HOH407 3.9 17.0 1.0 C A:LEU186 3.9 14.3 1.0 O A:LEU186 4.0 15.6 1.0 CA A:ASP153 4.1 16.9 1.0 N A:GLY187 4.1 12.8 1.0 O A:ALA152 4.1 16.2 1.0 CA A:GLY187 4.3 12.1 1.0 N A:ASP189 4.3 11.2 1.0 CA A:LEU186 4.3 15.2 1.0 N A:ILE154 4.4 15.9 1.0 O A:GLY183 4.4 15.3 1.0 N A:GLY188 4.4 12.0 1.0 N A:LEU186 4.4 14.9 1.0 N A:GLY185 4.4 15.9 1.0 CA A:GLY185 4.5 16.2 1.0 CA A:GLY188 4.6 11.8 1.0 CB A:ASP189 4.6 11.5 1.0 N A:MET155 4.6 14.2 1.0 C A:GLY188 4.6 11.8 1.0 CA A:ILE154 4.7 15.6 1.0 C A:THR184 4.8 15.5 1.0 O A:HOH410 4.8 20.9 1.0 CH2 A:TRP104 4.8 17.0 1.0 CG A:MET155 4.8 17.0 1.0 CA A:ASP189 4.8 11.1 1.0 C A:ALA152 5.0 17.3 1.0

Calcium binding site 2 out of 2 in the Crystal Structure of Human Mmp-7 in Complex with Inhibitor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Human Mmp-7 in Complex with Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca302 b:10.1 occ:1.00 OE2 A:GLU196 2.2 11.9 1.0 O A:GLY171 2.3 11.0 1.0 OD2 A:ASP193 2.3 8.7 1.0 OD1 A:ASP170 2.3 13.8 1.0 O A:THR175 2.3 10.8 1.0 O A:GLY173 2.4 12.2 1.0 CG A:ASP193 3.3 8.5 1.0 CD A:GLU196 3.4 11.8 1.0 C A:THR175 3.5 12.5 1.0 C A:GLY171 3.5 11.7 1.0 CG A:ASP170 3.6 14.0 1.0 C A:GLY173 3.6 13.0 1.0 N A:GLY173 3.9 11.7 1.0 CB A:ASP193 3.9 9.3 1.0 N A:THR175 4.0 14.1 1.0 N A:GLY171 4.1 11.2 1.0 C A:PRO172 4.1 11.9 1.0 OE1 A:GLU196 4.1 11.0 1.0 OD2 A:ASP170 4.2 15.5 1.0 OD1 A:ASP193 4.2 7.5 1.0 C A:ASP170 4.3 12.8 1.0 CA A:GLY173 4.3 12.8 1.0 CA A:THR175 4.3 13.8 1.0 C A:ASN174 4.3 14.5 1.0 N A:ASP170 4.3 13.1 1.0 CA A:GLY171 4.4 11.3 1.0 N A:PRO172 4.5 11.6 1.0 CA A:PRO172 4.5 11.4 1.0 CG A:GLU196 4.5 12.1 1.0 N A:LEU176 4.5 10.8 1.0 N A:ASN174 4.6 14.8 1.0 O A:PRO172 4.6 10.8 1.0 CA A:ASP170 4.7 12.9 1.0 CB A:ASP170 4.7 13.5 1.0 O A:ASP170 4.7 12.7 1.0 CA A:LEU176 4.7 10.7 1.0 O A:ASN174 4.7 13.7 1.0 O A:HOH425 4.7 24.4 1.0 CB A:THR175 4.8 15.8 1.0 CA A:ASN174 4.9 15.8 1.0

Y.Oka, K.Abe-Sato, H.Tabuse, Y.Yasukawa, T.Yahara, T.Nishimoto, M.Kamitani, T.Fukunaga, N.Ochiai, T.Kumasaka-Abe, K.Hitaka, E.Gunji, H.Ohara, T.Takeda, N.Kojima, T.Asami. Discovery of TP0628103: A Selective Mmp-7 Inhibitor Based on the Mitigation of Oatp Substrate Recognition Through Isoelectric Point Shift Strategy To Be Published.