Calcium in PDB 7wxx: 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: 7wxx was solved by M.Kamitani, Y.Oka, H.Tabuse, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	54.70 / 1.50
Space group	I 4
Cell size a, b, c (Å), α, β, γ (°)	77.36, 77.36, 62.71, 90, 90, 90
R / Rfree (%)	17 / 20.3

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

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

The binding sites of Calcium atom in the Crystal Structure of Human Mmp-7 in Complex with Inhibitor (pdb code 7wxx). 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: 7wxx:
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:16.2 occ:1.00 O A:ASP153 2.2 18.5 1.0 O A:GLY187 2.3 15.9 1.0 O A:HOH437 2.4 16.3 1.0 O A:GLY185 2.4 18.4 1.0 O A:HOH428 2.4 18.4 1.0 OD1 A:ASP189 2.4 16.5 1.0 CG A:ASP189 3.4 17.3 1.0 C A:ASP153 3.4 17.0 1.0 C A:GLY187 3.5 15.6 1.0 C A:GLY185 3.6 17.1 1.0 OD2 A:ASP189 3.8 18.7 1.0 C A:LEU186 3.9 16.0 1.0 N A:GLY187 4.0 16.8 1.0 O A:HOH409 4.1 22.5 1.0 O A:LEU186 4.1 16.0 1.0 O A:ALA152 4.2 20.1 1.0 CA A:ASP153 4.2 18.7 1.0 CA A:GLY187 4.3 16.6 1.0 N A:ASP189 4.3 15.4 1.0 O A:GLY183 4.4 17.4 1.0 CA A:LEU186 4.4 17.3 1.0 N A:ILE154 4.4 18.0 1.0 N A:LEU186 4.5 17.9 1.0 CA A:GLY185 4.5 18.3 1.0 N A:GLY188 4.5 13.6 1.0 N A:GLY185 4.5 17.8 1.0 CA A:GLY188 4.6 13.9 1.0 O A:HOH521 4.7 29.4 1.0 CA A:ILE154 4.7 15.7 1.0 CB A:ASP189 4.7 17.5 1.0 N A:MET155 4.7 16.1 1.0 C A:GLY188 4.7 14.3 1.0 C A:THR184 4.8 18.1 1.0 CH2 A:TRP104 4.8 17.2 1.0 CA A:ASP189 4.9 17.0 1.0 CG A:MET155 4.9 20.3 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:17.8 occ:1.00 OE2 A:GLU196 2.3 19.6 1.0 O A:GLY171 2.3 19.3 1.0 OD2 A:ASP193 2.4 17.0 1.0 O A:THR175 2.4 19.2 1.0 OD1 A:ASP170 2.4 21.7 1.0 O A:GLY173 2.4 20.4 1.0 CG A:ASP193 3.3 15.8 1.0 C A:THR175 3.5 20.1 1.0 CD A:GLU196 3.5 21.6 1.0 CG A:ASP170 3.6 22.0 1.0 C A:GLY171 3.6 20.5 1.0 C A:GLY173 3.6 22.3 1.0 N A:GLY173 4.0 18.7 1.0 CB A:ASP193 4.0 16.7 1.0 N A:THR175 4.1 21.8 1.0 N A:GLY171 4.1 19.1 1.0 OE1 A:GLU196 4.1 19.1 1.0 C A:PRO172 4.1 20.2 1.0 OD2 A:ASP170 4.2 25.2 1.0 C A:ASP170 4.3 20.7 1.0 OD1 A:ASP193 4.3 18.0 1.0 CA A:THR175 4.3 22.4 1.0 CA A:GLY173 4.3 20.2 1.0 C A:ASN174 4.4 24.9 1.0 N A:ASP170 4.4 22.0 1.0 CA A:GLY171 4.4 21.2 1.0 CA A:PRO172 4.5 19.4 1.0 N A:PRO172 4.5 20.6 1.0 N A:LEU176 4.5 16.2 1.0 O A:PRO172 4.6 23.4 1.0 CG A:GLU196 4.6 20.3 1.0 N A:ASN174 4.7 23.9 1.0 CA A:ASP170 4.7 23.3 1.0 CA A:LEU176 4.7 18.1 1.0 O A:ASN174 4.7 23.3 1.0 O A:ASP170 4.7 26.4 1.0 CB A:ASP170 4.7 23.3 1.0 O A:HOH418 4.8 31.4 1.0 CB A:THR175 4.9 24.4 1.0 CA A:ASN174 4.9 26.9 1.0 CB A:ASN174 5.0 31.0 1.0

H.Tabuse, K.Abe-Sato, H.Kanazawa, M.Yashiro, Y.Tamura, M.Kamitani, K.Hitaka, E.Gunji, A.Mitani, N.Kojima, Y.Oka. Discovery of Highly Potent and Selective Matrix Metalloproteinase-7 Inhibitors By Hybridizing the S1' Subsite Binder with Short Peptides. J.Med.Chem. V. 65 13253 2022.
ISSN: ISSN 0022-2623
PubMed: 36137271
DOI: 10.1021/ACS.JMEDCHEM.2C01088