Calcium in PDB 8jug: 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: 8jug was solved by M.Kamitani, K.Abe-Sato, Y.Oka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.05 / 1.30
Space group	I 4
Cell size a, b, c (Å), α, β, γ (°)	76.06, 76.06, 61.89, 90, 90, 90
R / Rfree (%)	22.1 / 23.8

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

Chlorine	(Cl)	2 atoms
Fluorine	(F)	6 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 8jug). 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: 8jug:
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:10.5 occ:1.00 O A:GLY185 2.3 10.7 1.0 O A:GLY187 2.3 9.8 1.0 O A:ASP153 2.3 11.0 1.0 OD1 A:ASP189 2.4 9.6 1.0 O A:HOH418 2.4 10.9 1.0 O A:HOH413 2.4 12.8 1.0 CG A:ASP189 3.3 9.8 1.0 C A:ASP153 3.5 11.2 1.0 C A:GLY185 3.5 11.4 1.0 C A:GLY187 3.5 9.4 1.0 OD2 A:ASP189 3.7 11.8 1.0 C A:LEU186 4.0 11.6 1.0 N A:GLY187 4.0 10.5 1.0 O A:LEU186 4.1 10.6 1.0 O A:HOH422 4.1 17.5 1.0 O A:ALA152 4.1 13.7 1.0 CA A:ASP153 4.2 12.5 1.0 N A:ASP189 4.2 9.6 1.0 N A:GLY185 4.3 12.0 1.0 CA A:GLY187 4.3 9.8 1.0 O A:GLY183 4.4 13.1 1.0 CA A:GLY185 4.4 12.3 1.0 N A:LEU186 4.4 11.9 1.0 N A:GLY188 4.4 9.9 1.0 CA A:LEU186 4.4 12.2 1.0 N A:ILE154 4.5 11.1 1.0 O A:HOH492 4.5 30.1 1.0 CB A:ASP189 4.5 9.0 1.0 N A:MET155 4.6 10.7 1.0 CA A:GLY188 4.6 9.6 1.0 C A:GLY188 4.6 10.0 1.0 CA A:ILE154 4.6 10.9 1.0 CH2 A:TRP104 4.7 10.8 1.0 C A:THR184 4.7 12.2 1.0 CA A:ASP189 4.7 9.1 1.0 CG A:MET155 4.7 12.3 1.0 O A:THR184 5.0 12.5 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 2.3 11.2 1.0 O A:GLY171 2.3 12.2 1.0 OD2 A:ASP193 2.3 8.6 1.0 O A:THR175 2.3 10.8 1.0 OD1 A:ASP170 2.4 11.0 1.0 O A:GLY173 2.4 10.5 1.0 CG A:ASP193 3.3 7.9 1.0 C A:GLY171 3.5 12.1 1.0 CD A:GLU196 3.5 9.6 1.0 C A:THR175 3.5 11.9 1.0 CG A:ASP170 3.6 12.4 1.0 C A:GLY173 3.6 12.1 1.0 N A:GLY173 3.9 11.0 1.0 N A:THR175 4.0 12.4 1.0 N A:GLY171 4.0 11.8 1.0 CB A:ASP193 4.0 8.2 1.0 OE1 A:GLU196 4.2 9.7 1.0 C A:PRO172 4.2 12.4 1.0 OD1 A:ASP193 4.2 8.7 1.0 C A:ASP170 4.2 11.5 1.0 OD2 A:ASP170 4.2 14.5 1.0 CA A:THR175 4.3 12.4 1.0 CA A:GLY173 4.3 11.7 1.0 N A:ASP170 4.3 11.7 1.0 C A:ASN174 4.3 14.2 1.0 CA A:GLY171 4.3 11.2 1.0 N A:PRO172 4.4 11.6 1.0 CA A:PRO172 4.5 11.9 1.0 N A:LEU176 4.5 10.3 1.0 CG A:GLU196 4.6 10.0 1.0 CA A:ASP170 4.6 11.7 1.0 N A:ASN174 4.6 13.6 1.0 O A:ASP170 4.7 14.7 1.0 CB A:ASP170 4.7 11.7 1.0 O A:PRO172 4.7 14.3 1.0 CA A:LEU176 4.7 10.5 1.0 O A:ASN174 4.7 15.0 1.0 O A:HOH421 4.7 23.8 1.0 CB A:THR175 4.8 13.1 1.0 CA A:ASN174 4.9 14.6 1.0 CB A:ASN174 5.0 15.9 1.0

K.Abe-Sato, H.Tabuse, H.Kanazawa, M.Kamitani, M.Endo, S.Tokura, S.Wakabayashi, T.Yahara, T.Takeda, K.Hitaka, E.Gunji, N.Kojima, Y.Oka. Structure-Based Optimization and Biological Evaluation of Potent and Selective Mmp-7 Inhibitors For Kidney Fibrosis. J.Med.Chem. 2023.
ISSN: ISSN 0022-2623
PubMed: 37861435
DOI: 10.1021/ACS.JMEDCHEM.3C01166