Calcium in PDB 8juf: 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: 8juf 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)	54.60 / 1.39
Space group	I 4
Cell size a, b, c (Å), α, β, γ (°)	77.22, 77.22, 62.98, 90, 90, 90
R / Rfree (%)	19.7 / 22

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

Chlorine	(Cl)	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 8juf). 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: 8juf:
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:18.8 occ:1.00 O A:GLY187 2.3 17.4 1.0 O A:ASP153 2.3 19.8 1.0 O A:GLY185 2.4 19.0 1.0 O A:HOH432 2.4 19.4 1.0 OD1 A:ASP189 2.4 19.9 1.0 O A:HOH427 2.4 21.1 1.0 CG A:ASP189 3.3 17.6 1.0 C A:ASP153 3.5 19.0 1.0 C A:GLY187 3.5 17.4 1.0 C A:GLY185 3.5 19.4 1.0 OD2 A:ASP189 3.8 20.7 1.0 C A:LEU186 4.0 19.4 1.0 N A:GLY187 4.0 20.3 1.0 O A:LEU186 4.1 18.5 1.0 O A:HOH414 4.2 26.9 1.0 O A:ALA152 4.2 24.6 1.0 CA A:ASP153 4.3 22.1 1.0 N A:ASP189 4.3 17.5 1.0 CA A:GLY187 4.3 19.7 1.0 O A:GLY183 4.4 22.3 1.0 N A:GLY185 4.5 22.8 1.0 N A:LEU186 4.5 20.6 1.0 CA A:GLY185 4.5 20.5 1.0 N A:GLY188 4.5 15.6 1.0 CA A:LEU186 4.5 19.9 1.0 N A:ILE154 4.5 21.0 1.0 CA A:GLY188 4.6 17.5 1.0 CB A:ASP189 4.6 16.9 1.0 O A:HOH522 4.6 35.1 1.0 N A:MET155 4.7 18.4 1.0 C A:GLY188 4.7 16.1 1.0 CA A:ILE154 4.7 19.8 1.0 CG A:MET155 4.7 22.5 1.0 C A:THR184 4.8 21.8 1.0 CH2 A:TRP104 4.8 19.8 1.0 CA A:ASP189 4.9 18.3 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:22.7 occ:1.00 OE2 A:GLU196 2.3 27.3 1.0 O A:GLY171 2.3 26.2 1.0 OD2 A:ASP193 2.3 18.9 1.0 O A:THR175 2.4 23.4 0.5 O A:GLY173 2.4 25.8 1.0 O A:THR175 2.4 25.2 0.5 OD1 A:ASP170 2.5 25.4 1.0 CG A:ASP193 3.3 16.1 1.0 CD A:GLU196 3.5 30.6 1.0 C A:GLY171 3.5 25.6 1.0 C A:THR175 3.6 25.0 0.5 C A:GLY173 3.6 27.1 1.0 C A:THR175 3.6 27.3 0.5 CG A:ASP170 3.7 24.2 1.0 N A:GLY173 3.9 23.3 1.0 N A:THR175 4.0 25.8 0.5 CB A:ASP193 4.0 20.5 1.0 N A:GLY171 4.1 24.4 1.0 OE1 A:GLU196 4.1 24.2 1.0 N A:THR175 4.1 29.7 0.5 C A:PRO172 4.1 25.6 1.0 C A:ASP170 4.2 27.0 1.0 OD1 A:ASP193 4.3 23.9 1.0 CA A:GLY173 4.3 22.5 1.0 CA A:THR175 4.3 24.9 0.5 OD2 A:ASP170 4.4 33.5 1.0 CA A:GLY171 4.4 28.7 1.0 N A:ASP170 4.4 27.1 1.0 N A:PRO172 4.4 25.6 1.0 C A:ASN174 4.4 29.8 1.0 CA A:THR175 4.5 28.8 0.5 CA A:PRO172 4.5 24.9 1.0 OG1 A:THR175 4.5 34.5 0.5 CG A:GLU196 4.6 26.6 1.0 O A:PRO172 4.6 29.1 1.0 N A:LEU176 4.6 21.2 1.0 N A:ASN174 4.6 27.4 1.0 O A:ASP170 4.7 33.3 1.0 CA A:ASP170 4.7 30.0 1.0 CA A:LEU176 4.7 23.4 1.0 CB A:ASP170 4.8 28.2 1.0 O A:ASN174 4.9 31.3 1.0 CA A:ASN174 4.9 33.7 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