Calcium in PDB 8jud: 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: 8jud 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)	54.69 / 1.50
Space group	I 4
Cell size a, b, c (Å), α, β, γ (°)	77.35, 77.35, 62.37, 90, 90, 90
R / Rfree (%)	23.1 / 26

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 8jud). 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: 8jud:
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:15.7 occ:1.00 O A:HOH436 2.3 13.6 1.0 O A:GLY187 2.3 14.5 1.0 O A:ASP153 2.4 19.9 1.0 O A:GLY185 2.4 18.1 1.0 O A:HOH406 2.4 14.6 1.0 OD1 A:ASP189 2.5 16.6 1.0 CG A:ASP189 3.4 18.9 1.0 C A:GLY187 3.5 15.4 1.0 C A:ASP153 3.5 16.3 1.0 C A:GLY185 3.6 15.9 1.0 OD2 A:ASP189 3.9 20.1 1.0 N A:GLY187 3.9 15.6 1.0 C A:LEU186 3.9 16.1 1.0 O A:HOH410 4.1 19.9 1.0 O A:LEU186 4.1 15.3 1.0 O A:ALA152 4.2 17.2 1.0 CA A:GLY187 4.2 15.2 1.0 CA A:ASP153 4.2 16.6 1.0 N A:ASP189 4.3 15.5 1.0 N A:LEU186 4.4 17.0 1.0 CA A:LEU186 4.4 17.4 1.0 O A:GLY183 4.4 16.7 1.0 N A:GLY188 4.5 14.7 1.0 N A:GLY185 4.5 16.6 1.0 CA A:GLY185 4.5 18.0 1.0 N A:ILE154 4.5 16.2 1.0 CA A:GLY188 4.6 15.6 1.0 C A:GLY188 4.7 14.6 1.0 O A:HOH489 4.7 30.7 1.0 CA A:ILE154 4.7 15.7 1.0 CB A:ASP189 4.7 17.2 1.0 O A:HOH415 4.8 20.7 1.0 C A:THR184 4.8 18.9 1.0 N A:MET155 4.8 15.3 1.0 CH2 A:TRP104 4.9 14.5 1.0 CA A:ASP189 4.9 16.3 1.0 CG A:MET155 4.9 18.9 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:15.9 occ:1.00 O A:THR175 2.3 14.6 1.0 OD2 A:ASP193 2.3 15.9 1.0 OD1 A:ASP170 2.3 20.1 1.0 O A:GLY171 2.4 16.7 1.0 O A:GLY173 2.4 17.8 1.0 OE2 A:GLU196 2.4 14.8 1.0 CG A:ASP193 3.4 17.0 1.0 C A:THR175 3.5 16.7 1.0 C A:GLY171 3.5 16.8 1.0 CG A:ASP170 3.6 20.6 1.0 C A:GLY173 3.6 18.4 1.0 CD A:GLU196 3.6 16.5 1.0 N A:GLY173 3.9 16.1 1.0 N A:THR175 4.0 19.3 1.0 CB A:ASP193 4.0 17.1 1.0 N A:GLY171 4.1 16.8 1.0 OD2 A:ASP170 4.2 23.5 1.0 C A:PRO172 4.2 19.6 1.0 CA A:THR175 4.3 17.8 1.0 CA A:GLY173 4.3 17.4 1.0 OD1 A:ASP193 4.3 17.3 1.0 OE1 A:GLU196 4.3 19.3 1.0 C A:ASP170 4.3 19.0 1.0 N A:ASP170 4.3 19.2 1.0 C A:ASN174 4.3 20.9 1.0 CA A:GLY171 4.4 17.8 1.0 N A:LEU176 4.5 13.9 1.0 N A:PRO172 4.5 18.7 1.0 CA A:PRO172 4.5 18.7 1.0 N A:ASN174 4.6 19.6 1.0 CA A:ASP170 4.6 20.9 1.0 CG A:GLU196 4.7 17.2 1.0 CB A:ASP170 4.7 19.5 1.0 CA A:LEU176 4.7 15.6 1.0 O A:ASP170 4.7 23.2 1.0 O A:PRO172 4.8 20.9 1.0 O A:ASN174 4.8 19.3 1.0 CB A:THR175 4.8 19.3 1.0 CA A:ASN174 4.9 21.7 1.0 CB A:ASN174 4.9 22.8 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