Zinc 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
Calcium	(Ca)	2 atoms
Fluorine	(F)	3 atoms

The binding sites of Zinc 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 Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of Human Mmp-7 in Complex with Inhibitor, PDB code: 8juf:
Jump to Zinc binding site number: 1; 2;

Zinc 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 Zinc with other atoms in the Zn 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:Zn303 b:21.5 occ:1.00 OD2 A:ASP165 2.0 19.8 1.0 NE2 A:HIS178 2.1 23.0 1.0 ND1 A:HIS191 2.1 27.0 1.0 NE2 A:HIS163 2.1 20.7 1.0 CG A:ASP165 2.9 25.8 1.0 CD2 A:HIS163 3.0 24.5 1.0 CE1 A:HIS178 3.0 22.3 1.0 CE1 A:HIS191 3.0 18.8 1.0 CD2 A:HIS178 3.1 22.7 1.0 CG A:HIS191 3.1 20.2 1.0 OD1 A:ASP165 3.1 29.1 1.0 CE1 A:HIS163 3.2 25.9 1.0 CB A:HIS191 3.5 22.4 1.0 ND1 A:HIS178 4.1 22.2 1.0 NE2 A:HIS191 4.1 20.4 1.0 CG A:HIS163 4.2 25.9 1.0 O A:TYR167 4.2 25.7 1.0 ND1 A:HIS163 4.2 25.1 1.0 CG A:HIS178 4.2 21.1 1.0 CD2 A:HIS191 4.2 20.9 1.0 CB A:ASP165 4.3 25.6 1.0 CE1 A:PHE180 4.3 23.9 1.0 CZ A:PHE180 4.6 26.6 1.0 O A:HOH455 4.9 24.7 1.0 CZ A:PHE169 4.9 25.6 1.0 CB A:TYR167 5.0 28.2 1.0 CE2 A:PHE169 5.0 24.4 1.0 CA A:HIS191 5.0 18.8 1.0

Zinc 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 Zinc with other atoms in the Zn 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:Zn304 b:22.4 occ:1.00 OXT B:GGL2 2.0 22.2 1.0 NE2 A:HIS218 2.1 20.2 1.0 NE2 A:HIS214 2.1 21.1 1.0 NE2 A:HIS224 2.1 28.8 1.0 C B:GGL2 2.8 25.4 1.0 O B:GGL2 2.9 28.3 1.0 CE1 A:HIS218 3.0 20.9 1.0 CD2 A:HIS214 3.1 17.9 1.0 CE1 A:HIS214 3.1 23.1 1.0 CD2 A:HIS224 3.1 23.0 1.0 CD2 A:HIS218 3.1 20.6 1.0 CE1 A:HIS224 3.1 27.4 1.0 ND1 A:HIS218 4.1 21.1 1.0 ND1 A:HIS214 4.2 23.4 1.0 CG A:HIS218 4.2 18.8 1.0 CA B:GGL2 4.2 25.7 1.0 ND1 A:HIS224 4.2 28.4 1.0 CG A:HIS214 4.2 19.5 1.0 CG A:HIS224 4.3 24.2 1.0 O A:HOH475 4.3 44.5 1.0 N B:GLY3 4.4 23.6 1.0 CD B:GGL2 4.4 21.8 1.0 C39 B:7SF1 4.6 25.1 1.0 C38 B:7SF1 4.6 28.1 1.0 CG B:GGL2 4.7 23.4 1.0 OE1 B:GGL2 4.7 24.9 1.0 CE A:MET232 4.7 20.1 1.0 CB B:GGL2 4.9 23.6 1.0 NE2 A:GLN215 4.9 22.7 1.0 CA B:GLY3 4.9 21.3 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