Zinc 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:

Calcium	(Ca)	2 atoms
Fluorine	(F)	3 atoms
Chlorine	(Cl)	1 atom

The binding sites of Zinc 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 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: 7wxx:
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:18.2 occ:1.00 OD2 A:ASP165 2.0 18.2 1.0 ND1 A:HIS191 2.0 18.7 1.0 NE2 A:HIS163 2.1 16.9 1.0 NE2 A:HIS178 2.1 18.6 1.0 CG A:ASP165 2.9 21.9 1.0 CE1 A:HIS191 2.9 15.4 1.0 CD2 A:HIS163 3.0 20.0 1.0 CE1 A:HIS178 3.1 17.1 1.0 CD2 A:HIS178 3.1 20.7 1.0 CE1 A:HIS163 3.1 20.7 1.0 CG A:HIS191 3.2 14.9 1.0 OD1 A:ASP165 3.2 23.2 1.0 CB A:HIS191 3.6 16.0 1.0 NE2 A:HIS191 4.1 17.6 1.0 CG A:HIS163 4.2 19.4 1.0 ND1 A:HIS163 4.2 18.6 1.0 ND1 A:HIS178 4.2 18.1 1.0 CD2 A:HIS191 4.2 16.7 1.0 CG A:HIS178 4.2 18.2 1.0 O A:TYR167 4.3 20.4 1.0 CB A:ASP165 4.3 21.2 1.0 CE1 A:PHE180 4.4 19.8 1.0 CZ A:PHE169 4.8 19.5 1.0 CZ A:PHE180 4.8 20.8 1.0 O A:HOH434 4.9 20.1 1.0 CE2 A:PHE169 4.9 19.6 1.0 CA A:HIS191 5.0 15.0 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:18.5 occ:1.00 O B:GGL2 2.0 22.0 1.0 NE2 A:HIS218 2.1 16.1 1.0 NE2 A:HIS224 2.1 22.2 1.0 NE2 A:HIS214 2.1 18.7 1.0 C B:GGL2 2.7 22.3 1.0 CE1 A:HIS218 3.0 18.1 1.0 CE1 A:HIS214 3.0 20.1 1.0 CE1 A:HIS224 3.1 27.3 1.0 CD2 A:HIS224 3.1 19.4 1.0 CD2 A:HIS214 3.1 16.6 1.0 CD2 A:HIS218 3.2 17.7 1.0 ND1 A:HIS218 4.2 17.3 1.0 ND1 A:HIS224 4.2 26.0 1.0 ND1 A:HIS214 4.2 20.0 1.0 CG A:HIS224 4.2 20.4 1.0 CA B:GGL2 4.2 21.1 1.0 CG A:HIS214 4.2 18.4 1.0 CG A:HIS218 4.3 16.9 1.0 N B:GLY3 4.3 17.8 1.0 CD B:GGL2 4.4 19.6 1.0 C38 B:7SF1 4.6 26.6 1.0 C39 B:7SF1 4.6 23.4 1.0 CG B:GGL2 4.7 21.3 1.0 CE A:MET232 4.7 17.5 1.0 NE2 A:GLN215 4.8 20.6 1.0 OE1 B:GGL2 4.9 18.9 1.0 CA B:GLY3 4.9 17.4 1.0 CB B:GGL2 4.9 21.3 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