Zinc in PDB 8k4z: 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: 8k4z was solved by M.Kamitani, M.Mima, Y.Oka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	53.60 / 1.70
Space group	I 4
Cell size a, b, c (Å), α, β, γ (°)	75.799, 75.799, 60.53, 90, 90, 90
R / Rfree (%)	20.3 / 23.9

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

Chlorine	(Cl)	2 atoms
Iodine	(I)	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 8k4z). 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: 8k4z:
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:11.1 occ:1.00 OD2 A:ASP165 1.9 13.1 1.0 ND1 A:HIS191 1.9 10.1 1.0 NE2 A:HIS163 2.0 12.4 1.0 NE2 A:HIS178 2.1 9.9 1.0 CE1 A:HIS191 2.8 10.7 1.0 CG A:ASP165 2.9 13.3 1.0 CD2 A:HIS163 2.9 11.7 1.0 CG A:HIS191 3.1 10.2 1.0 CD2 A:HIS178 3.1 9.5 1.0 CE1 A:HIS163 3.1 12.3 1.0 CE1 A:HIS178 3.2 10.2 1.0 OD1 A:ASP165 3.2 12.8 1.0 CB A:HIS191 3.5 10.0 1.0 NE2 A:HIS191 4.0 10.2 1.0 O A:TYR167 4.1 12.1 1.0 CG A:HIS163 4.1 11.5 1.0 CD2 A:HIS191 4.1 10.0 1.0 ND1 A:HIS163 4.1 11.4 1.0 CB A:ASP165 4.2 13.8 1.0 CG A:HIS178 4.2 9.5 1.0 ND1 A:HIS178 4.2 9.7 1.0 CE1 A:PHE180 4.5 14.1 1.0 CZ A:PHE169 4.8 10.0 1.0 CB A:TYR167 4.8 15.8 1.0 CE2 A:PHE169 4.8 10.3 1.0 CA A:HIS191 4.9 10.1 1.0 O A:HOH433 4.9 10.8 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:12.3 occ:1.00 NE2 A:HIS224 2.0 13.4 1.0 NE2 A:HIS214 2.0 10.0 1.0 O B:GGL2 2.0 14.1 1.0 NE2 A:HIS218 2.1 13.5 1.0 C B:GGL2 2.8 12.9 1.0 OXT B:GGL2 2.8 12.8 1.0 CE1 A:HIS214 2.9 10.2 1.0 CD2 A:HIS224 3.0 14.3 1.0 CE1 A:HIS224 3.0 14.7 1.0 CD2 A:HIS218 3.0 12.9 1.0 CE1 A:HIS218 3.1 13.6 1.0 CD2 A:HIS214 3.1 10.1 1.0 ND1 A:HIS214 4.1 10.1 1.0 ND1 A:HIS224 4.1 15.4 1.0 CG A:HIS224 4.1 15.0 1.0 CG A:HIS214 4.2 9.8 1.0 ND1 A:HIS218 4.2 13.3 1.0 CG A:HIS218 4.2 13.2 1.0 CA B:GGL2 4.2 12.7 1.0 CD B:GGL2 4.5 13.8 1.0 N B:GLY3 4.5 14.3 1.0 C38 B:7SF1 4.5 13.6 1.0 C39 B:7SF1 4.5 14.4 1.0 NE2 A:GLN215 4.7 12.0 1.0 CE A:MET232 4.7 13.0 1.0 CG B:GGL2 4.7 13.2 1.0 OE1 B:GGL2 4.8 14.1 1.0 CB B:GGL2 5.0 13.0 1.0 CA B:GLY3 5.0 15.4 1.0

Y.Oka, K.Abe-Sato, H.Tabuse, Y.Yasukawa, T.Yahara, T.Nishimoto, M.Kamitani, T.Fukunaga, N.Ochiai, T.Kumasaka-Abe, K.Hitaka, E.Gunji, H.Ohara, T.Takeda, N.Kojima, T.Asami. Discovery of TP0628103: A Selective Mmp-7 Inhibitor Based on the Mitigation of Oatp Substrate Recognition Through Isoelectric Point Shift Strategy To Be Published.