Zinc in PDB 8jug: 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: 8jug 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)	48.05 / 1.30
Space group	I 4
Cell size a, b, c (Å), α, β, γ (°)	76.06, 76.06, 61.89, 90, 90, 90
R / Rfree (%)	22.1 / 23.8

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

Calcium	(Ca)	2 atoms
Chlorine	(Cl)	2 atoms
Fluorine	(F)	6 atoms

The binding sites of Zinc atom in the Crystal Structure of Human Mmp-7 in Complex with Inhibitor (pdb code 8jug). 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: 8jug:
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:9.6 occ:1.00 OD2 A:ASP165 2.0 11.1 1.0 NE2 A:HIS178 2.0 8.5 1.0 ND1 A:HIS191 2.0 9.7 1.0 NE2 A:HIS163 2.0 9.6 1.0 CG A:ASP165 2.9 13.8 1.0 CE1 A:HIS191 2.9 8.7 1.0 CE1 A:HIS178 2.9 9.6 1.0 CD2 A:HIS163 2.9 10.2 1.0 CD2 A:HIS178 3.1 9.9 1.0 CG A:HIS191 3.1 8.5 1.0 CE1 A:HIS163 3.1 10.2 1.0 OD1 A:ASP165 3.2 12.9 1.0 CB A:HIS191 3.4 9.0 1.0 ND1 A:HIS178 4.1 9.4 1.0 NE2 A:HIS191 4.1 8.1 1.0 CG A:HIS163 4.1 10.4 1.0 O A:TYR167 4.1 12.0 1.0 ND1 A:HIS163 4.2 10.7 1.0 CG A:HIS178 4.2 9.3 1.0 CD2 A:HIS191 4.2 8.9 1.0 CE2 A:PHE180 4.2 11.8 1.0 CB A:ASP165 4.3 13.9 1.0 CZ A:PHE180 4.4 13.3 1.0 CZ A:PHE169 4.7 9.4 1.0 CB A:TYR167 4.8 16.1 1.0 CE2 A:PHE169 4.8 10.2 1.0 O A:HOH437 4.8 11.9 1.0 CA A:HIS191 4.9 8.8 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:10.3 occ:1.00 O C:GGL2 1.9 12.2 0.5 O C:GGL2 2.0 13.8 0.5 NE2 A:HIS224 2.0 12.5 1.0 NE2 A:HIS214 2.0 9.4 1.0 NE2 A:HIS218 2.0 11.1 1.0 C C:GGL2 2.8 11.2 0.5 C C:GGL2 2.8 12.8 0.5 CE1 A:HIS218 2.9 11.6 1.0 CE1 A:HIS224 3.0 12.6 1.0 CD2 A:HIS214 3.0 9.1 1.0 OXT C:GGL2 3.0 11.5 0.5 OXT C:GGL2 3.0 13.1 0.5 CE1 A:HIS214 3.0 9.8 1.0 CD2 A:HIS224 3.0 13.2 1.0 CD2 A:HIS218 3.1 10.2 1.0 ND1 A:HIS214 4.1 9.8 1.0 ND1 A:HIS224 4.1 14.4 1.0 ND1 A:HIS218 4.1 11.0 1.0 CG A:HIS214 4.1 9.2 1.0 CG A:HIS224 4.1 12.8 1.0 N C:GLY3 4.2 7.8 0.5 CG A:HIS218 4.2 9.1 1.0 CA C:GGL2 4.2 10.3 0.5 N C:GLY3 4.2 12.8 0.5 CA C:GGL2 4.2 11.9 0.5 CD C:GGL2 4.3 7.2 0.5 CD C:GGL2 4.3 10.5 0.5 CG C:GGL2 4.4 8.3 0.5 CA C:GLY3 4.5 13.3 0.5 OE1 C:GGL2 4.5 9.1 0.5 CE A:MET232 4.6 10.8 1.0 C38 C:7SF1 4.6 14.4 0.5 C38 C:7SF1 4.6 12.7 0.5 C39 C:7SF1 4.6 14.9 0.5 C39 C:7SF1 4.6 12.7 0.5 O A:HOH469 4.6 31.4 1.0 OE1 C:GGL2 4.6 6.5 0.5 NE2 A:GLN215 4.7 10.0 1.0 CG C:GGL2 4.7 11.0 0.5 CA C:GLY3 4.8 7.5 0.5 CB C:GGL2 4.8 9.5 0.5 CB C:GGL2 4.9 11.9 0.5

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