Zinc in PDB 3lil: Human MMP12 in Complex with Non-Zinc Chelating Inhibitor

All present enzymatic activity of Human MMP12 in Complex with Non-Zinc Chelating Inhibitor:
3.4.24.65;

The structure of Human MMP12 in Complex with Non-Zinc Chelating Inhibitor, PDB code: 3lil was solved by E.A.Stura, V.Dive, L.Devel, B.Czarny, L.Vera, F.Beau, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.32 / 1.80
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	68.782, 62.667, 37.648, 90.00, 90.00, 90.00
R / Rfree (%)	15.4 / 19

The structure of Human MMP12 in Complex with Non-Zinc Chelating Inhibitor also contains other interesting chemical elements:

Chlorine	(Cl)	1 atom
Calcium	(Ca)	3 atoms

The binding sites of Zinc atom in the Human MMP12 in Complex with Non-Zinc Chelating Inhibitor (pdb code 3lil). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Human MMP12 in Complex with Non-Zinc Chelating Inhibitor, PDB code: 3lil:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Human MMP12 in Complex with Non-Zinc Chelating Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Human MMP12 in Complex with Non-Zinc Chelating Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn264 b:13.2 occ:1.00 NE2 A:HIS218 2.1 10.6 1.0 NE2 A:HIS228 2.1 10.3 1.0 NE2 A:HIS222 2.1 12.1 1.0 O2 A:HAE302 2.2 13.9 0.8 O A:HAE302 2.3 16.4 1.0 C2 A:HAE302 3.0 19.1 0.7 CD2 A:HIS222 3.0 11.2 1.0 CD2 A:HIS218 3.0 11.5 1.0 CE1 A:HIS228 3.0 15.6 1.0 CD2 A:HIS228 3.0 15.5 1.0 CE1 A:HIS218 3.1 12.4 1.0 N A:HAE302 3.1 14.0 0.9 CE1 A:HIS222 3.2 13.5 1.0 C1 A:EEA301 4.0 16.3 1.0 ND1 A:HIS228 4.1 11.3 1.0 ND1 A:HIS218 4.2 10.2 1.0 CG A:HIS228 4.2 14.4 1.0 CG A:HIS218 4.2 8.1 1.0 CG A:HIS222 4.2 12.6 1.0 ND1 A:HIS222 4.2 11.1 1.0 O A:HOH1 4.2 14.7 1.0 OE1 A:GLU219 4.3 13.5 1.0 O A:HOH101 4.3 19.7 1.0 C1 A:HAE302 4.5 19.6 1.0 C2 A:EEA301 4.6 17.3 1.0 O A:HOH97 4.8 38.5 1.0 CE A:MET236 4.9 11.1 1.0

Zinc binding site 2 out of 2 in the Human MMP12 in Complex with Non-Zinc Chelating Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Human MMP12 in Complex with Non-Zinc Chelating Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn265 b:11.9 occ:1.00 NE2 A:HIS183 2.0 12.2 1.0 OD2 A:ASP170 2.0 10.3 1.0 NE2 A:HIS168 2.0 9.2 1.0 ND1 A:HIS196 2.1 18.4 1.0 CE1 A:HIS183 2.7 18.2 1.0 CG A:ASP170 2.9 11.6 1.0 CD2 A:HIS168 2.9 7.4 1.0 CE1 A:HIS196 3.1 10.1 1.0 CE1 A:HIS168 3.1 11.7 1.0 OD1 A:ASP170 3.1 13.2 1.0 CG A:HIS196 3.1 12.2 1.0 CD2 A:HIS183 3.2 18.6 1.0 CB A:HIS196 3.5 6.9 1.0 ND1 A:HIS183 3.9 19.8 1.0 CG A:HIS168 4.1 11.2 1.0 O A:HIS172 4.1 15.9 1.0 ND1 A:HIS168 4.2 8.6 1.0 CG A:HIS183 4.2 14.8 1.0 NE2 A:HIS196 4.2 11.9 1.0 CD2 A:HIS196 4.3 11.0 1.0 CB A:ASP170 4.3 15.3 1.0 CE2 A:PHE185 4.5 17.4 1.0 CB A:HIS172 4.5 16.2 1.0 O A:HOH100 4.7 27.9 1.0 CZ A:PHE174 4.7 11.6 1.0 O A:HOH3 4.9 12.7 1.0 CZ A:PHE185 4.9 18.1 1.0 C A:HIS172 4.9 14.5 1.0 CE1 A:PHE174 5.0 9.6 1.0 CA A:HIS196 5.0 8.4 1.0

L.Devel, S.Garcia, B.Czarny, F.Beau, E.Lajeunesse, L.Vera, D.Georgiadis, E.Stura, V.Dive. Insights From Selective Non-Phosphinic Inhibitors of Mmp-12 Tailored to Fit with An S1' Loop Canonical Conformation. J.Biol.Chem. V. 285 35900 2010.
ISSN: ISSN 0021-9258
PubMed: 20817735
DOI: 10.1074/JBC.M110.139634