Zinc in PDB 3lir: 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: 3lir 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)	46.59 / 1.90
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	68.997, 63.171, 37.573, 90.00, 90.00, 90.00
R / Rfree (%)	15.9 / 21.1

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

Calcium

(Ca)

3 atoms

The binding sites of Zinc atom in the Human MMP12 in Complex with Non-Zinc Chelating Inhibitor (pdb code 3lir). 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: 3lir:
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:12.1 occ:1.00 O A:GLY2 2.1 22.2 1.0 NE2 A:HIS222 2.1 9.4 1.0 NE2 A:HIS218 2.1 10.0 1.0 NE2 A:HIS228 2.1 13.1 1.0 OXT A:GLY2 2.6 17.1 1.0 C A:GLY2 2.7 23.6 1.0 CD2 A:HIS228 3.0 13.7 1.0 CE1 A:HIS218 3.0 8.4 1.0 CD2 A:HIS222 3.0 9.2 1.0 CE1 A:HIS222 3.1 11.8 1.0 CD2 A:HIS218 3.1 12.6 1.0 CE1 A:HIS228 3.2 19.8 1.0 ND1 A:HIS218 4.1 10.3 1.0 CA A:GLY2 4.2 21.3 1.0 ND1 A:HIS222 4.2 8.8 1.0 CG A:HIS222 4.2 10.1 1.0 CG A:HIS228 4.2 15.8 1.0 O A:HOH272 4.2 27.7 1.0 CG A:HIS218 4.2 13.6 1.0 ND1 A:HIS228 4.2 14.6 1.0 C12 A:EEC1 4.4 19.8 1.0 O A:HOH269 4.6 19.4 1.0 N A:GLY2 4.6 29.5 1.0 OE1 A:GLU219 4.7 13.1 1.0 CE A:MET236 4.8 13.2 1.0 O A:HOH102 4.8 30.6 1.0 C13 A:EEC1 5.0 21.3 1.0 O A:HOH56 5.0 37.8 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:11.0 occ:1.00 NE2 A:HIS168 2.1 10.2 1.0 OD1 A:ASP170 2.1 11.9 1.0 ND1 A:HIS196 2.1 10.6 1.0 NE2 A:HIS183 2.1 11.9 1.0 CE1 A:HIS183 2.9 19.9 1.0 CD2 A:HIS168 3.0 7.1 1.0 CG A:ASP170 3.0 16.0 1.0 CE1 A:HIS196 3.1 12.5 1.0 CG A:HIS196 3.1 10.7 1.0 CE1 A:HIS168 3.1 10.8 1.0 OD2 A:ASP170 3.2 10.2 1.0 CD2 A:HIS183 3.3 20.7 1.0 CB A:HIS196 3.4 8.0 1.0 CG A:HIS168 4.1 10.7 1.0 ND1 A:HIS183 4.1 18.1 1.0 ND1 A:HIS168 4.2 8.6 1.0 NE2 A:HIS196 4.2 11.6 1.0 O A:HIS172 4.2 12.6 1.0 CD2 A:HIS196 4.2 11.9 1.0 CG A:HIS183 4.3 14.3 1.0 CE2 A:PHE185 4.4 17.5 1.0 CB A:ASP170 4.4 15.3 1.0 CZ A:PHE174 4.6 9.8 1.0 CZ A:PHE185 4.7 23.1 1.0 CE1 A:PHE174 4.8 10.7 1.0 CA A:HIS196 4.9 11.1 1.0 O A:HOH3 5.0 11.2 1.0 CB A:HIS172 5.0 25.2 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