Calcium 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
Zinc	(Zn)	2 atoms

The binding sites of Calcium 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 Calcium atom.
In total 3 binding sites of Calcium where determined in the Human MMP12 in Complex with Non-Zinc Chelating Inhibitor, PDB code: 3lil:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Human MMP12 in Complex with Non-Zinc Chelating Inhibitor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca 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:Ca266 b:11.1 occ:1.00 O A:ASP158 2.3 11.2 1.0 O A:GLY192 2.3 10.7 1.0 O A:HOH24 2.4 11.4 1.0 O A:GLY190 2.4 13.0 1.0 O A:HOH17 2.4 16.7 1.0 OD2 A:ASP194 2.5 11.3 1.0 O A:HOH356 3.1 33.9 1.0 CG A:ASP194 3.4 12.8 1.0 C A:ASP158 3.5 12.2 1.0 C A:GLY192 3.5 14.5 1.0 C A:GLY190 3.6 19.0 1.0 OD1 A:ASP194 3.8 12.0 1.0 C A:ILE191 4.0 14.8 1.0 N A:GLY192 4.1 13.9 1.0 O A:ILE191 4.1 10.9 1.0 O A:ALA157 4.2 18.9 1.0 N A:ASP194 4.3 9.3 1.0 CA A:ASP158 4.3 11.5 1.0 CA A:GLY192 4.4 11.9 1.0 N A:GLY190 4.4 15.5 1.0 CA A:ILE191 4.4 15.1 1.0 O A:GLY188 4.4 16.1 1.0 N A:ILE159 4.4 10.3 1.0 N A:ILE191 4.4 14.7 1.0 CA A:GLY190 4.5 19.7 1.0 N A:GLY193 4.5 10.6 1.0 O A:HOH350 4.6 42.3 1.0 CA A:ILE159 4.6 9.1 1.0 N A:LEU160 4.6 9.7 0.3 CA A:GLY193 4.6 9.3 1.0 CB A:ASP194 4.6 10.3 1.0 N A:LEU160 4.6 9.7 0.7 C A:GLY193 4.6 11.5 1.0 O A:HOH9 4.7 18.8 1.0 O A:HOH354 4.8 34.1 1.0 CA A:ASP194 4.8 8.9 1.0 C A:SER189 4.8 16.6 1.0 CH2 A:TRP109 4.9 10.6 1.0 O A:HOH71 5.0 32.0 1.0

Calcium binding site 2 out of 3 in the Human MMP12 in Complex with Non-Zinc Chelating Inhibitor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca 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:Ca267 b:15.5 occ:1.00 O A:GLU199 2.4 12.6 1.0 OD2 A:ASP124 2.4 12.6 1.0 O A:GLU201 2.4 11.7 1.0 OE2 A:GLU199 2.5 13.6 1.0 O A:HOH25 2.5 14.9 1.0 O A:HOH36 2.6 16.1 1.0 OD1 A:ASP124 2.7 12.8 1.0 CG A:ASP124 2.9 13.8 1.0 CD A:GLU199 3.5 12.1 1.0 C A:GLU199 3.5 11.9 1.0 C A:GLU201 3.6 15.5 1.0 CG A:GLU199 3.9 12.2 1.0 OG1 A:THR122 4.1 11.8 1.0 CA A:GLU199 4.2 12.9 1.0 CA A:PHE202 4.2 15.5 1.0 CD1 A:TRP203 4.3 11.7 1.0 CB A:ASP124 4.4 9.5 1.0 N A:GLU201 4.4 14.3 1.0 N A:PHE202 4.4 10.6 1.0 O A:HOH68 4.5 29.9 1.0 O A:HOH50 4.5 28.6 1.0 C A:ASP200 4.5 21.0 1.0 N A:ASP200 4.6 13.1 1.0 OE1 A:GLU199 4.6 15.7 1.0 CB A:GLU199 4.7 12.8 1.0 CA A:GLU201 4.7 14.7 1.0 CA A:ASP200 4.7 17.2 1.0 O A:HOH89 4.7 22.1 1.0 N A:TRP203 4.8 12.7 1.0 NE1 A:TRP203 4.8 10.6 1.0 O A:HOH12 4.8 24.2 1.0 CD1 A:PHE202 4.9 18.3 1.0 O A:ASP200 5.0 18.9 1.0

Calcium binding site 3 out of 3 in the Human MMP12 in Complex with Non-Zinc Chelating Inhibitor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Human MMP12 in Complex with Non-Zinc Chelating Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca268 b:12.1 occ:1.00 OD1 A:ASP198 2.2 7.8 1.0 OE2 A:GLU201 2.3 16.8 1.0 O A:ILE180 2.3 12.2 1.0 O A:GLY178 2.4 15.1 1.0 O A:GLY176 2.4 15.0 1.0 OD2 A:ASP175 2.4 11.8 1.0 CG A:ASP198 3.3 11.0 1.0 C A:ILE180 3.5 11.9 1.0 CD A:GLU201 3.5 19.1 1.0 CG A:ASP175 3.5 15.2 1.0 C A:GLY178 3.5 20.6 1.0 C A:GLY176 3.6 17.9 1.0 N A:GLY178 3.8 15.3 1.0 N A:ILE180 3.9 14.5 1.0 CB A:ASP198 4.0 10.2 1.0 OD1 A:ASP175 4.1 16.0 1.0 N A:GLY176 4.2 13.7 1.0 C A:LYS177 4.2 18.8 1.0 CA A:ILE180 4.2 16.1 1.0 C A:GLY179 4.2 16.1 1.0 CA A:GLY178 4.3 22.6 1.0 OD2 A:ASP198 4.3 10.7 1.0 C A:ASP175 4.3 16.6 1.0 N A:ASP175 4.3 14.2 1.0 OE1 A:GLU201 4.3 16.4 1.0 CG A:GLU201 4.4 12.2 1.0 CA A:LYS177 4.4 17.1 1.0 N A:LYS177 4.4 15.3 1.0 CA A:GLY176 4.5 16.2 1.0 N A:LEU181 4.5 9.5 1.0 CB A:ILE180 4.5 13.0 1.0 N A:GLY179 4.6 16.4 1.0 CA A:LEU181 4.6 8.9 1.0 CA A:ASP175 4.7 14.1 1.0 CA A:GLY179 4.7 14.6 1.0 O A:ASP175 4.7 17.1 1.0 CB A:ASP175 4.7 12.0 1.0 O A:GLY179 4.7 13.4 1.0 O A:LYS177 4.8 22.4 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