Calcium 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:

Zinc

(Zn)

2 atoms

The binding sites of Calcium 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 Calcium atom.
In total 3 binding sites of Calcium where determined in the Human MMP12 in Complex with Non-Zinc Chelating Inhibitor, PDB code: 3lir:
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:14.3 occ:1.00 O A:ASP158 2.4 10.0 1.0 O A:GLY190 2.4 16.7 1.0 O A:GLY192 2.4 10.8 1.0 OD2 A:ASP194 2.4 10.7 1.0 O A:HOH17 2.5 19.5 1.0 O A:HOH24 2.5 15.4 1.0 O A:HOH73 3.4 31.2 1.0 CG A:ASP194 3.4 15.5 1.0 C A:ASP158 3.5 9.6 1.0 C A:GLY190 3.6 19.6 1.0 C A:GLY192 3.6 11.8 1.0 OD1 A:ASP194 3.8 14.9 1.0 C A:ILE191 4.0 15.9 1.0 N A:GLY192 4.1 15.2 1.0 O A:ILE191 4.2 13.6 1.0 N A:ASP194 4.2 12.3 1.0 O A:ALA157 4.3 14.7 1.0 CA A:ASP158 4.3 11.6 1.0 O A:GLY188 4.4 16.3 1.0 CA A:ILE191 4.4 15.9 1.0 N A:GLY190 4.4 19.6 1.0 CA A:GLY192 4.4 13.4 1.0 N A:ILE191 4.4 16.0 1.0 CA A:GLY190 4.5 23.5 1.0 N A:ILE159 4.5 9.6 1.0 N A:GLY193 4.6 12.9 1.0 CA A:ILE159 4.6 10.2 1.0 CB A:ASP194 4.6 10.1 1.0 N A:LEU160 4.6 11.7 1.0 O A:HOH9 4.6 14.0 1.0 C A:GLY193 4.6 14.4 1.0 CA A:GLY193 4.7 9.1 1.0 CA A:ASP194 4.8 9.8 1.0 C A:SER189 4.8 18.9 1.0 O A:HOH331 4.8 30.8 1.0 CH2 A:TRP109 4.9 13.9 1.0 O A:HOH339 4.9 45.8 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:15.6 occ:1.00 O A:GLU199 2.4 11.3 1.0 OE2 A:GLU199 2.4 11.4 1.0 O A:GLU201 2.5 15.1 1.0 OD2 A:ASP124 2.5 12.9 1.0 O A:HOH36 2.5 12.2 1.0 O A:HOH25 2.6 13.4 1.0 OD1 A:ASP124 2.6 11.9 1.0 CG A:ASP124 2.9 15.9 1.0 CD A:GLU199 3.5 12.3 1.0 C A:GLU199 3.5 12.4 1.0 C A:GLU201 3.6 13.8 1.0 CG A:GLU199 3.8 11.1 1.0 OG1 A:THR122 4.1 10.8 1.0 CA A:GLU199 4.1 11.8 1.0 CA A:PHE202 4.3 13.9 1.0 CD1 A:TRP203 4.4 10.1 1.0 N A:PHE202 4.4 13.6 1.0 CB A:ASP124 4.4 14.3 1.0 O A:HOH51 4.4 24.8 1.0 N A:GLU201 4.4 12.6 1.0 C A:ASP200 4.6 15.0 1.0 N A:ASP200 4.6 13.8 1.0 OE1 A:GLU199 4.6 12.0 1.0 O A:HOH69 4.6 25.7 1.0 O A:HOH93 4.6 21.6 1.0 CB A:GLU199 4.6 11.7 1.0 CA A:GLU201 4.7 14.8 1.0 CA A:ASP200 4.7 14.9 1.0 N A:TRP203 4.8 13.9 1.0 NE1 A:TRP203 4.8 10.6 1.0 CD1 A:PHE202 4.9 16.3 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:11.4 occ:1.00 O A:ILE180 2.3 11.2 1.0 OE2 A:GLU201 2.3 18.5 1.0 O A:GLY176 2.3 13.0 1.0 OD2 A:ASP175 2.4 12.9 1.0 OD1 A:ASP198 2.4 11.9 1.0 O A:GLY178 2.4 13.4 1.0 C A:ILE180 3.4 11.4 1.0 CG A:ASP198 3.4 11.6 1.0 CG A:ASP175 3.5 17.0 1.0 C A:GLY176 3.5 16.7 1.0 CD A:GLU201 3.6 14.7 1.0 C A:GLY178 3.6 19.6 1.0 N A:ILE180 3.9 15.6 1.0 N A:GLY178 3.9 21.6 1.0 CB A:ASP198 4.1 10.1 1.0 OD1 A:ASP175 4.1 13.5 1.0 CA A:ILE180 4.1 10.5 1.0 N A:GLY176 4.1 9.3 1.0 C A:LYS177 4.2 19.3 1.0 N A:ASP175 4.2 13.9 1.0 C A:GLY179 4.2 18.6 1.0 OE1 A:GLU201 4.3 16.7 1.0 C A:ASP175 4.3 14.2 1.0 CA A:GLY178 4.3 18.4 1.0 OD2 A:ASP198 4.4 8.4 1.0 CA A:LYS177 4.4 15.2 1.0 N A:LYS177 4.4 16.8 1.0 N A:LEU181 4.4 10.1 1.0 CA A:GLY176 4.5 16.3 1.0 CB A:ILE180 4.5 15.5 1.0 CG A:GLU201 4.5 14.2 1.0 CA A:ASP175 4.6 11.5 1.0 N A:GLY179 4.6 19.0 1.0 CA A:LEU181 4.6 10.0 1.0 CB A:ASP175 4.7 15.0 1.0 CA A:GLY179 4.7 18.1 1.0 O A:GLY179 4.7 11.9 1.0 O A:ASP175 4.8 11.1 1.0 O A:LYS177 4.8 23.5 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