Calcium in PDB 4efs: Human MMP12 in Complex with L-Glutamate Motif Inhibitor

All present enzymatic activity of Human MMP12 in Complex with L-Glutamate Motif Inhibitor:
3.4.24.65;

The structure of Human MMP12 in Complex with L-Glutamate Motif Inhibitor, PDB code: 4efs was solved by E.A.Stura, V.Dive, L.Devel, B.Czarny, F.Beau, L.Vera, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.59 / 1.63
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	68.970, 63.190, 37.510, 90.00, 90.00, 90.00
R / Rfree (%)	15.4 / 19

The structure of Human MMP12 in Complex with L-Glutamate Motif Inhibitor also contains other interesting chemical elements:

Zinc

(Zn)

2 atoms

The binding sites of Calcium atom in the Human MMP12 in Complex with L-Glutamate Motif Inhibitor (pdb code 4efs). 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 L-Glutamate Motif Inhibitor, PDB code: 4efs:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Human MMP12 in Complex with L-Glutamate Motif 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 L-Glutamate Motif Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca303 b:18.0 occ:1.00 O A:HOH435 2.3 22.1 1.0 O A:GLY192 2.3 15.2 1.0 O A:GLY190 2.3 20.2 1.0 O A:ASP158 2.4 15.1 1.0 OD1 A:ASP194 2.4 15.3 1.0 O A:HOH431 2.5 19.4 1.0 CG A:ASP194 3.4 14.7 1.0 C A:ASP158 3.5 13.6 1.0 C A:GLY192 3.5 14.1 1.0 C A:GLY190 3.5 20.6 1.0 O A:HOH436 3.7 39.0 1.0 OD2 A:ASP194 3.8 14.3 1.0 C A:ILE191 3.9 14.7 1.0 N A:GLY192 4.0 16.3 1.0 O A:ILE191 4.1 15.0 1.0 CA A:ASP158 4.3 12.4 1.0 N A:ASP194 4.3 12.6 1.0 CA A:GLY192 4.3 15.4 1.0 O A:ALA157 4.3 19.6 1.0 CA A:ILE191 4.3 16.3 1.0 O A:GLY188 4.4 20.0 1.0 N A:ILE191 4.4 16.9 1.0 N A:ILE159 4.4 11.7 1.0 N A:GLY190 4.4 21.2 1.0 N A:GLY193 4.5 12.9 1.0 CA A:GLY190 4.5 19.9 1.0 CA A:GLY193 4.5 14.2 1.0 CA A:ILE159 4.5 11.5 1.0 N A:LEU160 4.6 13.1 1.0 C A:GLY193 4.6 13.6 1.0 CB A:ASP194 4.6 13.9 1.0 C A:SER189 4.8 21.1 1.0 O A:HOH432 4.8 24.8 1.0 CA A:ASP194 4.8 11.9 1.0 O A:HOH434 4.8 48.1 1.0 O A:SER189 5.0 18.5 1.0 CH2 A:TRP109 5.0 17.4 1.0

Calcium binding site 2 out of 3 in the Human MMP12 in Complex with L-Glutamate Motif 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 L-Glutamate Motif Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca304 b:19.3 occ:1.00 O A:HOH456 2.3 22.9 1.0 O A:GLU199 2.4 15.9 1.0 O A:GLU201 2.4 16.3 1.0 OD1 A:ASP124 2.4 18.0 1.0 OE2 A:GLU199 2.4 20.3 1.0 O A:HOH455 2.4 24.6 1.0 OD2 A:ASP124 2.7 21.4 1.0 CG A:ASP124 2.9 20.6 1.0 CD A:GLU199 3.5 19.3 1.0 C A:GLU199 3.5 14.7 1.0 C A:GLU201 3.6 15.8 1.0 CG A:GLU199 3.8 18.6 1.0 CA A:GLU199 4.1 14.3 1.0 OG1 A:THR122 4.1 16.5 1.0 CA A:PHE202 4.2 16.2 1.0 CD1 A:TRP203 4.3 14.9 1.0 N A:PHE202 4.3 15.2 1.0 N A:GLU201 4.4 14.0 1.0 CB A:ASP124 4.4 17.7 1.0 O A:HOH460 4.4 37.8 1.0 O A:HOH459 4.5 30.4 1.0 N A:ASP200 4.6 13.7 1.0 C A:ASP200 4.6 16.7 1.0 CA A:GLU201 4.6 13.9 1.0 OE1 A:GLU199 4.6 18.4 1.0 CB A:GLU199 4.6 12.1 1.0 CA A:ASP200 4.7 16.0 1.0 N A:TRP203 4.8 14.9 1.0 O A:HOH461 4.8 33.9 1.0 NE1 A:TRP203 4.8 12.8 1.0 CD1 A:PHE202 4.9 22.2 1.0 O A:HOH458 4.9 28.3 1.0 O A:HOH457 4.9 39.3 1.0 O A:ASP200 5.0 19.9 1.0

Calcium binding site 3 out of 3 in the Human MMP12 in Complex with L-Glutamate Motif 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 L-Glutamate Motif Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca305 b:13.3 occ:1.00 OD2 A:ASP198 2.2 13.6 1.0 O A:ILE180 2.3 15.3 1.0 OE2 A:GLU201 2.3 22.1 1.0 O A:GLY176 2.3 18.3 1.0 OD1 A:ASP175 2.3 16.7 1.0 O A:GLY178 2.3 19.4 1.0 CG A:ASP198 3.4 13.9 1.0 C A:ILE180 3.4 15.1 1.0 CD A:GLU201 3.5 18.1 1.0 C A:GLY176 3.5 18.8 1.0 CG A:ASP175 3.5 20.6 1.0 C A:GLY178 3.6 19.6 1.0 N A:GLY178 3.8 20.8 1.0 N A:ILE180 3.9 15.0 1.0 CB A:ASP198 4.0 12.1 1.0 N A:GLY176 4.0 15.6 1.0 OD2 A:ASP175 4.1 18.9 1.0 CA A:ILE180 4.1 14.0 1.0 C A:LYS177 4.2 21.6 1.0 C A:GLY179 4.2 17.1 1.0 C A:ASP175 4.2 16.8 1.0 N A:ASP175 4.3 16.2 1.0 OE1 A:GLU201 4.3 19.3 1.0 CA A:GLY178 4.3 22.0 1.0 OD1 A:ASP198 4.3 12.8 1.0 CA A:GLY176 4.4 17.9 1.0 N A:LEU181 4.4 13.3 1.0 N A:LYS177 4.4 20.1 1.0 CA A:LYS177 4.4 21.0 1.0 CG A:GLU201 4.4 14.3 1.0 CB A:ILE180 4.5 15.9 1.0 N A:GLY179 4.6 18.4 1.0 CA A:ASP175 4.6 15.4 1.0 CA A:LEU181 4.6 12.1 1.0 CB A:ASP175 4.7 15.4 1.0 O A:ASP175 4.7 18.0 1.0 CA A:GLY179 4.7 16.8 1.0 O A:LYS177 4.7 24.1 1.0 O A:GLY179 4.8 17.9 1.0

L.Devel, F.Beau, M.Amoura, L.Vera, E.Cassar-Lajeunesse, S.Garcia, B.Czarny, E.A.Stura, V.Dive. Simple Pseudo-Dipeptides with A P2' Glutamate: A Novel Inhibitor Family of Matrix Metalloproteases and Other Metzincins. J.Biol.Chem. V. 287 26647 2012.
ISSN: ISSN 0021-9258
PubMed: 22689580
DOI: 10.1074/JBC.M112.380782