Calcium in PDB 3tsk: 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: 3tsk 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)	33.33 / 2.00
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	69.710, 63.060, 37.950, 90.00, 90.00, 90.00
R / Rfree (%)	16.2 / 23.2

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 3tsk). 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: 3tsk:
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:34.2 occ:1.00 O A:GLY190 2.3 26.2 1.0 OD2 A:ASP194 2.4 15.9 1.0 O A:HOH415 2.5 31.3 1.0 O A:GLY192 2.6 21.0 1.0 O A:ASP158 2.6 21.1 1.0 O A:HOH422 2.9 24.8 1.0 O A:HOH492 3.1 37.8 1.0 CG A:ASP194 3.3 16.7 1.0 C A:GLY190 3.5 26.0 1.0 C A:ASP158 3.7 22.2 1.0 OD1 A:ASP194 3.7 17.5 1.0 C A:GLY192 3.7 21.7 1.0 C A:ILE191 4.0 24.0 1.0 N A:GLY192 4.2 22.0 1.0 O A:ILE191 4.2 24.0 1.0 CA A:ILE191 4.3 24.8 1.0 N A:ILE191 4.3 25.4 1.0 O A:ALA157 4.3 24.8 1.0 O A:GLY188 4.4 25.2 1.0 N A:ASP194 4.4 19.0 1.0 CA A:GLY192 4.5 22.6 1.0 N A:GLY190 4.5 27.4 1.0 N A:ILE159 4.5 21.7 1.0 CA A:ASP158 4.5 23.5 1.0 CA A:GLY190 4.6 26.7 1.0 N A:LEU160 4.6 21.2 1.0 CA A:ILE159 4.6 21.5 1.0 CB A:ASP194 4.6 17.7 1.0 N A:GLY193 4.7 21.5 1.0 C A:GLY193 4.8 19.5 1.0 O A:HOH566 4.8 43.5 1.0 CA A:GLY193 4.8 19.4 1.0 C A:SER189 4.8 27.9 1.0 CA A:ASP194 4.9 18.3 1.0 O A:HOH408 5.0 38.3 1.0 CH2 A:TRP109 5.0 26.2 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:28.9 occ:1.00 OD2 A:ASP124 2.3 31.8 1.0 O A:GLU201 2.4 22.6 1.0 O A:GLU199 2.4 23.6 1.0 OE2 A:GLU199 2.5 26.6 1.0 O A:HOH434 2.6 22.6 1.0 O A:HOH423 2.8 35.7 1.0 OD1 A:ASP124 3.0 32.7 1.0 CG A:ASP124 3.0 29.6 1.0 C A:GLU199 3.5 23.3 1.0 C A:GLU201 3.5 24.0 1.0 CD A:GLU199 3.6 26.4 1.0 CA A:PHE202 4.0 24.2 1.0 CG A:GLU199 4.1 23.8 1.0 CA A:GLU199 4.2 23.0 1.0 N A:PHE202 4.2 23.3 1.0 OG1 A:THR122 4.2 21.9 1.0 CD1 A:TRP203 4.3 15.7 1.0 O A:HOH560 4.3 32.0 1.0 O A:HOH453 4.4 27.5 1.0 N A:GLU201 4.4 24.9 1.0 CB A:ASP124 4.5 28.9 1.0 C A:ASP200 4.5 26.6 1.0 N A:ASP200 4.5 25.1 1.0 CA A:GLU201 4.6 24.4 1.0 N A:TRP203 4.7 23.3 1.0 CA A:ASP200 4.7 26.5 1.0 OE1 A:GLU199 4.7 25.6 1.0 NE1 A:TRP203 4.8 14.1 1.0 CB A:GLU199 4.8 23.2 1.0 O A:HOH573 4.8 33.4 1.0 O A:ASP200 4.9 27.5 1.0 O A:HOH411 4.9 31.6 1.0 C A:PHE202 4.9 24.0 1.0 CB A:PHE202 5.0 25.0 1.0 CD1 A:PHE202 5.0 30.6 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:23.2 occ:1.00 OE2 A:GLU201 2.2 22.8 1.0 OD2 A:ASP175 2.3 20.1 1.0 O A:GLY176 2.3 20.8 1.0 O A:ILE180 2.3 19.8 1.0 OD1 A:ASP198 2.4 12.2 1.0 O A:GLY178 2.4 25.4 1.0 CD A:GLU201 3.4 23.4 1.0 CG A:ASP198 3.4 20.6 1.0 C A:ILE180 3.5 19.8 1.0 CG A:ASP175 3.5 20.1 1.0 C A:GLY176 3.5 22.2 1.0 C A:GLY178 3.6 24.7 1.0 N A:GLY178 3.9 25.6 1.0 N A:GLY176 4.0 20.1 1.0 OE1 A:GLU201 4.0 23.6 1.0 OD1 A:ASP175 4.1 17.5 1.0 N A:ILE180 4.1 20.8 1.0 CB A:ASP198 4.1 22.0 1.0 C A:LYS177 4.1 25.7 1.0 C A:ASP175 4.2 21.7 1.0 CA A:ILE180 4.3 19.7 1.0 C A:GLY179 4.3 22.7 1.0 N A:ASP175 4.3 20.3 1.0 CA A:GLY178 4.3 25.4 1.0 OD2 A:ASP198 4.4 19.8 1.0 CA A:GLY176 4.4 20.7 1.0 CA A:LYS177 4.4 25.5 1.0 N A:LYS177 4.4 22.2 1.0 N A:LEU181 4.4 19.5 1.0 CG A:GLU201 4.6 24.7 1.0 N A:GLY179 4.6 23.5 1.0 CA A:LEU181 4.6 18.5 1.0 CA A:ASP175 4.6 20.2 1.0 CB A:ASP175 4.6 19.4 1.0 O A:ASP175 4.7 22.3 1.0 CA A:GLY179 4.7 23.1 1.0 O A:LYS177 4.7 27.0 1.0 CB A:ILE180 4.7 20.0 1.0 O A:GLY179 4.8 23.1 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