Calcium in PDB 3tvc: Human MMP13 in Complex with L-Glutamate Motif Inhibitor

The structure of Human MMP13 in Complex with L-Glutamate Motif Inhibitor, PDB code: 3tvc was solved by E.A.Stura, V.Dive, L.Devel, B.Czarny, F.Beau, L.Vera, E.Cassar-Lajeunesse, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.92 / 2.43
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	60.303, 85.160, 40.916, 90.00, 90.00, 90.00
R / Rfree (%)	16.2 / 23.4

The structure of Human MMP13 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 MMP13 in Complex with L-Glutamate Motif Inhibitor (pdb code 3tvc). 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 MMP13 in Complex with L-Glutamate Motif Inhibitor, PDB code: 3tvc:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Human MMP13 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 MMP13 in Complex with L-Glutamate Motif Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:66.0 occ:1.00 OD2 A:ASP128 2.7 38.9 1.0 O A:ASP203 2.7 38.4 1.0 O A:HOH65 2.8 41.5 1.0 O A:GLU205 2.8 29.7 1.0 OD1 A:ASP203 2.8 29.2 1.0 OD1 A:ASP128 3.0 33.8 1.0 CG A:ASP128 3.2 36.0 1.0 C A:ASP203 3.7 33.5 1.0 CG A:ASP203 3.8 37.2 1.0 C A:GLU205 3.8 27.1 1.0 OG1 A:THR126 3.9 22.8 1.0 CA A:ASP203 4.2 30.8 1.0 CA A:THR206 4.4 24.4 1.0 CB A:ASP203 4.4 33.5 1.0 CD A:PRO127 4.5 18.4 1.0 N A:THR206 4.5 31.6 1.0 CB A:ASP128 4.6 27.0 1.0 N A:GLU205 4.6 35.0 1.0 C A:ASP204 4.6 35.2 1.0 OD2 A:ASP203 4.6 33.6 1.0 CD1 A:TRP207 4.6 16.0 1.0 N A:ASP204 4.7 27.4 1.0 CA A:ASP204 4.9 32.8 1.0 CA A:GLU205 4.9 33.2 1.0 O A:ASP204 4.9 42.3 1.0 N A:TRP207 4.9 31.7 1.0

Calcium binding site 2 out of 3 in the Human MMP13 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 MMP13 in Complex with L-Glutamate Motif Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca504 b:18.4 occ:1.00 OE2 A:GLU205 2.3 23.8 1.0 O A:LEU184 2.4 23.2 1.0 OD1 A:ASP179 2.4 21.1 1.0 O A:GLY180 2.4 24.1 1.0 O A:SER182 2.5 24.4 1.0 OD2 A:ASP202 2.5 25.7 1.0 CG A:ASP202 3.5 26.9 1.0 C A:LEU184 3.5 19.5 1.0 CD A:GLU205 3.6 29.6 1.0 C A:GLY180 3.6 28.2 1.0 CG A:ASP179 3.6 36.5 1.0 C A:SER182 3.7 30.8 1.0 N A:LEU184 3.9 24.3 1.0 CB A:ASP202 4.1 22.3 1.0 N A:ASP179 4.1 28.5 1.0 C A:GLY183 4.2 26.6 1.0 CA A:LEU184 4.2 27.0 1.0 N A:SER182 4.2 43.8 1.0 C A:PRO181 4.2 35.0 1.0 C A:ASP179 4.2 25.7 1.0 N A:GLY180 4.2 24.7 1.0 OD2 A:ASP179 4.3 45.9 1.0 OE1 A:GLU205 4.4 36.0 1.0 CG A:GLU205 4.4 32.1 1.0 CB A:LEU184 4.4 32.4 1.0 OD1 A:ASP202 4.5 28.4 1.0 CA A:PRO181 4.5 34.5 1.0 CA A:GLY183 4.5 23.3 1.0 N A:PRO181 4.5 39.2 1.0 N A:GLY183 4.5 39.8 1.0 O A:ASP179 4.5 35.5 1.0 CA A:GLY180 4.5 31.9 1.0 CA A:ASP179 4.5 29.7 1.0 O A:PRO181 4.5 37.3 1.0 CA A:SER182 4.6 37.5 1.0 N A:LEU185 4.6 16.4 1.0 O A:GLY183 4.7 35.1 1.0 CB A:ASP179 4.7 27.2 1.0 CA A:LEU185 4.8 17.2 1.0

Calcium binding site 3 out of 3 in the Human MMP13 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 MMP13 in Complex with L-Glutamate Motif Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca505 b:29.6 occ:1.00 O A:GLY196 2.4 18.2 1.0 O A:ASN194 2.4 30.9 1.0 O A:ASP162 2.5 21.3 1.0 O A:HOH14 2.5 19.6 1.0 OD1 A:ASP198 2.6 22.4 1.0 O A:HOH63 2.7 23.6 1.0 C A:ASN194 3.5 20.9 1.0 C A:GLY196 3.5 23.4 1.0 C A:ASP162 3.6 19.7 1.0 CG A:ASP198 3.7 22.4 1.0 C A:TYR195 3.8 22.6 0.5 O A:HOH30 3.8 16.9 1.0 O A:TYR195 3.9 21.4 0.5 N A:GLY196 3.9 20.3 1.0 C A:TYR195 3.9 22.6 0.5 O A:HOH70 3.9 42.6 1.0 CA A:TYR195 4.1 23.7 0.5 N A:TYR195 4.2 26.2 0.5 CA A:TYR195 4.2 23.7 0.5 N A:TYR195 4.2 26.2 0.5 CA A:GLY196 4.3 16.2 1.0 O A:ALA161 4.3 22.1 1.0 CA A:ASP162 4.3 22.4 1.0 OD2 A:ASP198 4.3 21.8 1.0 O A:TYR195 4.3 21.6 0.5 N A:ASP198 4.3 11.2 1.0 CA A:ASN194 4.5 20.9 1.0 N A:ASN194 4.5 23.1 1.0 O A:GLY192 4.5 28.3 1.0 N A:GLY197 4.6 18.9 1.0 O A:PRO193 4.6 25.0 1.0 N A:ILE163 4.6 19.0 1.0 C A:PRO193 4.7 26.1 1.0 CH2 A:TRP113 4.7 16.3 1.0 CA A:GLY197 4.7 19.4 1.0 CA A:ILE163 4.8 20.6 1.0 C A:GLY197 4.8 17.6 1.0 O A:HOH15 4.8 27.0 1.0 N A:MET164 4.8 23.3 1.0 CB A:ASP198 4.9 22.9 1.0 CA A:ASP198 5.0 19.2 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