Calcium in PDB 4i03: Human MMP12 in Complex with A Peg-Linked Bifunctional L-Glutamate Motif Inhibitor

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

The structure of Human MMP12 in Complex with A Peg-Linked Bifunctional L-Glutamate Motif Inhibitor, PDB code: 4i03 was solved by E.A.Stura, L.Vera, L.Devel, E.Cassar-Lajeunesse, V.Dive, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	36.67 / 1.70
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	51.790, 60.100, 54.920, 90.00, 116.67, 90.00
R / Rfree (%)	14.4 / 19.4

The structure of Human MMP12 in Complex with A Peg-Linked Bifunctional 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 A Peg-Linked Bifunctional L-Glutamate Motif Inhibitor (pdb code 4i03). 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 A Peg-Linked Bifunctional L-Glutamate Motif Inhibitor, PDB code: 4i03:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Human MMP12 in Complex with A Peg-Linked Bifunctional 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 A Peg-Linked Bifunctional L-Glutamate Motif Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca303 b:23.3 occ:1.00 O A:GLY192 2.2 17.2 1.0 O A:ASP158 2.2 16.8 1.0 O A:HOH414 2.3 28.7 1.0 O A:GLY190 2.4 23.3 1.0 O A:HOH419 2.5 20.4 1.0 OD1 A:ASP194 2.5 17.4 1.0 C A:GLY192 3.4 15.1 1.0 C A:ASP158 3.4 16.6 1.0 CG A:ASP194 3.5 17.5 1.0 C A:GLY190 3.6 22.4 1.0 O A:HOH479 3.9 36.5 1.0 N A:GLY192 3.9 17.8 1.0 C A:ILE191 3.9 19.3 1.0 OD2 A:ASP194 4.0 18.2 1.0 O A:ALA157 4.1 21.2 1.0 O A:ILE191 4.1 18.2 1.0 CA A:ASP158 4.2 17.1 1.0 CA A:GLY192 4.2 16.7 1.0 N A:ASP194 4.3 16.4 1.0 N A:GLY193 4.3 17.4 1.0 N A:ILE159 4.3 17.0 1.0 CA A:ILE191 4.4 19.7 1.0 N A:ILE191 4.4 20.9 1.0 O A:GLY188 4.5 24.9 1.0 CA A:GLY193 4.5 16.4 1.0 CA A:ILE159 4.5 15.6 1.0 CA A:GLY190 4.6 23.4 1.0 N A:GLY190 4.6 24.6 1.0 N A:LEU160 4.6 16.2 1.0 C A:GLY193 4.7 16.6 1.0 CB A:ASP194 4.7 14.0 1.0 O A:HOH407 4.8 25.6 1.0 CA A:ASP194 4.8 15.2 1.0 C A:SER189 4.9 25.0 1.0 C A:ALA157 5.0 20.3 1.0

Calcium binding site 2 out of 3 in the Human MMP12 in Complex with A Peg-Linked Bifunctional 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 A Peg-Linked Bifunctional L-Glutamate Motif Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca304 b:16.6 occ:1.00 OD2 A:ASP124 2.3 15.5 1.0 O A:GLU199 2.3 15.4 1.0 OE2 A:GLU199 2.4 20.6 1.0 O A:GLU201 2.5 15.7 1.0 O A:HOH420 2.5 19.9 1.0 O A:HOH429 2.5 23.6 1.0 OD1 A:ASP124 2.6 15.7 1.0 CG A:ASP124 2.8 15.0 1.0 C A:GLU199 3.4 16.1 1.0 CD A:GLU199 3.5 16.3 1.0 C A:GLU201 3.6 14.3 1.0 CG A:GLU199 4.0 17.2 1.0 CA A:GLU199 4.1 14.6 1.0 OG1 A:THR122 4.1 13.7 1.0 CA A:PHE202 4.2 14.5 1.0 CB A:ASP124 4.3 15.2 1.0 CD1 A:TRP203 4.3 16.9 1.0 N A:PHE202 4.3 14.6 1.0 N A:GLU201 4.4 15.3 1.0 C A:ASP200 4.5 16.9 1.0 N A:ASP200 4.5 15.6 1.0 OE1 A:GLU199 4.6 17.6 1.0 CB A:GLU199 4.6 16.6 1.0 CA A:GLU201 4.7 14.5 1.0 CA A:ASP200 4.7 16.5 1.0 O A:HOH410 4.7 47.6 1.0 O A:HOH442 4.7 26.4 1.0 O A:HOH490 4.8 42.7 1.0 N A:TRP203 4.8 13.3 1.0 NE1 A:TRP203 4.8 16.8 1.0 CD1 A:PHE202 4.9 14.5 1.0 O A:ASP200 5.0 18.2 1.0

Calcium binding site 3 out of 3 in the Human MMP12 in Complex with A Peg-Linked Bifunctional 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 A Peg-Linked Bifunctional L-Glutamate Motif Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca305 b:20.2 occ:1.00 OD2 A:ASP198 2.3 18.6 1.0 OD1 A:ASP175 2.3 22.0 1.0 OE2 A:GLU201 2.3 24.1 1.0 O A:ILE180 2.3 24.4 1.0 O A:GLY176 2.4 22.5 1.0 O A:GLY178 2.4 27.1 1.0 CG A:ASP198 3.4 18.0 1.0 C A:ILE180 3.4 22.4 1.0 CG A:ASP175 3.5 25.1 1.0 C A:GLY178 3.5 27.6 1.0 CD A:GLU201 3.5 23.9 1.0 C A:GLY176 3.6 24.8 1.0 N A:ILE180 3.7 25.1 1.0 N A:GLY178 3.9 27.6 1.0 OD2 A:ASP175 4.0 23.0 1.0 CA A:ILE180 4.0 25.2 1.0 CB A:ASP198 4.1 13.3 1.0 N A:GLY176 4.2 23.4 1.0 C A:GLY179 4.2 26.7 1.0 C A:LYS177 4.2 27.5 0.5 C A:LYS177 4.2 27.4 0.5 CB A:ILE180 4.3 24.0 1.0 CA A:GLY178 4.3 28.0 1.0 CG A:GLU201 4.3 19.9 1.0 C A:ASP175 4.3 24.3 1.0 OD1 A:ASP198 4.4 17.0 1.0 OE1 A:GLU201 4.4 21.4 1.0 CA A:LYS177 4.4 26.8 0.5 N A:ASP175 4.4 21.3 1.0 CA A:GLY176 4.4 24.0 1.0 N A:LYS177 4.5 25.5 0.5 N A:LYS177 4.5 25.6 0.5 CA A:LYS177 4.5 27.0 0.5 N A:GLY179 4.5 27.4 1.0 N A:LEU181 4.5 20.2 1.0 CB A:ASP175 4.7 22.7 1.0 CA A:GLY179 4.7 28.4 1.0 CA A:ASP175 4.7 22.8 1.0 O A:ASP175 4.7 27.0 1.0 O A:GLY179 4.8 27.1 1.0 O A:LYS177 4.8 29.0 0.5 CA A:LEU181 4.8 18.4 1.0 O A:LYS177 4.9 28.9 0.5

C.Antoni, L.Vera, L.Devel, M.P.Catalani, B.Czarny, E.Cassar-Lajeunesse, E.Nuti, A.Rossello, V.Dive, E.A.Stura. Crystallization of Bi-Functional Ligand Protein Complexes. J.Struct.Biol. V. 182 246 2013.
ISSN: ISSN 1047-8477
PubMed: 23567804
DOI: 10.1016/J.JSB.2013.03.015