Calcium in PDB 6ekn: Crystal Structure of MMP12 in Complex with Inhibitor BE7.

All present enzymatic activity of Crystal Structure of MMP12 in Complex with Inhibitor BE7.:
3.4.24.65;

The structure of Crystal Structure of MMP12 in Complex with Inhibitor BE7., PDB code: 6ekn was solved by L.Ciccone, L.Tepshi, E.Nuti, A.Rossello, E.A.Stura, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	36.74 / 1.20
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	51.560, 60.350, 54.560, 90.00, 116.10, 90.00
R / Rfree (%)	14.4 / 17.5

The structure of Crystal Structure of MMP12 in Complex with Inhibitor BE7. also contains other interesting chemical elements:

Zinc

(Zn)

2 atoms

The binding sites of Calcium atom in the Crystal Structure of MMP12 in Complex with Inhibitor BE7. (pdb code 6ekn). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Crystal Structure of MMP12 in Complex with Inhibitor BE7., PDB code: 6ekn:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Crystal Structure of MMP12 in Complex with Inhibitor BE7.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of MMP12 in Complex with Inhibitor BE7. within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca303 b:16.8 occ:1.00 O A:GLY192 2.3 15.1 1.0 O A:HOH414 2.3 22.8 1.0 O A:GLY190 2.3 19.2 1.0 O A:ASP158 2.3 14.2 1.0 OD1 A:ASP194 2.4 14.3 1.0 O A:HOH448 2.4 17.3 1.0 CG A:ASP194 3.4 14.1 1.0 C A:ASP158 3.5 13.3 1.0 C A:GLY192 3.5 14.4 1.0 C A:GLY190 3.5 16.8 1.0 OD2 A:ASP194 3.9 14.7 1.0 C A:ILE191 3.9 15.4 1.0 O A:HOH426 4.0 30.9 1.0 N A:GLY192 4.0 15.2 1.0 O A:ILE191 4.1 15.4 1.0 O A:ALA157 4.1 19.5 1.0 CA A:ASP158 4.3 13.4 1.0 N A:ASP194 4.3 11.8 1.0 CA A:ILE191 4.3 17.8 1.0 CA A:GLY192 4.3 15.2 1.0 N A:ILE191 4.4 18.6 1.0 N A:GLY193 4.4 12.3 1.0 N A:ILE159 4.4 12.8 1.0 O A:GLY188 4.4 19.0 1.0 N A:GLY190 4.5 20.3 1.0 CA A:GLY193 4.5 13.7 1.0 CA A:GLY190 4.5 20.3 1.0 CA A:ILE159 4.6 12.2 1.0 C A:GLY193 4.6 11.8 1.0 CB A:ASP194 4.6 12.8 1.0 N A:LEU160 4.7 12.0 1.0 O A:HOH421 4.8 22.7 1.0 CA A:ASP194 4.8 11.6 1.0 C A:SER189 4.9 18.6 1.0 CH2 A:TRP109 5.0 15.9 1.0

Calcium binding site 2 out of 3 in the Crystal Structure of MMP12 in Complex with Inhibitor BE7.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of MMP12 in Complex with Inhibitor BE7. within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca304 b:13.4 occ:1.00 O A:GLU199 2.3 12.7 1.0 O A:HOH515 2.4 21.4 1.0 O A:HOH507 2.4 19.1 1.0 O A:GLU201 2.4 13.7 1.0 OD2 A:ASP124 2.4 12.5 1.0 OE2 A:GLU199 2.4 12.8 1.0 OD1 A:ASP124 2.6 14.3 1.0 CG A:ASP124 2.9 14.3 1.0 C A:GLU199 3.5 12.5 1.0 CD A:GLU199 3.5 12.6 1.0 C A:GLU201 3.5 11.7 1.0 CG A:GLU199 3.9 14.2 1.0 CA A:GLU199 4.1 12.0 1.0 OG1 A:THR122 4.2 12.6 1.0 CA A:PHE202 4.2 12.1 1.0 N A:PHE202 4.3 11.4 1.0 CB A:ASP124 4.4 11.4 1.0 CD1 A:TRP203 4.4 11.9 1.0 N A:GLU201 4.4 12.4 1.0 C A:ASP200 4.4 14.6 1.0 N A:ASP200 4.5 12.5 1.0 CA A:GLU201 4.6 13.1 1.0 CB A:GLU199 4.6 13.3 1.0 OE1 A:GLU199 4.6 16.1 1.0 CA A:ASP200 4.6 12.7 1.0 O A:HOH434 4.7 25.4 1.0 N A:TRP203 4.8 11.9 1.0 O A:ASP200 4.9 20.1 1.0 NE1 A:TRP203 4.9 11.3 1.0 NH2 A:ARG165 4.9 30.2 1.0 CD1 A:PHE202 4.9 13.9 1.0

Calcium binding site 3 out of 3 in the Crystal Structure of MMP12 in Complex with Inhibitor BE7.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of MMP12 in Complex with Inhibitor BE7. within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca305 b:13.6 occ:1.00 O A:GLY176 2.3 15.3 1.0 OD2 A:ASP198 2.3 13.6 1.0 O A:GLY178 2.3 17.3 1.0 OE2 A:GLU201 2.3 18.0 1.0 O A:ILE180 2.3 11.9 0.7 OD1 A:ASP175 2.3 14.0 1.0 O A:ILE180 2.4 13.0 0.3 C A:GLY178 3.4 19.7 1.0 C A:ILE180 3.5 12.4 0.7 C A:GLY176 3.5 15.6 1.0 CG A:ASP198 3.5 12.9 1.0 CG A:ASP175 3.5 17.2 1.0 C A:ILE180 3.5 12.0 0.3 CD A:GLU201 3.5 17.0 1.0 N A:ILE180 3.8 14.5 0.7 N A:GLY178 3.8 19.1 1.0 N A:ILE180 3.9 14.2 0.3 OD2 A:ASP175 4.1 18.4 1.0 C A:LYS177 4.1 17.0 1.0 N A:GLY176 4.1 15.2 1.0 C A:GLY179 4.2 16.1 1.0 CA A:ILE180 4.2 15.2 0.7 CG A:GLU201 4.2 15.1 1.0 CB A:ASP198 4.2 10.6 1.0 CA A:GLY178 4.2 21.0 1.0 CA A:ILE180 4.3 13.8 0.3 C A:ASP175 4.3 17.4 1.0 CA A:LYS177 4.4 17.4 1.0 N A:ASP175 4.4 15.0 1.0 OD1 A:ASP198 4.4 13.1 1.0 N A:LYS177 4.4 18.3 1.0 CA A:GLY176 4.4 15.6 1.0 OE1 A:GLU201 4.5 18.1 1.0 N A:GLY179 4.5 19.0 1.0 CB A:ILE180 4.5 12.5 0.7 N A:LEU181 4.6 12.7 1.0 CA A:GLY179 4.6 19.5 1.0 CG1 A:ILE180 4.6 13.8 0.3 CB A:ASP175 4.6 16.4 1.0 CA A:ASP175 4.6 15.5 1.0 O A:GLY179 4.6 18.0 1.0 O A:ASP175 4.8 18.7 1.0 CA A:LEU181 4.8 11.6 1.0 O A:LYS177 4.9 25.4 1.0

E.Nuti, D.Cuffaro, E.Bernardini, C.Camodeca, L.Panelli, S.Chaves, L.Ciccone, L.Tepshi, L.Vera, E.Orlandini, S.Nencetti, E.A.Stura, M.A.Santos, V.Dive, A.Rossello. Development of Thioaryl-Based Matrix Metalloproteinase-12 Inhibitors with Alternative Zinc-Binding Groups: Synthesis, Potentiometric, uc(Nmr), and Crystallographic Studies. J. Med. Chem. V. 61 4421 2018.
ISSN: ISSN 1520-4804
PubMed: 29727184
DOI: 10.1021/ACS.JMEDCHEM.8B00096