Calcium in PDB 5n5j: Human MMP12 in Complex with 3-(5-(1,2-Dithiolan-3-Yl)Pentanamido) Propane-1-Sulfonate

All present enzymatic activity of Human MMP12 in Complex with 3-(5-(1,2-Dithiolan-3-Yl)Pentanamido) Propane-1-Sulfonate:
3.4.24.65;

The structure of Human MMP12 in Complex with 3-(5-(1,2-Dithiolan-3-Yl)Pentanamido) Propane-1-Sulfonate, PDB code: 5n5j was solved by V.Calderone, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.29 / 1.80
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	50.926, 60.470, 53.844, 90.00, 114.55, 90.00
R / Rfree (%)	12.5 / 19.5

The structure of Human MMP12 in Complex with 3-(5-(1,2-Dithiolan-3-Yl)Pentanamido) Propane-1-Sulfonate also contains other interesting chemical elements:

Zinc

(Zn)

2 atoms

The binding sites of Calcium atom in the Human MMP12 in Complex with 3-(5-(1,2-Dithiolan-3-Yl)Pentanamido) Propane-1-Sulfonate (pdb code 5n5j). 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 3-(5-(1,2-Dithiolan-3-Yl)Pentanamido) Propane-1-Sulfonate, PDB code: 5n5j:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Human MMP12 in Complex with 3-(5-(1,2-Dithiolan-3-Yl)Pentanamido) Propane-1-Sulfonate


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 3-(5-(1,2-Dithiolan-3-Yl)Pentanamido) Propane-1-Sulfonate within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca303 b:11.2 occ:1.00 O A:GLY192 2.3 9.4 1.0 O A:ASP158 2.3 10.7 1.0 O A:HOH416 2.3 14.0 1.0 O A:HOH431 2.3 10.5 1.0 OD1 A:ASP194 2.4 9.7 1.0 O A:GLY190 2.4 19.3 1.0 CG A:ASP194 3.4 9.5 1.0 C A:ASP158 3.4 11.4 1.0 C A:GLY192 3.5 8.9 1.0 C A:GLY190 3.6 18.0 1.0 OD2 A:ASP194 3.8 10.9 1.0 C A:ILE191 4.0 10.4 1.0 N A:GLY192 4.0 10.1 1.0 O A:ALA157 4.1 16.9 1.0 O A:ILE191 4.2 10.9 1.0 O A:HOH417 4.2 25.6 1.0 CA A:ASP158 4.2 10.4 1.0 N A:ASP194 4.2 8.4 1.0 CA A:GLY192 4.3 8.8 1.0 CA A:ILE191 4.3 13.6 1.0 O A:GLY188 4.3 13.7 1.0 O A:HOH503 4.3 36.8 1.0 N A:ILE159 4.4 9.0 1.0 N A:ILE191 4.4 13.5 1.0 N A:GLY193 4.4 9.2 1.0 N A:GLY190 4.5 12.9 1.0 CA A:GLY193 4.5 8.9 1.0 CA A:ILE159 4.5 7.7 1.0 CA A:GLY190 4.6 18.0 1.0 CB A:ASP194 4.6 6.6 1.0 C A:GLY193 4.6 8.2 1.0 N A:LEU160 4.7 6.5 1.0 CA A:ASP194 4.8 6.0 1.0 O A:HOH420 4.8 17.4 1.0 C A:SER189 4.8 14.1 1.0 C A:ALA157 5.0 11.5 1.0

Calcium binding site 2 out of 3 in the Human MMP12 in Complex with 3-(5-(1,2-Dithiolan-3-Yl)Pentanamido) Propane-1-Sulfonate


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 3-(5-(1,2-Dithiolan-3-Yl)Pentanamido) Propane-1-Sulfonate within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca304 b:8.4 occ:1.00 O A:GLU199 2.3 7.3 1.0 O A:HOH473 2.3 12.8 1.0 OE2 A:GLU199 2.4 10.0 1.0 O A:GLU201 2.4 8.9 1.0 OD2 A:ASP124 2.4 8.7 1.0 O A:HOH498 2.4 11.9 1.0 OD1 A:ASP124 2.5 7.5 1.0 CG A:ASP124 2.8 8.7 1.0 C A:GLU199 3.5 8.3 1.0 CD A:GLU199 3.5 9.7 1.0 C A:GLU201 3.6 8.1 1.0 CG A:GLU199 3.9 9.6 1.0 CA A:GLU199 4.1 7.9 1.0 OG1 A:THR122 4.1 6.9 1.0 CA A:PHE202 4.2 9.1 1.0 CB A:ASP124 4.3 8.1 1.0 N A:PHE202 4.3 8.7 1.0 CD1 A:TRP203 4.4 7.0 1.0 N A:GLU201 4.5 8.0 1.0 N A:ASP200 4.5 9.7 1.0 CB A:GLU199 4.6 8.5 1.0 C A:ASP200 4.6 9.4 1.0 OE1 A:GLU199 4.6 10.8 1.0 O A:HOH427 4.6 12.1 1.0 CA A:GLU201 4.7 7.7 1.0 CA A:ASP200 4.7 8.5 1.0 CD1 A:PHE202 4.8 9.7 1.0 N A:TRP203 4.8 8.3 1.0 NE1 A:TRP203 4.8 8.4 1.0 NH2 A:ARG165 4.9 17.7 1.0

Calcium binding site 3 out of 3 in the Human MMP12 in Complex with 3-(5-(1,2-Dithiolan-3-Yl)Pentanamido) Propane-1-Sulfonate


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 3-(5-(1,2-Dithiolan-3-Yl)Pentanamido) Propane-1-Sulfonate within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca305 b:11.4 occ:1.00 OE2 A:GLU201 2.3 15.2 1.0 OD2 A:ASP198 2.3 7.7 1.0 O A:ILE180 2.3 10.2 1.0 O A:GLY176 2.3 12.8 1.0 O A:GLY178 2.3 12.0 1.0 OD1 A:ASP175 2.3 14.2 1.0 CG A:ASP198 3.4 8.1 1.0 C A:ILE180 3.4 11.4 1.0 CD A:GLU201 3.5 10.3 1.0 C A:GLY178 3.5 13.4 1.0 CG A:ASP175 3.5 16.1 1.0 C A:GLY176 3.5 12.6 1.0 N A:GLY178 3.8 13.1 1.0 N A:ILE180 3.9 13.6 1.0 CB A:ASP198 4.0 5.8 1.0 C A:LYS177 4.1 14.4 1.0 OD2 A:ASP175 4.1 13.6 1.0 N A:GLY176 4.2 11.4 1.0 CA A:ILE180 4.3 12.0 1.0 OE1 A:GLU201 4.3 9.3 1.0 C A:GLY179 4.3 11.4 1.0 CA A:GLY178 4.3 13.5 1.0 C A:ASP175 4.3 16.4 1.0 N A:ASP175 4.3 13.4 1.0 OD1 A:ASP198 4.4 9.1 1.0 CA A:LYS177 4.4 14.4 1.0 N A:LYS177 4.4 12.2 1.0 N A:LEU181 4.4 7.1 1.0 CG A:GLU201 4.5 8.2 1.0 CA A:GLY176 4.5 11.7 1.0 N A:GLY179 4.6 12.3 1.0 CA A:LEU181 4.6 9.1 1.0 CA A:ASP175 4.6 14.6 1.0 CB A:ASP175 4.7 16.1 1.0 O A:LYS177 4.7 15.4 1.0 CB A:ILE180 4.7 11.8 1.0 CA A:GLY179 4.7 14.5 1.0 O A:ASP175 4.7 12.2 1.0 O A:GLY179 4.9 15.1 1.0 CD2 A:LEU181 5.0 13.9 1.0

M.Fragai, G.Comito, L.Di Cesare Mannelli, R.Gualdani, V.Calderone, A.Louka, B.Richichi, O.Francesconi, A.Angeli, A.Nocentini, P.Gratteri, P.Chiarugi, C.Ghelardini, F.Tadini-Buoninsegni, C.T.Supuran, C.Nativi. Lipoyl-Homotaurine Derivative (ADM_12) Reverts Oxaliplatin-Induced Neuropathy and Reduces Cancer Cells Malignancy By Inhibiting Carbonic Anhydrase IX (Caix). J. Med. Chem. V. 60 9003 2017.
ISSN: ISSN 1520-4804
PubMed: 29048889
DOI: 10.1021/ACS.JMEDCHEM.7B01237