Zinc 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:

Calcium

(Ca)

3 atoms

The binding sites of Zinc 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 Zinc atom.
In total 2 binding sites of Zinc 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 Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 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 Zinc with other atoms in the Zn 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:Zn301 b:9.1 occ:1.00 NE2 A:HIS218 2.1 8.3 1.0 O2 A:HAE306 2.1 24.4 1.0 NE2 A:HIS228 2.1 9.8 1.0 NE2 A:HIS222 2.1 5.3 1.0 O A:HAE306 2.2 13.2 1.0 C2 A:HAE306 2.9 22.9 1.0 N A:HAE306 3.0 12.4 1.0 CD2 A:HIS218 3.0 7.6 1.0 CD2 A:HIS222 3.0 6.5 1.0 CD2 A:HIS228 3.0 10.7 1.0 CE1 A:HIS228 3.1 11.8 1.0 CE1 A:HIS218 3.1 7.0 1.0 CE1 A:HIS222 3.2 7.9 1.0 O1 A:8NT307 3.5 55.9 1.0 O A:HOH494 4.1 12.1 1.0 ND1 A:HIS218 4.2 6.7 1.0 CG A:HIS218 4.2 6.3 1.0 ND1 A:HIS228 4.2 10.8 1.0 CG A:HIS228 4.2 10.7 1.0 CG A:HIS222 4.2 6.7 1.0 OE2 A:GLU219 4.2 6.8 1.0 ND1 A:HIS222 4.2 7.2 1.0 C1 A:HAE306 4.4 29.1 1.0 C10 A:8NT307 4.4 34.2 1.0 OE1 A:GLU219 4.9 8.7 1.0 C9 A:8NT307 4.9 34.7 1.0 O A:HOH510 4.9 31.6 1.0 CD A:GLU219 4.9 8.2 1.0

Zinc binding site 2 out of 2 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 Zinc with other atoms in the Zn 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:Zn302 b:12.3 occ:1.00 OD2 A:ASP170 2.0 13.1 1.0 ND1 A:HIS196 2.0 9.8 1.0 NE2 A:HIS183 2.0 17.9 1.0 NE2 A:HIS168 2.1 7.6 1.0 CE1 A:HIS183 2.6 23.8 1.0 CD2 A:HIS168 2.9 8.7 1.0 CG A:ASP170 2.9 17.1 1.0 CE1 A:HIS196 3.0 10.2 1.0 CG A:HIS196 3.1 10.7 1.0 CE1 A:HIS168 3.2 9.5 1.0 OD1 A:ASP170 3.2 14.1 1.0 CD2 A:HIS183 3.3 20.5 1.0 CB A:HIS196 3.5 10.2 1.0 ND1 A:HIS183 3.9 22.4 1.0 CG A:HIS168 4.1 10.4 1.0 NE2 A:HIS196 4.1 10.1 1.0 O A:HIS172 4.1 14.5 1.0 CG A:HIS183 4.2 15.1 1.0 ND1 A:HIS168 4.2 11.3 1.0 CD2 A:HIS196 4.2 9.5 1.0 CB A:ASP170 4.3 17.2 1.0 CE1 A:PHE185 4.4 20.4 1.0 CB A:HIS172 4.5 25.6 1.0 CZ A:PHE185 4.7 19.9 1.0 CZ A:PHE174 4.8 7.9 1.0 CE2 A:PHE174 4.8 8.2 1.0 C A:HIS172 5.0 14.7 1.0 CA A:HIS196 5.0 7.3 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