Zinc in PDB 5n5k: Human Catalytic Mmp-12 in Complex with 5-(1,2-Dithiolan-3-Yl)-N-(3- Hydroxypropyl)Pentanamide

All present enzymatic activity of Human Catalytic Mmp-12 in Complex with 5-(1,2-Dithiolan-3-Yl)-N-(3- Hydroxypropyl)Pentanamide:
3.4.24.65;

The structure of Human Catalytic Mmp-12 in Complex with 5-(1,2-Dithiolan-3-Yl)-N-(3- Hydroxypropyl)Pentanamide, PDB code: 5n5k was solved by V.Calderone, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.62 / 1.80
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	50.790, 60.170, 53.730, 90.00, 114.61, 90.00
R / Rfree (%)	16.7 / 22.7

The structure of Human Catalytic Mmp-12 in Complex with 5-(1,2-Dithiolan-3-Yl)-N-(3- Hydroxypropyl)Pentanamide also contains other interesting chemical elements:

Calcium

(Ca)

3 atoms

The binding sites of Zinc atom in the Human Catalytic Mmp-12 in Complex with 5-(1,2-Dithiolan-3-Yl)-N-(3- Hydroxypropyl)Pentanamide (pdb code 5n5k). 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 Catalytic Mmp-12 in Complex with 5-(1,2-Dithiolan-3-Yl)-N-(3- Hydroxypropyl)Pentanamide, PDB code: 5n5k:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Human Catalytic Mmp-12 in Complex with 5-(1,2-Dithiolan-3-Yl)-N-(3- Hydroxypropyl)Pentanamide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Human Catalytic Mmp-12 in Complex with 5-(1,2-Dithiolan-3-Yl)-N-(3- Hydroxypropyl)Pentanamide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:9.4 occ:1.00 NE2 A:HIS228 2.0 11.0 1.0 O2 A:HAE306 2.1 25.7 1.0 O A:HAE306 2.1 18.5 1.0 NE2 A:HIS222 2.1 9.8 1.0 NE2 A:HIS218 2.1 9.2 1.0 CE1 A:HIS228 2.9 11.6 1.0 C2 A:HAE306 2.9 25.0 1.0 N A:HAE306 3.0 21.7 1.0 CD2 A:HIS222 3.0 9.6 1.0 CD2 A:HIS228 3.1 11.2 1.0 CD2 A:HIS218 3.1 8.8 1.0 CE1 A:HIS218 3.1 9.2 1.0 CE1 A:HIS222 3.1 9.8 1.0 O1 A:8NW307 3.6 41.7 1.0 O A:HOH515 4.0 10.5 1.0 ND1 A:HIS228 4.1 12.0 1.0 CG A:HIS228 4.1 11.8 1.0 OE1 A:GLU219 4.2 10.4 1.0 CG A:HIS222 4.2 9.5 1.0 ND1 A:HIS222 4.2 9.6 1.0 ND1 A:HIS218 4.2 8.6 1.0 CG A:HIS218 4.2 8.7 1.0 C1 A:HAE306 4.4 27.4 1.0 C10 A:8NW307 4.7 34.6 1.0 OE2 A:GLU219 4.9 10.2 1.0 CD A:GLU219 4.9 10.0 1.0 O A:HOH560 4.9 43.5 1.0 CE A:MET236 5.0 10.5 1.0

Zinc binding site 2 out of 2 in the Human Catalytic Mmp-12 in Complex with 5-(1,2-Dithiolan-3-Yl)-N-(3- Hydroxypropyl)Pentanamide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Human Catalytic Mmp-12 in Complex with 5-(1,2-Dithiolan-3-Yl)-N-(3- Hydroxypropyl)Pentanamide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:11.5 occ:1.00 OD2 A:ASP170 2.0 16.3 1.0 ND1 A:HIS196 2.0 10.1 1.0 NE2 A:HIS168 2.0 12.0 1.0 NE2 A:HIS183 2.1 15.3 1.0 CE1 A:HIS183 2.7 16.7 1.0 CG A:ASP170 2.9 18.0 1.0 CD2 A:HIS168 2.9 12.3 1.0 CE1 A:HIS196 2.9 10.3 1.0 CG A:HIS196 3.1 9.7 1.0 CE1 A:HIS168 3.1 12.9 1.0 OD1 A:ASP170 3.2 16.1 1.0 CD2 A:HIS183 3.3 16.1 1.0 CB A:HIS196 3.5 9.3 1.0 ND1 A:HIS183 4.0 17.1 1.0 NE2 A:HIS196 4.1 10.2 1.0 CG A:HIS168 4.1 13.1 1.0 O A:HIS172 4.1 17.3 1.0 ND1 A:HIS168 4.2 12.8 1.0 CD2 A:HIS196 4.2 9.7 1.0 CB A:ASP170 4.2 19.5 1.0 CG A:HIS183 4.3 14.1 1.0 CE1 A:PHE185 4.4 16.3 1.0 CB A:HIS172 4.5 26.0 1.0 CZ A:PHE174 4.7 11.2 1.0 CE2 A:PHE174 4.7 11.4 1.0 CZ A:PHE185 4.8 17.1 1.0 C A:HIS172 4.9 19.3 1.0 O A:HOH443 4.9 39.6 1.0 O A:HOH460 5.0 11.7 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