Zinc in PDB 6enm: Crystal Structure of MMP12 in Complex with Hydroxamate Inhibitor LP168.

All present enzymatic activity of Crystal Structure of MMP12 in Complex with Hydroxamate Inhibitor LP168.:
3.4.24.65;

The structure of Crystal Structure of MMP12 in Complex with Hydroxamate Inhibitor LP168., PDB code: 6enm was solved by L.Vera, 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)	47.91 / 1.59
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	61.410, 67.090, 68.440, 90.00, 90.00, 90.00
R / Rfree (%)	17.4 / 20.2

The structure of Crystal Structure of MMP12 in Complex with Hydroxamate Inhibitor LP168. also contains other interesting chemical elements:

Calcium

(Ca)

6 atoms

The binding sites of Zinc atom in the Crystal Structure of MMP12 in Complex with Hydroxamate Inhibitor LP168. (pdb code 6enm). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of MMP12 in Complex with Hydroxamate Inhibitor LP168., PDB code: 6enm:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of MMP12 in Complex with Hydroxamate Inhibitor LP168.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of MMP12 in Complex with Hydroxamate Inhibitor LP168. within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:12.7 occ:1.00 O3 A:LPW301 2.0 16.1 1.0 NE2 A:HIS218 2.0 9.9 1.0 NE2 A:HIS222 2.0 13.5 1.0 NE2 A:HIS228 2.1 10.5 1.0 ON1 A:LPW301 2.3 13.4 1.0 C24 A:LPW301 2.8 18.4 1.0 CD2 A:HIS222 3.0 13.9 1.0 CD2 A:HIS218 3.0 10.8 1.0 N1 A:LPW301 3.0 16.1 1.0 CD2 A:HIS228 3.0 11.9 1.0 CE1 A:HIS228 3.1 15.8 1.0 CE1 A:HIS218 3.1 10.9 1.0 CE1 A:HIS222 3.1 14.2 1.0 O A:HOH517 4.1 15.5 1.0 CG A:HIS218 4.1 9.6 1.0 CG A:HIS222 4.2 14.1 1.0 ND1 A:HIS228 4.2 15.3 1.0 ND1 A:HIS218 4.2 10.5 1.0 CG A:HIS228 4.2 13.8 1.0 ND1 A:HIS222 4.2 12.9 1.0 OE2 A:GLU219 4.3 15.2 1.0 C23 A:LPW301 4.3 15.9 1.0 C22 A:LPW301 4.7 13.5 1.0 CB A:PRO238 4.8 18.2 1.0 O A:HOH561 4.8 23.9 1.0 CE A:MET236 4.8 15.3 1.0 C12 A:LPW301 4.9 16.3 1.0 OE1 A:GLU219 5.0 14.9 1.0 CD A:GLU219 5.0 15.8 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of MMP12 in Complex with Hydroxamate Inhibitor LP168.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of MMP12 in Complex with Hydroxamate Inhibitor LP168. within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn303 b:11.8 occ:1.00 OD2 A:ASP170 1.8 14.6 1.0 NE2 A:HIS168 1.9 8.8 1.0 NE2 A:HIS183 2.0 12.0 1.0 ND1 A:HIS196 2.0 11.3 1.0 CG A:ASP170 2.8 16.9 1.0 CE1 A:HIS196 2.9 11.4 1.0 CD2 A:HIS168 2.9 9.6 1.0 CE1 A:HIS168 2.9 9.2 1.0 CE1 A:HIS183 3.0 10.7 1.0 CD2 A:HIS183 3.0 11.0 1.0 CG A:HIS196 3.1 10.7 1.0 OD1 A:ASP170 3.2 16.6 1.0 CB A:HIS196 3.5 10.9 1.0 ND1 A:HIS168 4.1 9.7 1.0 CG A:HIS168 4.1 11.0 1.0 NE2 A:HIS196 4.1 11.5 1.0 ND1 A:HIS183 4.1 13.8 1.0 O A:HIS172 4.1 13.9 1.0 CE1 A:PHE185 4.1 17.3 1.0 CG A:HIS183 4.1 12.4 1.0 CD2 A:HIS196 4.2 12.7 1.0 CB A:ASP170 4.2 18.0 1.0 CZ A:PHE185 4.5 21.0 1.0 CZ A:PHE174 4.7 10.4 1.0 CE2 A:PHE174 4.8 9.4 1.0 CB A:HIS172 4.9 17.7 1.0 O A:HOH461 4.9 13.6 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of MMP12 in Complex with Hydroxamate Inhibitor LP168.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of MMP12 in Complex with Hydroxamate Inhibitor LP168. within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn302 b:12.1 occ:1.00 O3 B:LPW301 2.0 14.7 1.0 NE2 B:HIS222 2.0 12.4 1.0 NE2 B:HIS218 2.0 12.7 1.0 NE2 B:HIS228 2.1 12.5 1.0 ON1 B:LPW301 2.3 13.2 1.0 C24 B:LPW301 2.8 14.4 1.0 N1 B:LPW301 2.9 13.3 1.0 CD2 B:HIS222 3.0 11.5 1.0 CE1 B:HIS218 3.0 11.3 1.0 CE1 B:HIS222 3.1 14.8 1.0 CD2 B:HIS218 3.1 12.4 1.0 CD2 B:HIS228 3.1 12.9 1.0 CE1 B:HIS228 3.1 14.2 1.0 O B:HOH515 4.0 13.7 1.0 ND1 B:HIS218 4.1 11.7 1.0 CG B:HIS222 4.1 10.4 1.0 ND1 B:HIS222 4.2 13.5 1.0 CG B:HIS218 4.2 9.7 1.0 ND1 B:HIS228 4.2 12.5 1.0 CG B:HIS228 4.3 13.4 1.0 C23 B:LPW301 4.3 13.4 1.0 OE2 B:GLU219 4.3 14.5 1.0 C22 B:LPW301 4.7 13.8 1.0 CB B:PRO238 4.7 16.6 1.0 CE B:MET236 4.8 11.1 0.8 C12 B:LPW301 4.8 13.1 1.0 OE1 B:GLU219 5.0 15.9 1.0 O B:HOH568 5.0 31.4 1.0 CD B:GLU219 5.0 13.2 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of MMP12 in Complex with Hydroxamate Inhibitor LP168.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of MMP12 in Complex with Hydroxamate Inhibitor LP168. within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn303 b:12.1 occ:1.00 OD2 B:ASP170 2.0 12.3 1.0 NE2 B:HIS168 2.0 12.0 1.0 ND1 B:HIS196 2.0 11.0 1.0 NE2 B:HIS183 2.0 11.4 1.0 CG B:ASP170 2.9 13.2 1.0 CE1 B:HIS183 2.9 13.8 1.0 CE1 B:HIS196 3.0 11.2 1.0 CD2 B:HIS168 3.0 11.7 1.0 CE1 B:HIS168 3.0 10.2 1.0 CG B:HIS196 3.1 9.8 1.0 CD2 B:HIS183 3.1 12.5 1.0 OD1 B:ASP170 3.2 14.0 1.0 CB B:HIS196 3.5 11.8 1.0 ND1 B:HIS168 4.1 12.1 1.0 NE2 B:HIS196 4.1 11.3 1.0 ND1 B:HIS183 4.1 11.4 1.0 CE1 B:PHE185 4.1 15.2 1.0 O B:HIS172 4.1 16.0 1.0 CG B:HIS168 4.1 11.0 1.0 CD2 B:HIS196 4.2 10.2 1.0 CG B:HIS183 4.2 11.6 1.0 CB B:ASP170 4.3 15.3 1.0 CZ B:PHE185 4.5 18.1 1.0 CZ B:PHE174 4.6 9.9 1.0 CE2 B:PHE174 4.8 13.0 1.0 CB B:HIS172 4.9 17.9 1.0 CA B:HIS196 5.0 11.1 1.0 O B:HOH479 5.0 13.3 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