Zinc in PDB 5czm: Crystal Structure of A Mutated Catalytic Domain of Human MMP12 in Complex with RXP470

All present enzymatic activity of Crystal Structure of A Mutated Catalytic Domain of Human MMP12 in Complex with RXP470:
3.4.24.65;

The structure of Crystal Structure of A Mutated Catalytic Domain of Human MMP12 in Complex with RXP470, PDB code: 5czm was solved by C.Rouanet-Mehouas, L.Roselia, L.Devel, V.Dive, E.A.Stura, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.45 / 1.30
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	68.970, 63.290, 35.910, 90.00, 90.00, 90.00
R / Rfree (%)	14.5 / 17.4

The structure of Crystal Structure of A Mutated Catalytic Domain of Human MMP12 in Complex with RXP470 also contains other interesting chemical elements:

Bromine	(Br)	1 atom
Calcium	(Ca)	3 atoms
Chlorine	(Cl)	1 atom

The binding sites of Zinc atom in the Crystal Structure of A Mutated Catalytic Domain of Human MMP12 in Complex with RXP470 (pdb code 5czm). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of A Mutated Catalytic Domain of Human MMP12 in Complex with RXP470, PDB code: 5czm:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of A Mutated Catalytic Domain of Human MMP12 in Complex with RXP470


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 A Mutated Catalytic Domain of Human MMP12 in Complex with RXP470 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:11.6 occ:1.00 O3 A:R47306 1.9 9.6 1.0 NE2 A:HIS228 2.0 10.3 1.0 NE2 A:HIS218 2.0 8.3 1.0 NE2 A:HIS222 2.0 9.2 1.0 CE1 A:HIS218 2.9 8.5 1.0 CD2 A:HIS228 3.0 10.2 1.0 CE1 A:HIS222 3.0 10.9 1.0 CE1 A:HIS228 3.0 10.9 1.0 CD2 A:HIS218 3.0 8.7 1.0 CD2 A:HIS222 3.1 9.1 1.0 P1 A:R47306 3.1 10.6 1.0 O2 A:R47306 3.3 10.5 1.0 O A:HOH425 4.0 13.9 1.0 ND1 A:HIS218 4.1 8.6 1.0 ND1 A:HIS228 4.1 11.4 1.0 ND1 A:HIS222 4.1 11.3 1.0 CG A:HIS228 4.1 11.2 1.0 CG A:HIS218 4.2 8.4 1.0 CG A:HIS222 4.2 9.6 1.0 C19 A:R47306 4.3 13.6 1.0 O A:HOH626 4.3 23.1 0.5 C18 A:R47306 4.3 10.5 1.0 C17 A:R47306 4.3 11.3 1.0 C20 A:R47306 4.5 16.4 1.0 C16 A:R47306 4.6 11.8 1.0 CE A:MET236 4.7 10.9 1.0 O A:HOH478 4.8 13.4 1.0 O A:PRO238 4.9 12.7 1.0 C14 A:R47306 4.9 12.8 1.0 C15 A:R47306 4.9 13.1 1.0 OE2 A:GLU219 5.0 13.6 1.0 CA A:PRO238 5.0 10.4 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of A Mutated Catalytic Domain of Human MMP12 in Complex with RXP470


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 A Mutated Catalytic Domain of Human MMP12 in Complex with RXP470 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:10.2 occ:1.00 NE2 A:HIS183 2.0 9.8 1.0 NE2 A:HIS168 2.0 8.9 1.0 OD1 A:ASP170 2.0 12.0 1.0 ND1 A:HIS196 2.0 9.3 1.0 CE1 A:HIS183 2.8 10.1 1.0 CD2 A:HIS168 2.9 8.7 1.0 CG A:ASP170 2.9 12.1 1.0 CE1 A:HIS196 3.0 10.1 1.0 CE1 A:HIS168 3.0 8.6 1.0 CD2 A:HIS183 3.1 10.1 1.0 OD2 A:ASP170 3.1 12.3 1.0 CG A:HIS196 3.1 8.7 1.0 CB A:HIS196 3.5 9.1 1.0 ND1 A:HIS183 4.0 10.2 1.0 CG A:HIS168 4.0 9.0 1.0 ND1 A:HIS168 4.1 9.6 1.0 NE2 A:HIS196 4.1 9.7 1.0 CG A:HIS183 4.1 9.2 1.0 O A:HIS172 4.2 13.3 1.0 CD2 A:HIS196 4.2 9.7 1.0 CB A:ASP170 4.3 13.5 1.0 CE2 A:PHE185 4.5 14.3 1.0 O A:HOH513 4.6 30.0 1.0 CZ A:PHE185 4.7 14.8 1.0 CZ A:PHE174 4.7 9.8 1.0 O A:HOH511 4.8 11.7 1.0 CB A:HIS172 4.9 16.5 1.0 CE1 A:PHE174 4.9 9.5 1.0

C.Rouanet-Mehouas, B.Czarny, F.Beau, E.Cassar-Lajeunesse, E.A.Stura, V.Dive, L.Devel. Zinc-Metalloproteinase Inhibitors: Evaluation of the Complex Role Played By the Zinc-Binding Group on Potency and Selectivity. J. Med. Chem. V. 60 403 2017.
ISSN: ISSN 1520-4804
PubMed: 27996256
DOI: 10.1021/ACS.JMEDCHEM.6B01420