Calcium 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:

Zinc	(Zn)	2 atoms
Bromine	(Br)	1 atom
Chlorine	(Cl)	1 atom

The binding sites of Calcium 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 Calcium atom.
In total 3 binding sites of Calcium where determined in the Crystal Structure of A Mutated Catalytic Domain of Human MMP12 in Complex with RXP470, PDB code: 5czm:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 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 Calcium with other atoms in the Ca 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:Ca303 b:12.2 occ:1.00 O A:GLY192 2.3 12.0 1.0 O A:GLY190 2.3 13.6 1.0 O A:HOH420 2.3 18.3 1.0 O A:ASP158 2.3 10.1 1.0 OD2 A:ASP194 2.4 11.1 1.0 O A:HOH441 2.4 12.5 1.0 CG A:ASP194 3.3 10.0 1.0 C A:GLY192 3.5 11.2 1.0 C A:ASP158 3.5 9.5 1.0 C A:GLY190 3.5 13.5 1.0 OD1 A:ASP194 3.8 10.7 1.0 C A:ILE191 4.0 12.7 1.0 N A:GLY192 4.0 12.6 1.0 O A:ILE191 4.2 12.4 1.0 N A:ASP194 4.2 10.0 1.0 CA A:GLY192 4.3 11.8 1.0 O A:ALA157 4.3 11.8 1.0 CA A:ASP158 4.3 9.8 1.0 CA A:ILE191 4.3 13.9 1.0 N A:ILE191 4.4 13.7 1.0 O A:GLY188 4.4 16.1 1.0 N A:GLY190 4.4 15.1 1.0 N A:ILE159 4.4 8.5 1.0 N A:GLY193 4.4 10.6 1.0 CA A:GLY190 4.4 14.2 1.0 CA A:ILE159 4.5 8.9 1.0 CA A:GLY193 4.5 10.6 1.0 N A:LEU160 4.5 8.7 1.0 CB A:ASP194 4.6 10.2 1.0 C A:GLY193 4.6 10.5 1.0 O A:HOH636 4.7 28.6 1.0 CA A:ASP194 4.7 9.7 1.0 O A:HOH447 4.7 20.5 1.0 C A:SER189 4.7 16.1 1.0 O A:HOH434 4.9 13.9 1.0 CH2 A:TRP109 5.0 13.1 1.0

Calcium binding site 2 out of 3 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 Calcium with other atoms in the Ca 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:Ca304 b:11.9 occ:1.00 O A:HOH564 2.4 17.0 1.0 O A:GLU199 2.4 10.3 1.0 O A:GLU201 2.4 12.0 1.0 O A:HOH533 2.4 17.1 1.0 OD2 A:ASP124 2.4 11.9 1.0 OE2 A:GLU199 2.4 12.2 1.0 OD1 A:ASP124 2.6 13.7 1.0 CG A:ASP124 2.9 12.3 1.0 CD A:GLU199 3.5 11.7 1.0 C A:GLU199 3.5 9.7 1.0 C A:GLU201 3.6 11.1 1.0 CG A:GLU199 3.9 10.7 1.0 OG1 A:THR122 4.1 12.1 1.0 CA A:GLU199 4.2 9.2 1.0 CA A:PHE202 4.2 11.3 1.0 CD1 A:TRP203 4.3 9.9 1.0 N A:PHE202 4.3 10.9 1.0 CB A:ASP124 4.4 12.6 1.0 N A:GLU201 4.4 10.7 1.0 O A:HOH497 4.4 27.6 1.0 O A:HOH619 4.4 32.7 1.0 C A:ASP200 4.5 10.8 1.0 N A:ASP200 4.5 10.2 1.0 OE1 A:GLU199 4.6 12.1 1.0 O A:HOH458 4.6 21.4 1.0 O A:HOH409 4.6 24.0 1.0 CB A:GLU199 4.6 9.7 1.0 CA A:GLU201 4.6 10.6 1.0 CA A:ASP200 4.7 10.9 1.0 N A:TRP203 4.7 10.8 1.0 NE1 A:TRP203 4.8 9.7 1.0 CD1 A:PHE202 4.9 17.1 1.0 O A:HOH655 4.9 22.3 1.0 O A:ASP200 5.0 12.1 1.0

Calcium binding site 3 out of 3 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 Calcium with other atoms in the Ca binding site number 3 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:Ca305 b:10.5 occ:1.00 OE2 A:GLU201 2.2 14.6 1.0 O A:GLY176 2.3 12.1 1.0 OD1 A:ASP198 2.3 9.2 1.0 O A:GLY178 2.3 12.2 1.0 O A:ILE180 2.3 10.3 1.0 OD2 A:ASP175 2.3 10.8 1.0 CG A:ASP198 3.4 8.4 1.0 CD A:GLU201 3.5 13.4 1.0 C A:ILE180 3.5 10.1 1.0 C A:GLY178 3.5 11.8 1.0 C A:GLY176 3.5 11.4 1.0 CG A:ASP175 3.5 11.3 1.0 N A:GLY178 3.8 13.4 1.0 N A:ILE180 4.0 10.4 1.0 CB A:ASP198 4.1 8.4 1.0 OD1 A:ASP175 4.1 12.6 1.0 N A:GLY176 4.1 11.8 1.0 C A:LYS177 4.1 14.0 1.0 OE1 A:GLU201 4.2 14.7 1.0 CG2 A:ILE180 4.2 15.6 1.0 CA A:GLY178 4.2 12.9 1.0 N A:ASP175 4.3 9.9 1.0 CA A:ILE180 4.3 11.0 1.0 C A:ASP175 4.3 11.0 1.0 OD2 A:ASP198 4.3 9.2 1.0 C A:GLY179 4.3 10.4 1.0 CA A:LYS177 4.4 13.9 1.0 CA A:GLY176 4.4 11.5 1.0 N A:LYS177 4.4 13.2 1.0 N A:LEU181 4.4 10.1 1.0 CG A:GLU201 4.5 11.5 1.0 N A:GLY179 4.5 11.2 1.0 CA A:LEU181 4.6 9.6 1.0 CA A:ASP175 4.6 10.4 1.0 CA A:GLY179 4.7 10.5 1.0 CB A:ASP175 4.7 10.8 1.0 O A:HOH436 4.7 26.9 1.0 O A:ASP175 4.8 12.7 1.0 O A:LYS177 4.8 15.8 1.0 O A:GLY179 4.8 11.1 1.0 CB A:ILE180 4.9 14.2 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