Calcium in PDB 6rly: Human MMP12 (Catalytic Domain) in Complex with AP316

All present enzymatic activity of Human MMP12 (Catalytic Domain) in Complex with AP316:
3.4.24.65;

The structure of Human MMP12 (Catalytic Domain) in Complex with AP316, PDB code: 6rly was solved by V.Calderone, M.Fragai, C.Luchinat, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.66 / 2.20
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	69.420, 63.020, 37.420, 90.00, 90.00, 90.00
R / Rfree (%)	17.8 / 22.7

The structure of Human MMP12 (Catalytic Domain) in Complex with AP316 also contains other interesting chemical elements:

Zinc

(Zn)

2 atoms

The binding sites of Calcium atom in the Human MMP12 (Catalytic Domain) in Complex with AP316 (pdb code 6rly). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Human MMP12 (Catalytic Domain) in Complex with AP316, PDB code: 6rly:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Human MMP12 (Catalytic Domain) in Complex with AP316


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Human MMP12 (Catalytic Domain) in Complex with AP316 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca303 b:20.7 occ:1.00 O A:HOH422 2.2 26.2 1.0 O A:GLY192 2.2 18.0 1.0 O A:ASP158 2.2 17.6 1.0 OD1 A:ASP194 2.3 15.6 1.0 O A:GLY190 2.4 20.9 1.0 O A:HOH418 2.4 28.4 1.0 CG A:ASP194 3.3 15.9 1.0 C A:ASP158 3.4 18.9 1.0 C A:GLY192 3.5 17.6 1.0 C A:GLY190 3.5 21.7 1.0 O A:HOH410 3.6 39.4 1.0 OD2 A:ASP194 3.7 16.5 1.0 C A:ILE191 3.9 19.5 1.0 N A:GLY192 4.0 19.6 1.0 O A:ILE191 4.0 18.6 1.0 O A:ALA157 4.2 24.0 1.0 N A:ASP194 4.2 14.9 1.0 CA A:GLY192 4.3 19.2 1.0 CA A:ILE191 4.3 20.4 1.0 CA A:ASP158 4.3 21.2 1.0 N A:ILE191 4.3 21.5 1.0 N A:ILE159 4.4 17.4 1.0 O A:GLY188 4.4 23.4 1.0 N A:GLY193 4.4 16.4 1.0 N A:GLY190 4.5 25.1 1.0 CA A:GLY190 4.5 23.5 1.0 CB A:ASP194 4.5 15.2 1.0 N A:LEU160 4.5 15.9 1.0 CA A:ILE159 4.5 16.3 1.0 CA A:GLY193 4.6 15.9 1.0 C A:GLY193 4.6 15.0 1.0 CA A:ASP194 4.7 14.9 1.0 C A:SER189 4.8 25.0 1.0 CH2 A:TRP109 4.8 27.1 1.0 O A:SER189 5.0 24.1 1.0

Calcium binding site 2 out of 3 in the Human MMP12 (Catalytic Domain) in Complex with AP316


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Human MMP12 (Catalytic Domain) in Complex with AP316 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca304 b:23.7 occ:1.00 O A:GLU199 2.2 21.6 1.0 OE2 A:GLU199 2.3 22.4 1.0 O A:GLU201 2.4 22.7 1.0 O A:HOH467 2.4 30.1 1.0 OD2 A:ASP124 2.4 22.6 1.0 O A:HOH482 2.5 24.5 1.0 OD1 A:ASP124 2.6 23.9 1.0 CG A:ASP124 2.8 23.7 1.0 C A:GLU199 3.4 20.7 1.0 CD A:GLU199 3.4 21.9 1.0 C A:GLU201 3.6 23.0 1.0 CG A:GLU199 3.8 21.1 1.0 CA A:GLU199 4.0 19.8 1.0 OG1 A:THR122 4.1 21.6 1.0 CD1 A:TRP203 4.3 19.2 1.0 CA A:PHE202 4.3 24.4 1.0 O A:HOH519 4.3 44.2 1.0 N A:GLU201 4.3 21.9 1.0 CB A:ASP124 4.3 24.6 1.0 N A:PHE202 4.3 23.5 1.0 O A:HOH478 4.4 32.5 1.0 N A:ASP200 4.4 21.3 1.0 C A:ASP200 4.5 23.4 1.0 OE1 A:GLU199 4.5 22.2 1.0 O A:HOH532 4.5 47.1 1.0 CB A:GLU199 4.6 20.2 1.0 O A:HOH464 4.6 31.4 1.0 O A:HOH512 4.6 31.3 1.0 CA A:GLU201 4.6 22.9 1.0 O A:HOH416 4.7 39.6 1.0 NE1 A:TRP203 4.7 18.8 1.0 CA A:ASP200 4.7 22.7 1.0 N A:TRP203 4.8 22.2 1.0 O A:ASP200 5.0 26.0 1.0

Calcium binding site 3 out of 3 in the Human MMP12 (Catalytic Domain) in Complex with AP316


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Human MMP12 (Catalytic Domain) in Complex with AP316 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca305 b:23.5 occ:1.00 OE2 A:GLU201 2.1 23.9 1.0 O A:ILE180 2.2 20.2 1.0 O A:GLY178 2.2 27.4 1.0 OD2 A:ASP198 2.3 21.3 1.0 OD1 A:ASP175 2.3 20.0 1.0 O A:GLY176 2.4 22.6 1.0 CG A:ASP198 3.3 20.3 1.0 C A:ILE180 3.4 20.3 1.0 CD A:GLU201 3.4 23.2 1.0 CG A:ASP175 3.5 21.0 1.0 C A:GLY178 3.5 28.8 1.0 C A:GLY176 3.6 24.3 1.0 N A:ILE180 3.9 24.0 1.0 N A:GLY178 3.9 30.2 1.0 CB A:ASP198 3.9 19.5 1.0 N A:GLY176 4.0 22.6 1.0 OD2 A:ASP175 4.1 20.7 1.0 OE1 A:GLU201 4.2 24.5 1.0 CA A:ILE180 4.2 21.8 1.0 C A:ASP175 4.2 23.4 1.0 CA A:GLY178 4.3 29.9 1.0 C A:GLY179 4.3 24.8 1.0 N A:ASP175 4.3 21.6 1.0 OD1 A:ASP198 4.3 21.0 1.0 C A:LYS177 4.3 31.2 1.0 N A:LEU181 4.3 19.0 1.0 CA A:GLY176 4.4 24.1 1.0 CG A:GLU201 4.4 22.4 1.0 CA A:LEU181 4.5 18.5 1.0 N A:LYS177 4.5 27.1 1.0 N A:GLY179 4.5 28.0 1.0 CA A:LYS177 4.6 30.4 1.0 O A:ASP175 4.6 25.1 1.0 CA A:ASP175 4.6 22.8 1.0 CB A:ASP175 4.6 22.1 1.0 CB A:ILE180 4.7 22.1 1.0 CA A:GLY179 4.8 27.2 1.0 O A:GLY179 4.8 23.6 1.0 O A:LYS177 4.8 33.1 1.0 O A:HOH413 5.0 19.2 1.0 CB A:PHE174 5.0 21.2 1.0

S.Tsoukalidou, M.Kakou, I.Mavridis, D.Koumantou, V.Calderone, M.Fragai, E.Stratikos, A.Papakyriakou, D.Vourloumis. Exploration of Zinc-Binding Groups For the Design of Inhibitors For the Oxytocinase Subfamily of M1 Aminopeptidases. Bioorg.Med.Chem. V. 27 15177 2019.
ISSN: ESSN 1464-3391
PubMed: 31711716
DOI: 10.1016/J.BMC.2019.115177