Calcium in PDB 6rd0: Human MMP12 Catalytic Domain in Complex with AP280

All present enzymatic activity of Human MMP12 Catalytic Domain in Complex with AP280:
3.4.24.65;

The structure of Human MMP12 Catalytic Domain in Complex with AP280, PDB code: 6rd0 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)	46.48 / 1.90
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	69.430, 62.580, 37.500, 90.00, 90.00, 90.00
R / Rfree (%)	16.7 / 20.9

The structure of Human MMP12 Catalytic Domain in Complex with AP280 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 AP280 (pdb code 6rd0). 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 AP280, PDB code: 6rd0:
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 AP280


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 AP280 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca303 b:20.1 occ:1.00 O A:ASP158 2.3 20.0 1.0 O A:GLY192 2.3 18.3 1.0 O A:GLY190 2.3 23.2 1.0 O A:HOH427 2.3 22.6 1.0 OD1 A:ASP194 2.3 18.0 1.0 O A:HOH410 2.4 24.8 1.0 CG A:ASP194 3.3 18.2 1.0 C A:ASP158 3.4 21.1 1.0 C A:GLY192 3.4 19.1 1.0 C A:GLY190 3.5 23.7 1.0 OD2 A:ASP194 3.7 19.9 1.0 O A:HOH413 3.9 36.0 1.0 C A:ILE191 4.0 20.4 1.0 N A:GLY192 4.1 20.0 1.0 O A:ILE191 4.1 18.4 1.0 CA A:ASP158 4.3 23.2 1.0 CA A:GLY192 4.3 20.5 1.0 N A:ASP194 4.3 16.6 1.0 O A:ALA157 4.3 21.7 1.0 O A:GLY188 4.3 25.3 1.0 N A:GLY190 4.3 25.9 1.0 CA A:ILE191 4.4 23.3 1.0 N A:GLY193 4.4 17.1 1.0 N A:ILE191 4.4 22.2 1.0 N A:ILE159 4.4 20.3 1.0 CA A:GLY190 4.5 25.6 1.0 CB A:ASP194 4.6 17.5 1.0 CA A:GLY193 4.6 16.7 1.0 CA A:ILE159 4.6 18.7 1.0 C A:GLY193 4.7 16.2 1.0 N A:LEU160 4.7 17.8 1.0 C A:SER189 4.7 26.1 1.0 O A:HOH446 4.7 27.7 1.0 CA A:ASP194 4.8 16.3 1.0 CH2 A:TRP109 4.9 24.2 1.0

Calcium binding site 2 out of 3 in the Human MMP12 Catalytic Domain in Complex with AP280


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 AP280 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca304 b:27.5 occ:1.00 O A:GLU199 2.3 25.1 1.0 OD2 A:ASP124 2.3 28.5 1.0 O A:HOH500 2.3 33.5 1.0 O A:GLU201 2.3 25.0 1.0 OE2 A:GLU199 2.4 25.9 1.0 O A:HOH512 2.5 26.3 1.0 OD1 A:ASP124 2.7 30.1 1.0 CG A:ASP124 2.8 31.8 1.0 C A:GLU199 3.4 23.1 1.0 CD A:GLU199 3.4 24.2 1.0 C A:GLU201 3.6 26.6 1.0 CG A:GLU199 3.8 23.2 1.0 CA A:GLU199 4.0 21.4 1.0 OG1 A:THR122 4.1 24.2 1.0 CD1 A:TRP203 4.2 22.4 1.0 CA A:PHE202 4.3 29.9 1.0 N A:PHE202 4.3 28.1 1.0 CB A:ASP124 4.3 31.9 1.0 N A:GLU201 4.3 23.5 1.0 O A:HOH547 4.5 49.1 1.0 N A:ASP200 4.5 24.8 1.0 O A:HOH565 4.5 55.3 1.0 C A:ASP200 4.5 26.4 1.0 O A:HOH463 4.5 39.4 1.0 O A:HOH499 4.5 38.2 1.0 OE1 A:GLU199 4.6 23.5 1.0 O A:HOH405 4.6 40.0 1.0 CB A:GLU199 4.6 22.4 1.0 CA A:GLU201 4.6 24.8 1.0 NE1 A:TRP203 4.7 20.3 1.0 CA A:ASP200 4.7 25.7 1.0 N A:TRP203 4.8 27.8 1.0 O A:HOH517 4.8 30.6 1.0

Calcium binding site 3 out of 3 in the Human MMP12 Catalytic Domain in Complex with AP280


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 AP280 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca305 b:23.7 occ:1.00 OE2 A:GLU201 2.2 25.8 1.0 O A:GLY178 2.2 25.6 1.0 OD2 A:ASP198 2.3 21.0 1.0 OD1 A:ASP175 2.3 25.2 1.0 O A:ILE180 2.3 19.9 1.0 O A:GLY176 2.3 26.3 1.0 CG A:ASP198 3.4 19.6 1.0 CD A:GLU201 3.4 25.5 1.0 C A:ILE180 3.4 21.5 1.0 CG A:ASP175 3.5 24.1 1.0 C A:GLY178 3.5 27.7 1.0 C A:GLY176 3.5 28.4 1.0 N A:ILE180 3.9 25.3 1.0 N A:GLY178 3.9 29.4 1.0 CB A:ASP198 4.0 18.4 1.0 N A:GLY176 4.0 26.6 1.0 OE1 A:GLU201 4.0 25.9 1.0 OD2 A:ASP175 4.0 22.4 1.0 CA A:ILE180 4.2 23.1 1.0 C A:LYS177 4.2 32.9 1.0 C A:ASP175 4.2 26.5 1.0 N A:ASP175 4.2 22.5 1.0 C A:GLY179 4.2 26.4 1.0 CA A:GLY178 4.3 29.9 1.0 OD1 A:ASP198 4.3 19.9 1.0 CA A:GLY176 4.4 28.5 1.0 N A:LEU181 4.4 19.6 1.0 CG A:GLU201 4.5 24.4 1.0 N A:LYS177 4.5 30.4 1.0 N A:GLY179 4.5 27.2 1.0 CA A:LYS177 4.5 32.6 1.0 CA A:LEU181 4.6 20.6 1.0 CA A:ASP175 4.6 24.9 1.0 CB A:ASP175 4.6 24.9 1.0 O A:ASP175 4.7 28.5 1.0 O A:LYS177 4.7 34.0 1.0 CA A:GLY179 4.7 27.1 1.0 CB A:ILE180 4.8 23.6 1.0 O A:GLY179 4.8 25.5 1.0 O A:HOH443 5.0 21.4 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