Calcium in PDB 6esm: Crystal Structure of MMP9 in Complex with Inhibitor BE4.

All present enzymatic activity of Crystal Structure of MMP9 in Complex with Inhibitor BE4.:
3.4.24.35;

The structure of Crystal Structure of MMP9 in Complex with Inhibitor BE4., PDB code: 6esm was solved by L.Ciccone, L.Tepshi, 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)	31.69 / 1.10
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	39.690, 39.690, 163.660, 90.00, 90.00, 120.00
R / Rfree (%)	15.6 / 17.2

The structure of Crystal Structure of MMP9 in Complex with Inhibitor BE4. also contains other interesting chemical elements:

Zinc

(Zn)

2 atoms

The binding sites of Calcium atom in the Crystal Structure of MMP9 in Complex with Inhibitor BE4. (pdb code 6esm). 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 MMP9 in Complex with Inhibitor BE4., PDB code: 6esm:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Crystal Structure of MMP9 in Complex with Inhibitor BE4.


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 MMP9 in Complex with Inhibitor BE4. within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca303 b:8.7 occ:1.00 O A:LEU187 2.2 10.1 0.6 O A:GLY183 2.2 9.6 1.0 OE2 A:GLU208 2.3 10.1 1.0 OD2 A:ASP205 2.3 8.7 1.0 OD1 A:ASP182 2.3 9.4 1.0 O A:LEU187 2.3 8.3 0.4 O A:ASP185 2.4 10.5 1.0 C A:LEU187 3.4 9.0 0.6 CG A:ASP205 3.4 8.2 1.0 C A:LEU187 3.4 9.0 0.4 C A:GLY183 3.5 9.9 1.0 CD A:GLU208 3.5 8.9 1.0 CG A:ASP182 3.5 10.6 1.0 C A:ASP185 3.5 11.4 1.0 N A:ASP185 3.8 9.5 1.0 N A:LEU187 3.9 9.4 0.4 C A:LYS184 3.9 10.5 0.5 N A:LEU187 4.0 9.6 0.6 OD2 A:ASP182 4.0 12.1 1.0 C A:LYS184 4.0 10.8 0.5 CB A:ASP205 4.1 7.7 1.0 N A:GLY183 4.1 9.9 1.0 CA A:LEU187 4.2 9.7 0.4 CA A:LEU187 4.2 9.7 0.6 OE1 A:GLU208 4.2 9.7 1.0 CA A:ASP185 4.2 9.8 1.0 O A:LYS184 4.3 10.4 0.5 C A:GLY186 4.3 10.0 1.0 C A:ASP182 4.3 10.1 1.0 N A:ASP182 4.3 10.0 1.0 OD1 A:ASP205 4.3 8.7 1.0 CA A:LYS184 4.4 11.6 0.5 N A:LEU188 4.4 9.0 1.0 N A:LYS184 4.4 10.7 0.5 N A:LYS184 4.4 10.7 0.5 CA A:LYS184 4.4 10.8 0.5 CA A:GLY183 4.4 9.9 1.0 CG A:GLU208 4.4 8.9 1.0 CB A:LEU187 4.5 10.1 0.6 O A:LYS184 4.5 10.4 0.5 CB A:LEU187 4.5 10.4 0.4 CA A:LEU188 4.5 7.7 1.0 N A:GLY186 4.6 11.1 1.0 O A:HOH432 4.7 12.9 1.0 CA A:ASP182 4.7 10.1 1.0 CB A:ASP182 4.7 10.6 1.0 CA A:GLY186 4.7 11.3 1.0 O A:ASP182 4.8 10.8 1.0 O A:GLY186 4.9 11.2 1.0 CD2 A:LEU188 5.0 10.6 1.0

Calcium binding site 2 out of 3 in the Crystal Structure of MMP9 in Complex with Inhibitor BE4.


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 MMP9 in Complex with Inhibitor BE4. within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca304 b:10.4 occ:1.00 O A:GLY197 2.3 12.9 1.0 O A:GLN199 2.3 11.0 1.0 O A:HOH407 2.4 11.3 1.0 O A:ASP165 2.4 9.8 1.0 OD1 A:ASP201 2.4 9.8 1.0 O A:HOH413 2.4 13.0 1.0 CG A:ASP201 3.4 10.6 1.0 C A:ASP165 3.5 8.5 1.0 C A:GLY197 3.5 13.9 1.0 C A:GLN199 3.5 11.1 1.0 OD2 A:ASP201 3.9 11.5 1.0 C A:ILE198 4.0 12.7 1.0 O A:ALA164 4.1 13.3 1.0 N A:ASP201 4.1 9.2 1.0 N A:GLN199 4.2 12.4 1.0 O A:ILE198 4.2 11.9 1.0 CA A:ASP165 4.3 8.5 1.0 O A:GLY195 4.3 15.1 1.0 N A:GLY197 4.3 16.2 1.0 CA A:GLY200 4.3 9.7 1.0 C A:GLY200 4.4 9.3 1.0 N A:GLY200 4.4 10.3 1.0 N A:ILE198 4.4 14.3 1.0 CA A:ILE198 4.4 14.7 1.0 CA A:GLY197 4.4 14.6 1.0 O A:HOH598 4.5 24.6 1.0 CA A:GLN199 4.5 11.2 1.0 N A:ILE166 4.5 8.6 1.0 O A:HOH422 4.5 23.9 1.0 CB A:ASP201 4.6 9.5 1.0 N A:VAL167 4.6 9.1 1.0 CA A:ILE166 4.7 8.9 1.0 CA A:ASP201 4.7 8.9 1.0 C A:PRO196 4.7 14.9 1.0 CH2 A:TRP116 4.7 12.1 1.0 O A:HOH448 4.8 14.0 1.0 CG2 A:VAL167 4.8 13.4 1.0 O A:PRO196 5.0 16.9 1.0

Calcium binding site 3 out of 3 in the Crystal Structure of MMP9 in Complex with Inhibitor BE4.


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 MMP9 in Complex with Inhibitor BE4. within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca305 b:9.4 occ:1.00 O A:GLU208 2.4 8.5 1.0 O A:HOH550 2.4 16.2 1.0 O A:ASP206 2.4 8.5 1.0 OD2 A:ASP131 2.4 10.2 1.0 O A:HOH564 2.4 15.2 1.0 OD1 A:ASP206 2.4 8.8 1.0 OD1 A:ASP131 2.7 14.1 1.0 CG A:ASP131 2.9 10.3 1.0 CG A:ASP206 3.4 8.4 1.0 C A:ASP206 3.4 8.9 1.0 C A:GLU208 3.5 7.5 1.0 CA A:ASP206 3.9 7.6 1.0 OG A:SER129 4.0 8.6 1.0 CB A:ASP206 4.1 8.8 1.0 CA A:LEU209 4.2 8.2 1.0 OD2 A:ASP206 4.2 11.2 1.0 N A:LEU209 4.3 8.2 1.0 CD1 A:TRP210 4.3 9.1 1.0 N A:GLU208 4.4 7.9 1.0 CB A:ASP131 4.4 9.1 1.0 O A:HOH511 4.4 16.8 1.0 N A:ASP207 4.5 7.7 1.0 C A:ASP207 4.6 8.5 1.0 O A:HOH477 4.6 15.0 1.0 O A:HOH414 4.6 30.9 1.0 CA A:GLU208 4.6 8.4 1.0 O A:HOH443 4.6 33.8 1.0 N A:TRP210 4.7 8.2 1.0 CA A:ASP207 4.7 8.5 1.0 NE1 A:TRP210 4.9 7.8 1.0 C A:LEU209 5.0 8.4 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