Calcium in PDB 4l19: Matrix Metalloproteinase-13 Complexed with Selective Inhibitor Compound Q1

The structure of Matrix Metalloproteinase-13 Complexed with Selective Inhibitor Compound Q1, PDB code: 4l19 was solved by D.Minond, T.P.Spicer, J.Jiang, A.B.Taylor, P.J.Hart, W.R.Roush, G.B.Fields, P.S.Hodder, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.75 / 1.66
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	135.320, 36.029, 95.814, 90.00, 130.23, 90.00
R / Rfree (%)	13.4 / 19.9

The structure of Matrix Metalloproteinase-13 Complexed with Selective Inhibitor Compound Q1 also contains other interesting chemical elements:

Zinc

(Zn)

5 atoms

The binding sites of Calcium atom in the Matrix Metalloproteinase-13 Complexed with Selective Inhibitor Compound Q1 (pdb code 4l19). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Matrix Metalloproteinase-13 Complexed with Selective Inhibitor Compound Q1, PDB code: 4l19:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Matrix Metalloproteinase-13 Complexed with Selective Inhibitor Compound Q1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Matrix Metalloproteinase-13 Complexed with Selective Inhibitor Compound Q1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca304 b:30.2 occ:1.00 OE2 A:GLU205 2.2 34.1 1.0 O A:GLY180 2.3 37.4 1.0 O A:LEU184 2.3 34.9 1.0 O A:SER182 2.3 36.5 1.0 OD2 A:ASP202 2.3 29.5 1.0 OD1 A:ASP179 2.4 35.2 1.0 C A:SER182 3.4 39.8 1.0 CD A:GLU205 3.4 35.1 1.0 CG A:ASP202 3.4 25.7 1.0 C A:LEU184 3.5 31.5 1.0 C A:GLY180 3.5 36.5 1.0 CG A:ASP179 3.5 34.2 1.0 N A:SER182 3.8 42.0 1.0 N A:LEU184 3.9 34.8 1.0 C A:PRO181 4.0 38.6 1.0 OD2 A:ASP179 4.1 38.8 1.0 CB A:ASP202 4.1 23.9 1.0 CA A:SER182 4.1 38.7 1.0 N A:GLY180 4.2 39.1 1.0 CA A:LEU184 4.2 32.4 1.0 C A:GLY183 4.2 39.4 1.0 OE1 A:GLU205 4.2 34.5 1.0 N A:ASP179 4.3 32.4 1.0 C A:ASP179 4.3 35.5 1.0 CG A:GLU205 4.3 30.9 1.0 O A:PRO181 4.4 40.5 1.0 OD1 A:ASP202 4.4 26.6 1.0 N A:PRO181 4.4 35.8 1.0 N A:GLY183 4.4 40.4 1.0 CA A:PRO181 4.4 35.6 1.0 CA A:GLY180 4.5 37.6 1.0 N A:LEU185 4.5 30.9 1.0 CB A:LEU184 4.6 37.4 1.0 CA A:GLY183 4.6 41.6 1.0 CA A:ASP179 4.6 33.8 1.0 O A:ASP179 4.7 33.1 1.0 CB A:ASP179 4.7 37.1 1.0 CA A:LEU185 4.7 31.9 1.0 O A:GLY183 4.7 43.0 1.0

Calcium binding site 2 out of 4 in the Matrix Metalloproteinase-13 Complexed with Selective Inhibitor Compound Q1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Matrix Metalloproteinase-13 Complexed with Selective Inhibitor Compound Q1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca305 b:28.4 occ:1.00 O A:ASP162 2.3 26.9 1.0 O A:ASN194 2.3 36.0 1.0 O A:HOH458 2.4 31.3 1.0 O A:HOH407 2.4 32.5 1.0 O A:GLY196 2.4 29.9 1.0 OD1 A:ASP198 2.4 25.6 1.0 CG A:ASP198 3.4 28.9 1.0 C A:ASP162 3.4 26.9 1.0 C A:ASN194 3.5 36.2 1.0 C A:GLY196 3.5 28.2 1.0 OD2 A:ASP198 3.8 27.7 1.0 C A:TYR195 4.0 30.1 1.0 O A:ALA161 4.0 27.4 1.0 N A:GLY196 4.0 29.6 1.0 O A:HOH445 4.1 39.0 1.0 N A:ASP198 4.1 25.2 1.0 CA A:ASP162 4.1 23.8 1.0 O A:TYR195 4.2 29.8 1.0 CA A:GLY196 4.3 29.5 1.0 N A:ILE163 4.4 28.2 1.0 CA A:TYR195 4.4 33.7 1.0 O A:GLY192 4.4 31.6 1.0 N A:TYR195 4.4 36.4 1.0 N A:ASN194 4.4 37.6 1.0 CA A:ASN194 4.4 38.7 1.0 N A:GLY197 4.5 25.5 1.0 CB A:ASP198 4.6 28.8 1.0 N A:MET164 4.6 24.4 1.0 CA A:GLY197 4.6 25.2 1.0 O A:HOH412 4.6 37.4 1.0 CA A:ILE163 4.6 23.2 1.0 C A:GLY197 4.7 26.2 1.0 CA A:ASP198 4.7 24.8 1.0 C A:PRO193 4.8 42.9 1.0 CG A:MET164 4.8 22.8 1.0 CH2 A:TRP113 4.9 34.9 1.0 C A:ALA161 5.0 24.7 1.0 O A:PRO193 5.0 33.7 1.0

Calcium binding site 3 out of 4 in the Matrix Metalloproteinase-13 Complexed with Selective Inhibitor Compound Q1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Matrix Metalloproteinase-13 Complexed with Selective Inhibitor Compound Q1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca303 b:27.0 occ:1.00 O B:GLY196 2.3 24.6 1.0 O B:HOH505 2.3 31.1 1.0 O B:ASP162 2.4 23.4 1.0 OD1 B:ASP198 2.4 25.2 1.0 O B:HOH489 2.4 30.7 1.0 O B:ASN194 2.4 32.1 1.0 CG B:ASP198 3.4 28.9 1.0 C B:GLY196 3.5 24.3 1.0 C B:ASP162 3.5 21.1 1.0 C B:ASN194 3.6 32.0 1.0 OD2 B:ASP198 3.9 24.9 1.0 N B:GLY196 4.0 28.4 1.0 C B:TYR195 4.0 28.1 1.0 O B:HOH447 4.1 40.3 1.0 O B:ALA161 4.1 27.6 1.0 N B:ASP198 4.1 20.4 1.0 O B:TYR195 4.2 28.1 1.0 CA B:GLY196 4.2 26.1 1.0 CA B:ASP162 4.3 23.6 1.0 O B:GLY192 4.4 28.9 1.0 N B:GLY197 4.5 23.1 1.0 O B:HOH490 4.5 37.4 1.0 N B:ILE163 4.5 20.4 1.0 CA B:TYR195 4.5 28.9 1.0 N B:TYR195 4.5 33.3 1.0 CA B:ASN194 4.5 38.2 1.0 CB B:ASP198 4.6 23.3 1.0 N B:ASN194 4.6 33.7 1.0 CA B:GLY197 4.6 21.6 1.0 C B:GLY197 4.6 20.4 1.0 N B:MET164 4.7 20.0 1.0 CA B:ILE163 4.7 22.1 1.0 CA B:ASP198 4.7 20.7 1.0 CG B:MET164 4.8 23.6 1.0 CH2 B:TRP113 4.8 31.2 1.0 C B:PRO193 4.9 41.0 1.0

Calcium binding site 4 out of 4 in the Matrix Metalloproteinase-13 Complexed with Selective Inhibitor Compound Q1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Matrix Metalloproteinase-13 Complexed with Selective Inhibitor Compound Q1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca304 b:22.9 occ:1.00 OE2 B:GLU205 2.2 29.8 1.0 O B:LEU184 2.2 26.8 1.0 O B:GLY180 2.3 24.8 1.0 OD2 B:ASP202 2.3 22.1 1.0 OD1 B:ASP179 2.4 28.1 1.0 O B:SER182 2.4 33.8 0.3 O B:SER182 2.4 32.5 0.7 C B:LEU184 3.4 27.0 1.0 CG B:ASP202 3.4 21.9 1.0 CD B:GLU205 3.5 25.2 1.0 C B:GLY180 3.5 26.4 1.0 C B:SER182 3.5 34.0 0.3 C B:SER182 3.5 33.9 0.7 CG B:ASP179 3.5 30.2 1.0 N B:LEU184 3.9 24.4 1.0 N B:SER182 4.0 25.8 0.7 N B:SER182 4.0 31.2 0.3 C B:PRO181 4.0 30.6 1.0 CA B:LEU184 4.1 24.2 1.0 OD2 B:ASP179 4.1 31.3 1.0 N B:GLY180 4.1 25.0 1.0 CB B:ASP202 4.2 20.6 1.0 C B:GLY183 4.2 28.9 1.0 N B:ASP179 4.3 25.3 1.0 CA B:SER182 4.3 27.9 0.7 CA B:SER182 4.3 32.3 0.3 OD1 B:ASP202 4.3 20.7 1.0 OE1 B:GLU205 4.3 28.1 1.0 CG B:GLU205 4.3 25.4 1.0 C B:ASP179 4.3 24.8 1.0 O B:PRO181 4.3 31.0 1.0 N B:PRO181 4.4 27.4 1.0 CA B:PRO181 4.4 31.2 1.0 CA B:GLY180 4.4 27.8 1.0 CB B:LEU184 4.5 27.0 1.0 N B:GLY183 4.5 31.0 1.0 N B:LEU185 4.5 24.5 1.0 O B:HOH481 4.6 45.8 1.0 CA B:GLY183 4.6 30.6 1.0 CA B:ASP179 4.6 26.6 1.0 CB B:ASP179 4.7 29.8 1.0 O B:GLY183 4.8 33.6 1.0 O B:ASP179 4.8 26.5 1.0 CA B:LEU185 4.8 25.6 1.0

T.P.Spicer, J.Jiang, A.B.Taylor, J.Y.Choi, P.J.Hart, W.R.Roush, G.B.Fields, P.S.Hodder, D.Minond. Characterization of Selective Exosite-Binding Inhibitors of Matrix Metalloproteinase 13 That Prevent Articular Cartilage Degradation in Vitro. J.Med.Chem. V. 57 9598 2014.
ISSN: ISSN 0022-2623
PubMed: 25330343
DOI: 10.1021/JM501284E