Zinc 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:

Calcium

(Ca)

4 atoms

The binding sites of Zinc 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 Zinc atom.
In total 5 binding sites of Zinc where determined in the Matrix Metalloproteinase-13 Complexed with Selective Inhibitor Compound Q1, PDB code: 4l19:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in the Matrix Metalloproteinase-13 Complexed with Selective Inhibitor Compound Q1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn 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:Zn301 b:26.5 occ:1.00 NE2 A:HIS172 2.0 23.1 1.0 OD2 A:ASP174 2.0 26.9 1.0 NE2 A:HIS187 2.1 26.6 1.0 ND1 A:HIS200 2.1 26.8 1.0 CD2 A:HIS172 2.9 23.7 1.0 CG A:ASP174 2.9 29.2 1.0 CE1 A:HIS187 3.0 31.1 1.0 CE1 A:HIS172 3.0 27.5 1.0 CE1 A:HIS200 3.0 28.0 1.0 CG A:HIS200 3.1 24.4 1.0 CD2 A:HIS187 3.2 28.4 1.0 OD1 A:ASP174 3.2 29.9 1.0 CB A:HIS200 3.5 23.6 1.0 CG A:HIS172 4.1 20.9 1.0 ND1 A:HIS172 4.1 22.2 1.0 ND1 A:HIS187 4.1 28.5 1.0 NE2 A:HIS200 4.2 25.6 1.0 O A:TYR176 4.2 28.1 1.0 CD2 A:HIS200 4.2 26.6 1.0 CG A:HIS187 4.2 29.9 1.0 CB A:ASP174 4.3 26.9 1.0 CZ A:PHE178 4.6 26.1 1.0 CE2 A:PHE178 4.7 25.4 1.0 O A:HOH404 4.8 29.5 1.0 CE1 A:PHE189 4.8 33.2 1.0 CA A:HIS200 5.0 19.8 1.0 CB A:TYR176 5.0 31.3 1.0

Zinc binding site 2 out of 5 in the Matrix Metalloproteinase-13 Complexed with Selective Inhibitor Compound Q1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn 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:Zn302 b:34.3 occ:1.00 NE2 A:HIS222 2.1 30.9 1.0 NE2 A:HIS226 2.1 32.8 1.0 NE2 A:HIS232 2.1 40.6 1.0 O1 A:FMT306 2.2 59.5 1.0 C A:FMT306 2.4 54.3 1.0 O2 A:FMT306 2.6 43.3 1.0 CD2 A:HIS232 3.0 37.2 1.0 CD2 A:HIS222 3.0 28.6 1.0 CE1 A:HIS226 3.0 32.9 1.0 CE1 A:HIS222 3.0 33.3 1.0 CD2 A:HIS226 3.1 33.1 1.0 CE1 A:HIS232 3.2 44.3 1.0 ND1 A:HIS222 4.1 31.6 1.0 CG A:HIS232 4.1 38.7 1.0 CG A:HIS222 4.2 29.4 1.0 ND1 A:HIS226 4.2 32.6 1.0 ND1 A:HIS232 4.2 44.6 1.0 CG A:HIS226 4.2 31.0 1.0 C1 A:1UA308 4.5 65.3 1.0 OE2 A:GLU223 4.5 34.6 1.0 OE1 A:GLU223 4.8 38.6 1.0 O A:HOH494 4.8 39.8 1.0 CE A:MET240 4.8 29.5 1.0 C15 A:1UA307 4.9 48.1 1.0 CD A:GLU223 4.9 31.0 1.0

Zinc binding site 3 out of 5 in the Matrix Metalloproteinase-13 Complexed with Selective Inhibitor Compound Q1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn 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 A:Zn303 b:39.7 occ:0.31 NE2 A:HIS251 1.9 42.7 1.0 O2 A:GOL309 2.3 65.3 0.9 CD2 A:HIS251 2.5 43.4 1.0 CE1 A:HIS251 2.8 34.1 1.0 OG A:SER250 3.0 60.0 1.0 CB A:SER250 3.2 50.6 1.0 C2 A:GOL309 3.2 65.1 0.9 CG A:HIS251 3.5 41.1 1.0 ND1 A:HIS251 3.7 36.1 1.0 C1 A:GOL309 4.1 65.3 0.9 C A:SER250 4.2 45.8 1.0 O A:HOH506 4.2 51.9 1.0 CA A:SER250 4.3 51.7 1.0 O1 A:GOL309 4.4 69.9 0.9 C3 A:GOL309 4.4 63.3 0.9 O3 A:GOL309 4.4 62.5 0.9 O A:SER250 4.4 47.1 1.0 N A:HIS251 4.5 43.0 1.0 CB A:HIS251 4.8 40.3 1.0

Zinc binding site 4 out of 5 in the Matrix Metalloproteinase-13 Complexed with Selective Inhibitor Compound Q1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn 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:Zn301 b:23.5 occ:1.00 OD2 B:ASP174 2.0 23.8 1.0 NE2 B:HIS172 2.0 21.1 1.0 ND1 B:HIS200 2.0 19.5 1.0 NE2 B:HIS187 2.1 24.1 1.0 CD2 B:HIS172 2.9 19.9 1.0 CG B:ASP174 2.9 24.5 1.0 CE1 B:HIS200 2.9 20.9 1.0 CE1 B:HIS187 3.0 25.2 1.0 CG B:HIS200 3.1 22.1 1.0 CE1 B:HIS172 3.1 20.5 1.0 CD2 B:HIS187 3.1 23.4 1.0 OD1 B:ASP174 3.1 22.0 1.0 CB B:HIS200 3.5 18.6 1.0 CG B:HIS172 4.1 19.6 1.0 NE2 B:HIS200 4.1 23.5 1.0 ND1 B:HIS187 4.1 24.9 1.0 ND1 B:HIS172 4.1 22.9 1.0 CD2 B:HIS200 4.2 19.6 1.0 O B:TYR176 4.2 24.6 1.0 CG B:HIS187 4.2 22.3 1.0 CB B:ASP174 4.3 23.5 1.0 CE1 B:PHE189 4.6 29.7 1.0 CB B:TYR176 4.7 25.8 1.0 CZ B:PHE178 4.8 20.2 1.0 CZ B:PHE189 4.8 36.7 1.0 CE2 B:PHE178 4.8 21.2 1.0 O B:HOH412 4.9 27.0 1.0 CA B:HIS200 5.0 21.8 1.0

Zinc binding site 5 out of 5 in the Matrix Metalloproteinase-13 Complexed with Selective Inhibitor Compound Q1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Matrix Metalloproteinase-13 Complexed with Selective Inhibitor Compound Q1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn302 b:22.9 occ:1.00 NE2 B:HIS226 2.1 23.0 1.0 NE2 B:HIS222 2.1 19.7 1.0 NE2 B:HIS232 2.1 22.1 1.0 O1 B:FMT305 2.2 42.7 1.0 O2 B:FMT305 2.3 29.2 1.0 C B:FMT305 2.5 32.9 1.0 CD2 B:HIS232 3.0 22.8 1.0 CD2 B:HIS226 3.0 20.8 1.0 CD2 B:HIS222 3.0 20.7 1.0 CE1 B:HIS222 3.1 21.6 1.0 CE1 B:HIS232 3.1 24.8 1.0 CE1 B:HIS226 3.1 22.9 1.0 ND1 B:HIS232 4.2 27.3 1.0 CG B:HIS232 4.2 21.7 1.0 ND1 B:HIS222 4.2 20.1 1.0 ND1 B:HIS226 4.2 20.3 1.0 CG B:HIS226 4.2 17.9 1.0 CG B:HIS222 4.2 20.3 1.0 O B:HOH458 4.2 41.0 1.0 O B:HOH470 4.4 35.9 1.0 OE2 B:GLU223 4.5 22.8 1.0 C15 B:1UA309 4.7 32.9 1.0 CE B:MET240 4.8 21.8 1.0 O B:HOH521 4.8 57.7 1.0 OE1 B:GLU223 4.9 24.4 1.0 O B:HOH555 5.0 61.9 1.0 CD B:GLU223 5.0 20.6 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