Zinc in PDB 5uwl: Matrix Metalloproteinase-13 Complexed with Selective Inhibitor Compound (S)-17A

The structure of Matrix Metalloproteinase-13 Complexed with Selective Inhibitor Compound (S)-17A, PDB code: 5uwl was solved by A.B.Taylor, X.Cao, P.J.Hart, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	60.07 / 2.55
Space group	P 64 2 2
Cell size a, b, c (Å), α, β, γ (°)	129.962, 129.962, 142.076, 90.00, 90.00, 120.00
R / Rfree (%)	19.9 / 24

The structure of Matrix Metalloproteinase-13 Complexed with Selective Inhibitor Compound (S)-17A also contains other interesting chemical elements:

Calcium

(Ca)

5 atoms

The binding sites of Zinc atom in the Matrix Metalloproteinase-13 Complexed with Selective Inhibitor Compound (S)-17A (pdb code 5uwl). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Matrix Metalloproteinase-13 Complexed with Selective Inhibitor Compound (S)-17A, PDB code: 5uwl:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Matrix Metalloproteinase-13 Complexed with Selective Inhibitor Compound (S)-17A


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 (S)-17A within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:36.3 occ:1.00 NE2 A:HIS232 1.9 32.6 1.0 NE2 A:HIS222 2.0 28.9 1.0 NE2 A:HIS226 2.1 28.2 1.0 CD2 A:HIS232 2.8 32.9 1.0 CD2 A:HIS226 3.0 29.7 1.0 CE1 A:HIS232 3.0 33.6 1.0 CD2 A:HIS222 3.0 35.6 1.0 CE1 A:HIS222 3.0 30.5 1.0 CE1 A:HIS226 3.3 32.4 1.0 CG A:HIS232 4.0 26.8 1.0 ND1 A:HIS232 4.0 29.6 1.0 OE2 A:GLU223 4.1 37.0 1.0 ND1 A:HIS222 4.1 30.7 1.0 CG A:HIS222 4.2 32.1 1.0 CG A:HIS226 4.2 33.6 1.0 ND1 A:HIS226 4.3 29.0 1.0 C13 A:8OJ306 4.4 31.6 1.0 OE1 A:GLU223 4.4 35.8 1.0 CD A:GLU223 4.5 36.3 1.0 C12 A:8OJ306 4.7 32.5 1.0 CE A:MET240 4.8 23.4 1.0 C14 A:8OJ306 4.8 34.5 1.0

Zinc binding site 2 out of 3 in the Matrix Metalloproteinase-13 Complexed with Selective Inhibitor Compound (S)-17A


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 (S)-17A within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:46.5 occ:1.00 NE2 A:HIS172 1.9 37.2 1.0 ND1 A:HIS200 1.9 42.2 1.0 OD2 A:ASP174 1.9 47.2 1.0 NE2 A:HIS187 2.2 45.2 1.0 CD2 A:HIS172 2.7 45.7 1.0 CG A:ASP174 2.8 56.0 1.0 CE1 A:HIS200 2.8 42.5 1.0 OD1 A:ASP174 3.0 53.0 1.0 CE1 A:HIS172 3.0 44.5 1.0 CG A:HIS200 3.1 40.8 1.0 CE1 A:HIS187 3.1 40.2 1.0 CD2 A:HIS187 3.3 41.2 1.0 CB A:HIS200 3.5 34.7 1.0 CG A:HIS172 3.9 45.9 1.0 NE2 A:HIS200 4.0 35.6 1.0 ND1 A:HIS172 4.0 43.0 1.0 CD2 A:HIS200 4.1 40.2 1.0 CB A:ASP174 4.2 58.5 1.0 ND1 A:HIS187 4.3 44.3 1.0 O A:TYR176 4.4 47.8 1.0 CG A:HIS187 4.4 43.3 1.0 CZ A:PHE178 4.4 42.0 1.0 O A:HOH414 4.8 48.4 1.0 CE2 A:PHE178 4.8 43.4 1.0 CE2 A:PHE189 4.9 42.5 1.0 CA A:HIS200 5.0 33.3 1.0 CE1 A:PHE178 5.0 40.5 1.0

Zinc binding site 3 out of 3 in the Matrix Metalloproteinase-13 Complexed with Selective Inhibitor Compound (S)-17A


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 (S)-17A within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:36.0 occ:1.00 NE2 B:HIS232 1.9 31.9 1.0 NE2 B:HIS222 2.2 34.9 1.0 NE2 B:HIS226 2.2 31.9 1.0 CE1 B:HIS232 2.8 30.5 1.0 CD2 B:HIS232 3.0 37.3 1.0 CD2 B:HIS222 3.0 32.9 1.0 CD2 B:HIS226 3.1 36.4 1.0 CE1 B:HIS222 3.2 36.3 1.0 CE1 B:HIS226 3.3 31.2 1.0 ND1 B:HIS232 3.9 27.4 1.0 CG B:HIS232 4.1 32.8 1.0 CG B:HIS222 4.2 34.8 1.0 ND1 B:HIS222 4.3 32.9 1.0 CG B:HIS226 4.3 36.1 1.0 ND1 B:HIS226 4.3 31.0 1.0 OE2 B:GLU223 4.4 40.2 1.0 C13 B:8OJ304 4.5 28.9 1.0 OE1 B:GLU223 4.6 38.7 1.0 CE B:MET240 4.8 35.3 1.0 CD B:GLU223 4.8 39.8 1.0 C12 B:8OJ304 4.9 25.8 1.0 C14 B:8OJ304 4.9 32.4 1.0

J.Y.Choi, R.Fuerst, A.M.Knapinska, A.B.Taylor, L.Smith, X.Cao, P.J.Hart, G.B.Fields, W.R.Roush. Structure-Based Design and Synthesis of Potent and Selective Matrix Metalloproteinase 13 Inhibitors. J. Med. Chem. V. 60 5816 2017.
ISSN: ISSN 1520-4804
PubMed: 28653849
DOI: 10.1021/ACS.JMEDCHEM.7B00514