Zinc in PDB 5uwk: Matrix Metalloproteinase-13 Complexed with Selective Inhibitor Compound (S)-10A

The structure of Matrix Metalloproteinase-13 Complexed with Selective Inhibitor Compound (S)-10A, PDB code: 5uwk 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)	51.65 / 1.60
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	45.784, 57.155, 120.564, 90.00, 90.00, 90.00
R / Rfree (%)	14.8 / 19.9

The structure of Matrix Metalloproteinase-13 Complexed with Selective Inhibitor Compound (S)-10A also contains other interesting chemical elements:

Calcium

(Ca)

6 atoms

The binding sites of Zinc atom in the Matrix Metalloproteinase-13 Complexed with Selective Inhibitor Compound (S)-10A (pdb code 5uwk). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Matrix Metalloproteinase-13 Complexed with Selective Inhibitor Compound (S)-10A, PDB code: 5uwk:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Matrix Metalloproteinase-13 Complexed with Selective Inhibitor Compound (S)-10A


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)-10A within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:17.5 occ:1.00 O2 A:8OM306 2.0 16.1 1.0 NE2 A:HIS232 2.0 18.2 1.0 NE2 A:HIS226 2.1 15.2 1.0 NE2 A:HIS222 2.1 15.8 1.0 C1 A:8OM306 2.9 18.2 1.0 CE1 A:HIS232 3.0 21.1 1.0 CE1 A:HIS226 3.0 17.9 1.0 CD2 A:HIS232 3.0 16.7 1.0 CE1 A:HIS222 3.0 16.4 1.0 CD2 A:HIS222 3.1 12.8 1.0 CD2 A:HIS226 3.1 18.3 1.0 O1 A:8OM306 3.1 16.5 1.0 ND1 A:HIS232 4.1 21.0 1.0 O A:HOH460 4.1 22.0 1.0 CG A:HIS232 4.1 20.3 1.0 ND1 A:HIS226 4.1 17.6 1.0 ND1 A:HIS222 4.1 15.5 1.0 CG A:HIS222 4.2 13.6 1.0 CG A:HIS226 4.2 15.6 1.0 C21 A:8OM306 4.3 19.3 1.0 C17 A:8OM306 4.4 25.0 1.0 OE2 A:GLU223 4.5 14.9 1.0 C12 A:8OM306 4.7 17.7 1.0 CE A:MET240 4.7 14.4 1.0 C11 A:8OM306 4.8 17.0 1.0 C13 A:8OM306 4.9 17.7 1.0 C22 A:8OM306 4.9 21.9 1.0 O A:HOH493 5.0 17.3 1.0

Zinc binding site 2 out of 4 in the Matrix Metalloproteinase-13 Complexed with Selective Inhibitor Compound (S)-10A


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)-10A within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:16.2 occ:1.00 OD2 A:ASP174 2.0 19.7 1.0 ND1 A:HIS200 2.0 13.1 1.0 NE2 A:HIS172 2.1 13.9 1.0 NE2 A:HIS187 2.1 14.7 1.0 CE1 A:HIS200 2.9 12.9 1.0 CD2 A:HIS172 2.9 14.0 1.0 CG A:ASP174 3.0 18.9 1.0 CE1 A:HIS187 3.0 19.4 1.0 CG A:HIS200 3.1 12.7 1.0 CE1 A:HIS172 3.1 13.7 1.0 CD2 A:HIS187 3.2 17.2 1.0 OD1 A:ASP174 3.2 16.5 1.0 CB A:HIS200 3.5 12.9 1.0 O A:TYR176 4.0 16.0 1.0 NE2 A:HIS200 4.1 14.7 1.0 CG A:HIS172 4.1 15.0 1.0 ND1 A:HIS187 4.2 19.6 1.0 ND1 A:HIS172 4.2 16.0 1.0 CD2 A:HIS200 4.2 13.4 1.0 CG A:HIS187 4.3 17.2 1.0 CB A:ASP174 4.3 17.9 1.0 CE1 A:PHE189 4.5 21.4 1.0 CB A:TYR176 4.7 22.7 1.0 CZ A:PHE178 4.7 15.4 1.0 CZ A:PHE189 4.7 23.2 1.0 CE2 A:PHE178 4.9 15.1 1.0 O A:HOH457 4.9 17.4 1.0 C A:TYR176 5.0 16.0 1.0 CA A:HIS200 5.0 11.5 1.0

Zinc binding site 3 out of 4 in the Matrix Metalloproteinase-13 Complexed with Selective Inhibitor Compound (S)-10A


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)-10A within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:19.9 occ:1.00 O2 B:8OM306 2.0 19.2 1.0 NE2 B:HIS222 2.0 18.7 1.0 NE2 B:HIS232 2.0 21.2 1.0 NE2 B:HIS226 2.1 17.7 1.0 C1 B:8OM306 2.8 19.4 1.0 CE1 B:HIS222 2.9 19.4 1.0 CE1 B:HIS232 3.0 22.1 1.0 CE1 B:HIS226 3.0 22.5 1.0 CD2 B:HIS232 3.0 21.1 1.0 CD2 B:HIS222 3.0 17.2 1.0 O1 B:8OM306 3.1 21.2 1.0 CD2 B:HIS226 3.1 17.5 1.0 ND1 B:HIS222 4.0 18.8 1.0 O B:HOH450 4.0 25.0 1.0 ND1 B:HIS232 4.1 21.3 1.0 CG B:HIS222 4.1 17.1 1.0 ND1 B:HIS226 4.1 21.7 1.0 CG B:HIS232 4.2 20.5 1.0 C21 B:8OM306 4.2 19.8 1.0 CG B:HIS226 4.2 18.9 1.0 C17 B:8OM306 4.4 26.7 1.0 OE2 B:GLU223 4.6 14.3 1.0 C12 B:8OM306 4.6 17.1 1.0 CE B:MET240 4.7 19.6 1.0 C11 B:8OM306 4.8 16.9 1.0 C13 B:8OM306 4.8 18.3 1.0 C22 B:8OM306 4.9 23.4 1.0 O B:HOH497 4.9 19.6 1.0

Zinc binding site 4 out of 4 in the Matrix Metalloproteinase-13 Complexed with Selective Inhibitor Compound (S)-10A


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 (S)-10A within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn302 b:16.7 occ:1.00 OD2 B:ASP174 1.9 18.3 1.0 NE2 B:HIS172 2.0 12.8 1.0 ND1 B:HIS200 2.0 13.4 1.0 NE2 B:HIS187 2.1 16.7 1.0 CG B:ASP174 2.9 19.4 1.0 CE1 B:HIS200 2.9 15.9 1.0 CE1 B:HIS187 3.0 16.4 1.0 CD2 B:HIS172 3.0 14.8 1.0 CE1 B:HIS172 3.0 14.8 1.0 CG B:HIS200 3.1 14.5 1.0 CD2 B:HIS187 3.1 16.8 1.0 OD1 B:ASP174 3.2 18.9 1.0 CB B:HIS200 3.5 12.7 1.0 NE2 B:HIS200 4.1 15.7 1.0 ND1 B:HIS172 4.1 16.6 1.0 CG B:HIS172 4.1 16.6 1.0 ND1 B:HIS187 4.1 16.0 1.0 O B:TYR176 4.2 18.7 1.0 CD2 B:HIS200 4.2 15.6 1.0 CB B:ASP174 4.2 19.1 1.0 CG B:HIS187 4.2 16.6 1.0 CE1 B:PHE189 4.6 19.7 1.0 CZ B:PHE178 4.7 15.2 1.0 CE2 B:PHE178 4.8 17.3 1.0 O B:HOH438 4.9 17.7 1.0 CZ B:PHE189 4.9 19.3 1.0 CB B:TYR176 4.9 18.7 1.0 CA B:HIS200 5.0 11.7 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