Zinc in PDB 3kec: Crystal Structure of Human Mmp-13 Complexed with A Phenyl-2H-Tetrazole Compound

The structure of Crystal Structure of Human Mmp-13 Complexed with A Phenyl-2H-Tetrazole Compound, PDB code: 3kec was solved by H.-S.Shieh, A.G.Pavlovsky, B.Collins, M.E.Schnute, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.05
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	133.209, 72.348, 36.356, 90.00, 90.00, 90.00
R / Rfree (%)	16.9 / 20.4

The structure of Crystal Structure of Human Mmp-13 Complexed with A Phenyl-2H-Tetrazole Compound also contains other interesting chemical elements:

Calcium

(Ca)

6 atoms

The binding sites of Zinc atom in the Crystal Structure of Human Mmp-13 Complexed with A Phenyl-2H-Tetrazole Compound (pdb code 3kec). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of Human Mmp-13 Complexed with A Phenyl-2H-Tetrazole Compound, PDB code: 3kec:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of Human Mmp-13 Complexed with A Phenyl-2H-Tetrazole Compound


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Human Mmp-13 Complexed with A Phenyl-2H-Tetrazole Compound within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn901 b:14.5 occ:1.00 NE2 A:HIS222 2.1 9.1 1.0 NE2 A:HIS226 2.2 11.2 1.0 NE2 A:HIS232 2.2 16.9 1.0 O2 A:HAE272 2.5 38.0 1.0 C2 A:HAE272 2.7 40.0 1.0 CD2 A:HIS222 3.0 9.3 1.0 CD2 A:HIS232 3.1 16.6 1.0 C1 A:HAE272 3.1 40.7 1.0 CD2 A:HIS226 3.1 11.0 1.0 CE1 A:HIS222 3.1 10.2 1.0 CE1 A:HIS226 3.2 12.1 1.0 CE1 A:HIS232 3.2 18.1 1.0 O A:HAE272 3.4 42.3 1.0 N A:HAE272 3.6 40.3 1.0 CG A:HIS222 4.2 10.5 1.0 ND1 A:HIS222 4.2 10.3 1.0 CG A:HIS232 4.2 16.6 1.0 CG A:HIS226 4.3 12.1 1.0 ND1 A:HIS232 4.3 16.8 1.0 OE2 A:GLU223 4.3 16.2 1.0 O A:HOH15 4.3 15.4 1.0 ND1 A:HIS226 4.3 12.3 1.0 OE1 A:GLU223 4.8 16.6 1.0 CE A:MET240 4.8 11.2 1.0 C13 A:3KE271 4.9 15.6 1.0 CD A:GLU223 4.9 14.2 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of Human Mmp-13 Complexed with A Phenyl-2H-Tetrazole Compound


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Human Mmp-13 Complexed with A Phenyl-2H-Tetrazole Compound within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn902 b:13.7 occ:1.00 OD2 A:ASP174 1.9 10.5 1.0 NE2 A:HIS187 1.9 12.8 1.0 NE2 A:HIS172 2.1 10.4 1.0 ND1 A:HIS200 2.2 11.1 1.0 CE1 A:HIS187 2.8 14.1 1.0 CG A:ASP174 2.8 11.8 1.0 CD2 A:HIS172 2.9 11.0 1.0 CD2 A:HIS187 3.0 13.5 1.0 OD1 A:ASP174 3.1 12.5 1.0 CE1 A:HIS200 3.1 11.6 1.0 CE1 A:HIS172 3.1 12.5 1.0 CG A:HIS200 3.2 11.2 1.0 CB A:HIS200 3.5 11.3 1.0 ND1 A:HIS187 4.0 15.0 1.0 O A:TYR176 4.1 13.5 1.0 CG A:HIS172 4.1 11.5 1.0 CG A:HIS187 4.1 14.0 1.0 ND1 A:HIS172 4.1 12.1 1.0 NE2 A:HIS200 4.2 10.9 1.0 CB A:ASP174 4.2 12.6 1.0 CD2 A:HIS200 4.3 11.5 1.0 CB A:TYR176 4.7 15.7 1.0 O A:HOH19 4.8 13.1 1.0 C A:TYR176 4.9 14.3 1.0 CZ A:PHE178 4.9 13.7 1.0 CE1 A:PHE189 4.9 16.2 1.0 CE2 A:PHE178 4.9 13.3 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of Human Mmp-13 Complexed with A Phenyl-2H-Tetrazole Compound


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Human Mmp-13 Complexed with A Phenyl-2H-Tetrazole Compound within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn901 b:18.2 occ:1.00 NE2 B:HIS222 2.1 14.7 1.0 NE2 B:HIS226 2.1 14.0 1.0 NE2 B:HIS232 2.2 19.1 1.0 O B:HAE271 2.2 38.8 1.0 CD2 B:HIS222 2.9 12.4 1.0 N B:HAE271 2.9 40.7 1.0 CD2 B:HIS226 3.1 13.0 1.0 CD2 B:HIS232 3.1 19.7 1.0 CE1 B:HIS226 3.1 15.2 1.0 CE1 B:HIS232 3.2 20.3 1.0 CE1 B:HIS222 3.2 15.3 1.0 C2 B:HAE271 3.7 43.1 1.0 OE2 B:GLU223 4.1 16.5 1.0 O2 B:HAE271 4.1 44.0 1.0 CG B:HIS222 4.1 13.8 1.0 ND1 B:HIS222 4.2 14.3 1.0 ND1 B:HIS226 4.2 14.6 1.0 CG B:HIS232 4.2 19.8 1.0 ND1 B:HIS232 4.2 18.9 1.0 CG B:HIS226 4.2 13.4 1.0 O B:HOH67 4.3 20.6 1.0 C1 B:HAE271 4.6 42.6 1.0 CD B:GLU223 4.7 14.6 1.0 OE1 B:GLU223 4.8 15.8 1.0 CE B:MET240 4.9 9.5 1.0 C13 B:3KE2 5.0 15.3 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of Human Mmp-13 Complexed with A Phenyl-2H-Tetrazole Compound


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Human Mmp-13 Complexed with A Phenyl-2H-Tetrazole Compound within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn902 b:14.7 occ:1.00 OD2 B:ASP174 1.8 13.0 1.0 ND1 B:HIS200 2.1 14.3 1.0 NE2 B:HIS172 2.1 13.4 1.0 NE2 B:HIS187 2.1 15.3 1.0 CG B:ASP174 2.8 14.3 1.0 CD2 B:HIS172 2.9 12.8 1.0 CE1 B:HIS200 3.0 15.6 1.0 CE1 B:HIS187 3.1 16.0 1.0 CG B:HIS200 3.1 14.0 1.0 CE1 B:HIS172 3.1 13.7 1.0 CD2 B:HIS187 3.2 14.6 1.0 OD1 B:ASP174 3.2 13.2 1.0 CB B:HIS200 3.5 13.8 1.0 NE2 B:HIS200 4.1 16.2 1.0 CG B:HIS172 4.1 13.2 1.0 ND1 B:HIS172 4.2 15.0 1.0 CB B:ASP174 4.2 15.2 1.0 CD2 B:HIS200 4.2 14.8 1.0 ND1 B:HIS187 4.2 15.8 1.0 CG B:HIS187 4.3 14.9 1.0 O B:TYR176 4.5 16.4 1.0 CE1 B:PHE189 4.6 18.9 1.0 CZ B:PHE178 4.6 13.4 1.0 CZ B:PHE189 4.8 19.3 1.0 O B:HOH44 4.8 12.6 1.0 O B:HOH282 4.8 27.5 1.0 CE2 B:PHE178 4.9 13.8 1.0 CA B:HIS200 4.9 13.4 1.0

M.E.Schnute, P.M.O'brien, J.Nahra, M.Morris, W.Howard Roark, C.E.Hanau, P.G.Ruminski, J.A.Scholten, T.R.Fletcher, B.C.Hamper, J.N.Carroll, W.C.Patt, H.S.Shieh, B.Collins, A.G.Pavlovsky, K.E.Palmquist, K.W.Aston, J.Hitchcock, M.D.Rogers, J.Mcdonald, A.R.Johnson, G.E.Munie, A.J.Wittwer, C.F.Man, S.L.Settle, O.Nemirovskiy, L.E.Vickery, A.Agawal, R.D.Dyer, T.Sunyer. Discovery of (Pyridin-4-Yl)-2H-Tetrazole As A Novel Scaffold to Identify Highly Selective Matrix Metalloproteinase-13 Inhibitors For the Treatment of Osteoarthritis. Bioorg.Med.Chem.Lett. V. 20 576 2010.
ISSN: ISSN 0960-894X
PubMed: 20005097
DOI: 10.1016/J.BMCL.2009.11.081