Zinc in PDB 3elm: Crystal Structure of Mmp-13 Complexed with Inhibitor 24F

The structure of Crystal Structure of Mmp-13 Complexed with Inhibitor 24F, PDB code: 3elm was solved by R.Kulathila, L.Monovich, J.Koehn, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.56 / 1.90
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	134.500, 36.070, 95.180, 90.00, 130.53, 90.00
R / Rfree (%)	n/a / n/a

The structure of Crystal Structure of Mmp-13 Complexed with Inhibitor 24F also contains other interesting chemical elements:

Calcium

(Ca)

7 atoms

The binding sites of Zinc atom in the Crystal Structure of Mmp-13 Complexed with Inhibitor 24F (pdb code 3elm). 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 Mmp-13 Complexed with Inhibitor 24F, PDB code: 3elm:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of Mmp-13 Complexed with Inhibitor 24F


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 Mmp-13 Complexed with Inhibitor 24F within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn300 b:16.4 occ:1.00 NE2 A:HIS232 2.0 17.1 1.0 NE2 A:HIS226 2.1 14.3 1.0 NE2 A:HIS222 2.1 14.1 1.0 O21 A:24F400 2.1 22.5 1.0 OM0 A:24F400 2.6 18.7 1.0 C19 A:24F400 2.6 24.2 1.0 CE1 A:HIS232 2.9 18.0 1.0 CD2 A:HIS232 3.0 16.2 1.0 CE1 A:HIS226 3.0 12.3 1.0 CD2 A:HIS222 3.1 12.1 1.0 CD2 A:HIS226 3.1 13.1 1.0 CE1 A:HIS222 3.1 12.6 1.0 ND1 A:HIS232 4.1 17.9 1.0 CG A:HIS232 4.1 16.6 1.0 ND1 A:HIS226 4.1 13.0 1.0 C18 A:24F400 4.1 25.4 1.0 ND1 A:HIS222 4.2 11.3 1.0 CG A:HIS226 4.2 12.8 1.0 CG A:HIS222 4.2 13.0 1.0 O A:HOH1202 4.5 22.2 1.0 C23 A:24F400 4.5 28.8 1.0 OE2 A:GLU223 4.6 11.6 1.0 CE A:MET240 4.7 9.8 1.0 C22 A:24F400 4.7 27.5 1.0 N15 A:24F400 4.7 24.8 1.0 S13 A:24F400 4.9 25.9 1.0 C09 A:24F400 4.9 25.6 1.0 C12 A:24F400 4.9 25.5 1.0 OE1 A:GLU223 5.0 14.5 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of Mmp-13 Complexed with Inhibitor 24F


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 Mmp-13 Complexed with Inhibitor 24F within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:15.4 occ:1.00 NE2 A:HIS172 1.9 10.6 1.0 OD2 A:ASP174 2.0 14.4 1.0 ND1 A:HIS200 2.0 14.7 1.0 NE2 A:HIS187 2.0 20.1 1.0 CD2 A:HIS172 2.8 12.4 1.0 CE1 A:HIS187 2.9 20.9 1.0 CG A:ASP174 2.9 14.0 1.0 CE1 A:HIS200 2.9 18.0 1.0 CE1 A:HIS172 3.0 10.4 1.0 CG A:HIS200 3.0 14.4 1.0 OD1 A:ASP174 3.1 13.6 1.0 CD2 A:HIS187 3.1 18.3 1.0 CB A:HIS200 3.4 11.8 1.0 CG A:HIS172 4.0 11.8 1.0 ND1 A:HIS172 4.0 13.6 1.0 ND1 A:HIS187 4.1 21.9 1.0 NE2 A:HIS200 4.1 15.4 1.0 CD2 A:HIS200 4.1 14.7 1.0 O A:TYR176 4.2 16.6 1.0 CG A:HIS187 4.2 18.1 1.0 CB A:ASP174 4.3 12.9 1.0 CE1 A:PHE189 4.5 20.2 1.0 CZ A:PHE178 4.6 14.3 1.0 CE2 A:PHE178 4.8 13.9 1.0 CZ A:PHE189 4.8 19.5 1.0 CB A:TYR176 4.9 20.2 1.0 CA A:HIS200 4.9 12.1 1.0 O A:HOH1012 5.0 13.3 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of Mmp-13 Complexed with Inhibitor 24F


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 Mmp-13 Complexed with Inhibitor 24F within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn300 b:19.8 occ:1.00 O21 B:24F400 1.9 21.9 1.0 NE2 B:HIS226 2.1 17.5 1.0 NE2 B:HIS222 2.1 15.0 1.0 NE2 B:HIS232 2.1 16.4 1.0 C19 B:24F400 2.6 23.9 1.0 OM0 B:24F400 2.7 23.4 1.0 CD2 B:HIS232 3.0 16.4 1.0 CE1 B:HIS222 3.0 14.3 1.0 CD2 B:HIS222 3.0 14.5 1.0 CE1 B:HIS226 3.0 16.9 1.0 CD2 B:HIS226 3.0 16.9 1.0 CE1 B:HIS232 3.1 21.1 1.0 C18 B:24F400 4.1 24.5 1.0 ND1 B:HIS222 4.1 15.8 1.0 ND1 B:HIS226 4.1 16.8 1.0 CG B:HIS222 4.1 14.8 1.0 CG B:HIS232 4.2 18.5 1.0 ND1 B:HIS232 4.2 20.1 1.0 CG B:HIS226 4.2 16.7 1.0 CE B:MET240 4.7 13.3 1.0 N15 B:24F400 4.7 26.8 1.0 C23 B:24F400 4.7 23.6 1.0 OE2 B:GLU223 4.7 14.2 1.0 C22 B:24F400 4.7 24.6 1.0 S13 B:24F400 4.8 24.6 1.0 O B:HOH1226 4.8 40.7 1.0 C09 B:24F400 4.9 22.4 1.0 C12 B:24F400 4.9 25.0 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of Mmp-13 Complexed with Inhibitor 24F


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 Mmp-13 Complexed with Inhibitor 24F within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:16.8 occ:1.00 NE2 B:HIS172 2.0 11.4 1.0 OD2 B:ASP174 2.0 15.4 1.0 ND1 B:HIS200 2.0 13.3 1.0 NE2 B:HIS187 2.0 14.5 1.0 CD2 B:HIS172 2.9 11.2 1.0 CG B:ASP174 2.9 16.0 1.0 CE1 B:HIS187 2.9 16.6 1.0 CE1 B:HIS200 3.0 12.7 1.0 CE1 B:HIS172 3.0 14.6 1.0 CG B:HIS200 3.1 11.4 1.0 CD2 B:HIS187 3.1 15.3 1.0 OD1 B:ASP174 3.2 13.1 1.0 CB B:HIS200 3.5 11.7 1.0 CG B:HIS172 4.0 13.5 1.0 ND1 B:HIS172 4.1 13.1 1.0 ND1 B:HIS187 4.1 14.8 1.0 NE2 B:HIS200 4.1 14.0 1.0 CD2 B:HIS200 4.2 13.9 1.0 CG B:HIS187 4.2 14.4 1.0 CB B:ASP174 4.3 13.4 1.0 O B:TYR176 4.3 14.8 1.0 CZ B:PHE178 4.6 12.2 1.0 CE2 B:PHE178 4.6 11.6 1.0 CE1 B:PHE189 4.7 18.5 1.0 CB B:TYR176 4.9 17.9 1.0 CZ B:PHE189 4.9 19.9 1.0 O B:HOH1014 4.9 16.1 1.0 O B:HOH1150 4.9 39.4 1.0 CA B:HIS200 5.0 12.2 1.0

L.G.Monovich, R.A.Tommasi, R.A.Fujimoto, V.Blancuzzi, K.Clark, W.D.Cornell, R.Doti, J.Doughty, J.Fang, D.Farley, J.Fitt, V.Ganu, R.Goldberg, R.Goldstein, S.Lavoie, R.Kulathila, W.Macchia, D.T.Parker, R.Melton, E.O'byrne, G.Pastor, T.Pellas, E.Quadros, N.Reel, D.M.Roland, Y.Sakane, H.Singh, J.Skiles, J.Somers, K.Toscano, A.Wigg, S.Zhou, L.Zhu, W.C.Shieh, S.Xue, L.W.Mcquire. Discovery of Potent, Selective, and Orally Active Carboxylic Acid Based Inhibitors of Matrix Metalloproteinase-13 J.Med.Chem. V. 52 3523 2009.
ISSN: ISSN 0022-2623
PubMed: 19422229
DOI: 10.1021/JM801394M