Zinc in PDB 3zxh: Mmp-13 Complexed with 2-Napthylsulfonamide Hydroxamic Acid Inhibitor

The structure of Mmp-13 Complexed with 2-Napthylsulfonamide Hydroxamic Acid Inhibitor, PDB code: 3zxh was solved by K.L.Clark, R.Kulathila, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	9.00 / 1.30
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	134.904, 36.141, 95.069, 90.00, 131.02, 90.00
R / Rfree (%)	14.5 / 15.9

The structure of Mmp-13 Complexed with 2-Napthylsulfonamide Hydroxamic Acid Inhibitor also contains other interesting chemical elements:

Calcium

(Ca)

7 atoms

The binding sites of Zinc atom in the Mmp-13 Complexed with 2-Napthylsulfonamide Hydroxamic Acid Inhibitor (pdb code 3zxh). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Mmp-13 Complexed with 2-Napthylsulfonamide Hydroxamic Acid Inhibitor, PDB code: 3zxh:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Mmp-13 Complexed with 2-Napthylsulfonamide Hydroxamic Acid Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Mmp-13 Complexed with 2-Napthylsulfonamide Hydroxamic Acid Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn300 b:7.6 occ:1.00 O A:E41401 2.0 9.2 1.0 NE2 A:HIS222 2.1 7.8 1.0 NE2 A:HIS226 2.1 6.4 1.0 NE2 A:HIS232 2.1 7.5 1.0 O1 A:E41401 2.2 7.9 1.0 C A:E41401 2.9 8.7 1.0 N1 A:E41401 3.0 8.1 1.0 CD2 A:HIS222 3.0 6.8 1.0 CE1 A:HIS226 3.1 7.5 1.0 CE1 A:HIS232 3.1 9.5 1.0 CE1 A:HIS222 3.1 7.0 1.0 CD2 A:HIS226 3.1 6.0 1.0 CD2 A:HIS232 3.2 7.5 1.0 HD2 A:HIS222 3.2 8.2 1.0 HE1 A:HIS232 3.2 11.4 1.0 HE1 A:HIS226 3.2 8.9 1.0 HE1 A:HIS222 3.3 8.4 1.0 HD2 A:HIS226 3.3 7.2 1.0 HD2 A:HIS232 3.3 9.1 1.0 HB3 A:PRO242 4.0 16.4 1.0 OE2 A:GLU223 4.1 8.3 1.0 O A:HOH2142 4.1 8.8 1.0 ND1 A:HIS222 4.2 6.9 1.0 CG A:HIS222 4.2 7.1 1.0 ND1 A:HIS232 4.2 9.4 1.0 ND1 A:HIS226 4.2 7.3 1.0 CG A:HIS226 4.3 6.6 1.0 CG A:HIS232 4.3 8.0 1.0 HE2 A:MET240 4.3 9.7 1.0 HE1 A:MET240 4.3 9.7 1.0 CA A:E41401 4.3 9.2 1.0 HA A:PRO242 4.7 14.3 1.0 C8 A:E41401 4.7 8.9 1.0 CG2 A:E41401 4.8 13.0 1.0 C7 A:E41401 4.8 7.9 1.0 CE A:MET240 4.8 8.1 1.0 CB A:PRO242 4.9 13.7 1.0 CB A:E41401 4.9 10.9 1.0 C11 A:E41401 4.9 8.2 1.0 C18 A:E41401 5.0 11.5 1.0 HD1 A:HIS222 5.0 8.3 1.0 HD1 A:HIS232 5.0 11.3 1.0 HD1 A:HIS226 5.0 8.7 1.0 N A:E41401 5.0 10.3 1.0

Zinc binding site 2 out of 4 in the Mmp-13 Complexed with 2-Napthylsulfonamide Hydroxamic Acid Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Mmp-13 Complexed with 2-Napthylsulfonamide Hydroxamic Acid Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:8.0 occ:1.00 OD2 A:ASP174 1.9 8.6 1.0 NE2 A:HIS187 2.0 9.9 1.0 NE2 A:HIS172 2.0 7.3 1.0 ND1 A:HIS200 2.1 8.1 1.0 CG A:ASP174 2.9 8.1 1.0 CE1 A:HIS187 2.9 12.5 1.0 CD2 A:HIS172 2.9 7.3 1.0 CE1 A:HIS200 3.0 8.1 1.0 CE1 A:HIS172 3.0 7.3 1.0 HE1 A:HIS187 3.1 15.0 1.0 CD2 A:HIS187 3.1 12.8 1.0 HD2 A:HIS172 3.1 8.8 1.0 CG A:HIS200 3.1 7.2 1.0 HB2 A:HIS200 3.1 7.6 1.0 HE1 A:HIS200 3.1 9.7 1.0 OD1 A:ASP174 3.1 8.3 1.0 HE1 A:HIS172 3.3 8.7 1.0 HD2 A:HIS187 3.3 15.3 1.0 CB A:HIS200 3.5 6.3 1.0 HB3 A:HIS200 3.5 7.6 1.0 HB2 A:TYR176 3.8 17.5 1.0 HE1 A:PHE189 3.9 16.5 1.0 ND1 A:HIS187 4.1 12.5 1.0 CG A:HIS172 4.1 8.0 1.0 ND1 A:HIS172 4.1 7.4 1.0 NE2 A:HIS200 4.1 7.9 1.0 O A:TYR176 4.1 10.3 1.0 CG A:HIS187 4.2 8.9 1.0 CD2 A:HIS200 4.2 8.3 1.0 CB A:ASP174 4.2 8.9 1.0 HB3 A:ASP174 4.3 10.7 1.0 HZ A:PHE189 4.3 16.8 1.0 HZ A:PHE178 4.5 11.6 1.0 CE1 A:PHE189 4.6 13.8 1.0 HB2 A:ASP174 4.6 10.7 1.0 HE2 A:PHE178 4.7 11.8 1.0 CB A:TYR176 4.7 14.6 1.0 CZ A:PHE178 4.7 9.7 1.0 HD2 A:TYR176 4.7 19.1 1.0 H A:TYR176 4.8 14.4 1.0 CE2 A:PHE178 4.8 9.9 1.0 CZ A:PHE189 4.8 14.0 1.0 HD1 A:HIS187 4.8 15.0 1.0 HE2 A:HIS200 4.9 9.5 1.0 HD1 A:HIS172 4.9 8.9 1.0 C A:TYR176 4.9 9.6 1.0 CA A:HIS200 5.0 5.9 1.0 O A:HOH2122 5.0 8.3 1.0

Zinc binding site 3 out of 4 in the Mmp-13 Complexed with 2-Napthylsulfonamide Hydroxamic Acid Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Mmp-13 Complexed with 2-Napthylsulfonamide Hydroxamic Acid Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn300 b:8.1 occ:1.00 O B:E41401 2.0 9.0 1.0 NE2 B:HIS222 2.1 7.2 1.0 NE2 B:HIS226 2.1 7.8 1.0 NE2 B:HIS232 2.1 7.6 1.0 O1 B:E41401 2.2 8.5 1.0 C B:E41401 2.8 8.2 1.0 N1 B:E41401 3.0 9.0 1.0 CD2 B:HIS222 3.0 7.7 1.0 CE1 B:HIS222 3.1 7.0 1.0 CE1 B:HIS226 3.1 8.3 1.0 CE1 B:HIS232 3.1 9.5 1.0 CD2 B:HIS226 3.1 7.0 1.0 CD2 B:HIS232 3.1 7.9 1.0 HD2 B:HIS222 3.2 9.2 1.0 HE1 B:HIS226 3.2 10.0 1.0 HE1 B:HIS232 3.2 11.3 1.0 HE1 B:HIS222 3.2 8.4 1.0 HD2 B:HIS226 3.3 8.4 1.0 HD2 B:HIS232 3.3 9.5 1.0 OE2 B:GLU223 4.2 8.7 1.0 ND1 B:HIS222 4.2 7.7 1.0 HB3 B:PRO242 4.2 16.7 1.0 ND1 B:HIS232 4.2 9.9 1.0 CG B:HIS222 4.2 7.0 1.0 ND1 B:HIS226 4.2 7.8 1.0 CG B:HIS226 4.2 7.7 1.0 CG B:HIS232 4.3 8.1 1.0 O B:HOH2138 4.3 9.1 1.0 CA B:E41401 4.3 9.5 1.0 HE2 B:MET240 4.4 10.6 1.0 HE1 B:MET240 4.4 10.6 1.0 C8 B:E41401 4.6 8.7 1.0 C7 B:E41401 4.7 7.8 1.0 CG2 B:E41401 4.8 11.4 1.0 HA B:PRO242 4.8 13.3 1.0 O B:HOH2106 4.8 21.9 1.0 CE B:MET240 4.9 8.8 1.0 C18 B:E41401 4.9 10.1 1.0 CB B:E41401 4.9 9.5 1.0 C11 B:E41401 4.9 8.5 1.0 N B:E41401 4.9 9.1 1.0 HD1 B:HIS222 4.9 9.3 1.0 HD1 B:HIS232 5.0 11.9 1.0 C6 B:E41401 5.0 8.8 1.0 HD1 B:HIS226 5.0 9.4 1.0

Zinc binding site 4 out of 4 in the Mmp-13 Complexed with 2-Napthylsulfonamide Hydroxamic Acid Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Mmp-13 Complexed with 2-Napthylsulfonamide Hydroxamic Acid Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:7.5 occ:1.00 OD2 B:ASP174 2.0 8.2 1.0 NE2 B:HIS187 2.0 7.5 1.0 NE2 B:HIS172 2.0 6.9 1.0 ND1 B:HIS200 2.0 6.4 1.0 CG B:ASP174 2.9 7.7 1.0 CE1 B:HIS200 2.9 6.8 1.0 CE1 B:HIS187 2.9 7.7 1.0 CD2 B:HIS172 3.0 7.1 1.0 CE1 B:HIS172 3.0 7.2 1.0 HE1 B:HIS200 3.1 8.2 1.0 CD2 B:HIS187 3.1 8.0 1.0 HE1 B:HIS187 3.1 9.2 1.0 CG B:HIS200 3.1 6.5 1.0 HD2 B:HIS172 3.2 8.6 1.0 HB2 B:HIS200 3.2 7.7 1.0 OD1 B:ASP174 3.2 8.2 1.0 HE1 B:HIS172 3.2 8.7 1.0 HD2 B:HIS187 3.3 9.6 1.0 CB B:HIS200 3.5 6.5 1.0 HB3 B:HIS200 3.5 7.7 1.0 HB2 B:TYR176 3.8 12.9 1.0 HE1 B:PHE189 4.0 15.6 1.0 ND1 B:HIS187 4.1 8.2 1.0 NE2 B:HIS200 4.1 7.6 1.0 ND1 B:HIS172 4.1 6.8 1.0 CG B:HIS172 4.1 7.3 1.0 CG B:HIS187 4.2 7.6 1.0 CD2 B:HIS200 4.2 7.5 1.0 CB B:ASP174 4.2 8.7 1.0 HB3 B:ASP174 4.3 10.4 1.0 O B:TYR176 4.3 8.5 1.0 HZ B:PHE189 4.3 16.8 1.0 HZ B:PHE178 4.4 10.8 1.0 HD2 B:TYR176 4.5 15.3 1.0 CZ B:PHE178 4.6 9.0 1.0 HB2 B:ASP174 4.6 10.4 1.0 HE2 B:PHE178 4.7 10.9 1.0 O B:HOH2123 4.7 19.0 1.0 CE1 B:PHE189 4.7 13.0 1.0 CE2 B:PHE178 4.8 9.1 1.0 CB B:TYR176 4.8 10.8 1.0 O B:HOH2121 4.8 8.5 1.0 HE2 B:HIS200 4.9 9.2 1.0 HD1 B:HIS187 4.9 9.8 1.0 CZ B:PHE189 4.9 14.0 1.0 HD1 B:HIS172 4.9 8.1 1.0 H B:TYR176 4.9 10.9 1.0 H B:ASP174 5.0 10.2 1.0 CA B:HIS200 5.0 5.6 1.0

R.A.Tommasi, S.Weiler, L.W.Mcquire, O.Rogel, M.Chambers, K.L.Clark, J.Doughty, J.Fang, V.Ganu, J.Grob, R.Goldberg, R.Goldstein, S.Lavoie, R.Kulathila, W.Macchia, R.Melton, C.Springer, M.Walker, J.Zhang, L.Zhu, M.Shultz. Potent and Selective 2-Naphthylsulfonamide Substituted Hydroxamic Acid Inhibitors of Matrix Metalloproteinase-13. Bioorg.Med.Chem.Lett. V. 21 6440 2011.
ISSN: ISSN 0960-894X
PubMed: 21937229
DOI: 10.1016/J.BMCL.2011.08.087