Zinc in PDB 3o2x: Mmp-13 in Complex with Selective Tetrazole Core Inhibitor

The structure of Mmp-13 in Complex with Selective Tetrazole Core Inhibitor, PDB code: 3o2x was solved by J.R.Kiefer, T.E.Barta, D.P.Becker, K.J.Mathis, J.Williams, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.72 / 1.90
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	73.864, 95.257, 120.076, 90.00, 90.00, 90.00
R / Rfree (%)	17.7 / 21

The structure of Mmp-13 in Complex with Selective Tetrazole Core Inhibitor also contains other interesting chemical elements:

Fluorine	(F)	12 atoms
Calcium	(Ca)	8 atoms

The binding sites of Zinc atom in the Mmp-13 in Complex with Selective Tetrazole Core Inhibitor (pdb code 3o2x). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Mmp-13 in Complex with Selective Tetrazole Core Inhibitor, PDB code: 3o2x:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in the Mmp-13 in Complex with Selective Tetrazole Core 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 in Complex with Selective Tetrazole Core Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1998 b:8.0 occ:1.00 OD2 A:ASP1174 1.9 6.5 1.0 NE2 A:HIS1187 2.0 7.9 1.0 ND1 A:HIS1200 2.0 8.3 1.0 NE2 A:HIS1172 2.1 6.3 1.0 CG A:ASP1174 2.9 5.7 1.0 CD2 A:HIS1172 2.9 6.4 1.0 CE1 A:HIS1187 2.9 7.8 1.0 CE1 A:HIS1200 3.0 8.5 1.0 CD2 A:HIS1187 3.0 7.7 1.0 CG A:HIS1200 3.0 8.7 1.0 CE1 A:HIS1172 3.1 6.4 1.0 OD1 A:ASP1174 3.2 5.6 1.0 CB A:HIS1200 3.4 8.9 1.0 ND1 A:HIS1187 4.1 8.2 1.0 NE2 A:HIS1200 4.1 8.3 1.0 CG A:HIS1172 4.1 5.5 1.0 CG A:HIS1187 4.1 7.8 1.0 CD2 A:HIS1200 4.1 8.2 1.0 ND1 A:HIS1172 4.2 5.7 1.0 CB A:ASP1174 4.3 5.2 1.0 O A:TYR1176 4.4 5.8 1.0 CZ A:PHE1178 4.5 8.3 1.0 CE1 A:PHE1189 4.6 13.1 1.0 O A:HOH3 4.6 5.6 1.0 CE2 A:PHE1178 4.7 7.9 1.0 CZ A:PHE1189 4.8 13.4 1.0 O A:HOH481 4.9 20.9 1.0 CA A:HIS1200 4.9 9.1 1.0 O A:HOH325 4.9 12.4 1.0

Zinc binding site 2 out of 8 in the Mmp-13 in Complex with Selective Tetrazole Core 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 in Complex with Selective Tetrazole Core Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1999 b:8.4 occ:1.00 NE2 A:HIS1232 2.0 9.2 1.0 NE2 A:HIS1222 2.1 6.0 1.0 O6 A:3O21801 2.1 11.8 1.0 O5 A:3O21801 2.2 14.5 1.0 NE2 A:HIS1226 2.2 7.2 1.0 C6 A:3O21801 2.9 14.3 1.0 CD2 A:HIS1232 3.0 9.1 1.0 N2 A:3O21801 3.0 13.6 1.0 CE1 A:HIS1222 3.0 6.2 1.0 CD2 A:HIS1222 3.0 6.7 1.0 CE1 A:HIS1232 3.1 10.3 1.0 CD2 A:HIS1226 3.1 7.7 1.0 CE1 A:HIS1226 3.2 8.0 1.0 O A:HOH26 4.0 7.0 1.0 OE2 A:GLU1223 4.1 10.7 1.0 CG A:HIS1232 4.1 8.9 1.0 ND1 A:HIS1222 4.1 7.2 1.0 ND1 A:HIS1232 4.1 9.8 1.0 CG A:HIS1222 4.2 6.8 1.0 ND1 A:HIS1226 4.3 8.2 1.0 CG A:HIS1226 4.3 7.6 1.0 C1 A:3O21801 4.4 15.2 1.0 OE1 A:GLU1223 4.7 9.2 1.0 CD A:GLU1223 4.7 9.8 1.0 C12 A:3O21801 4.7 13.2 1.0 CE A:MET1240 4.8 8.7 1.0 C5 A:3O21801 4.8 16.1 1.0 C2 A:3O21801 4.9 17.3 1.0 C15 A:3O21801 5.0 13.4 1.0 C10 A:3O21801 5.0 13.3 1.0

Zinc binding site 3 out of 8 in the Mmp-13 in Complex with Selective Tetrazole Core 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 in Complex with Selective Tetrazole Core Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn2998 b:13.2 occ:1.00 OD2 B:ASP2174 1.9 7.7 1.0 NE2 B:HIS2172 2.0 7.0 1.0 ND1 B:HIS2200 2.1 9.4 1.0 NE2 B:HIS2187 2.1 6.8 1.0 CG B:ASP2174 2.9 6.8 1.0 CD2 B:HIS2172 3.0 6.8 1.0 CE1 B:HIS2200 3.0 9.3 1.0 CE1 B:HIS2172 3.0 7.3 1.0 CE1 B:HIS2187 3.0 7.0 1.0 CG B:HIS2200 3.1 8.2 1.0 CD2 B:HIS2187 3.1 6.6 1.0 OD1 B:ASP2174 3.2 6.5 1.0 CB B:HIS2200 3.5 8.0 1.0 ND1 B:HIS2172 4.1 6.2 1.0 CG B:HIS2172 4.1 6.2 1.0 NE2 B:HIS2200 4.1 9.0 1.0 ND1 B:HIS2187 4.2 6.1 1.0 CD2 B:HIS2200 4.2 8.8 1.0 CB B:ASP2174 4.2 6.5 1.0 CG B:HIS2187 4.3 7.7 1.0 O B:TYR2176 4.3 6.4 1.0 CE1 B:PHE2189 4.7 10.4 1.0 CZ B:PHE2189 4.7 10.4 1.0 O B:HOH55 4.7 4.5 1.0 CZ B:PHE2178 4.7 7.0 1.0 CE2 B:PHE2178 4.8 6.7 1.0 O B:HOH168 4.9 7.0 1.0 CA B:HIS2200 5.0 7.9 1.0

Zinc binding site 4 out of 8 in the Mmp-13 in Complex with Selective Tetrazole Core 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 in Complex with Selective Tetrazole Core Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn2999 b:15.0 occ:1.00 NE2 B:HIS2232 2.1 11.1 1.0 O5 B:3O21801 2.1 21.1 1.0 NE2 B:HIS2222 2.1 7.6 1.0 NE2 B:HIS2226 2.1 7.6 1.0 O6 B:3O21801 2.2 19.4 1.0 C6 B:3O21801 2.9 21.8 1.0 CD2 B:HIS2232 3.0 10.9 1.0 CD2 B:HIS2222 3.0 8.3 1.0 N2 B:3O21801 3.0 20.1 1.0 CE1 B:HIS2232 3.1 11.4 1.0 CE1 B:HIS2226 3.1 7.7 1.0 CD2 B:HIS2226 3.1 8.0 1.0 CE1 B:HIS2222 3.2 9.2 1.0 O B:HOH41 4.0 13.3 1.0 OE2 B:GLU2223 4.0 9.6 1.0 CG B:HIS2232 4.1 10.8 1.0 ND1 B:HIS2232 4.2 10.5 1.0 CG B:HIS2222 4.2 8.1 1.0 ND1 B:HIS2226 4.2 8.2 1.0 ND1 B:HIS2222 4.2 8.0 1.0 CG B:HIS2226 4.3 8.0 1.0 C1 B:3O21801 4.3 22.8 1.0 C12 B:3O21801 4.6 22.7 1.0 CD B:GLU2223 4.7 9.1 1.0 OE1 B:GLU2223 4.7 9.2 1.0 CE B:MET2240 4.8 7.8 1.0 C5 B:3O21801 4.8 23.4 1.0 C15 B:3O21801 4.9 24.0 1.0 C2 B:3O21801 4.9 24.5 1.0 C10 B:3O21801 4.9 23.0 1.0

Zinc binding site 5 out of 8 in the Mmp-13 in Complex with Selective Tetrazole Core Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Mmp-13 in Complex with Selective Tetrazole Core Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn1998 b:9.0 occ:1.00 OD2 C:ASP1174 1.9 7.2 1.0 NE2 C:HIS1187 2.0 8.7 1.0 ND1 C:HIS1200 2.0 8.6 1.0 NE2 C:HIS1172 2.0 8.3 1.0 CG C:ASP1174 2.8 7.1 1.0 CD2 C:HIS1172 2.9 7.8 1.0 CE1 C:HIS1187 2.9 9.0 1.0 CE1 C:HIS1200 3.0 8.8 1.0 CD2 C:HIS1187 3.0 9.0 1.0 CG C:HIS1200 3.1 8.1 1.0 CE1 C:HIS1172 3.1 6.9 1.0 OD1 C:ASP1174 3.1 6.8 1.0 CB C:HIS1200 3.4 8.3 1.0 ND1 C:HIS1187 4.0 9.5 1.0 CG C:HIS1172 4.1 7.3 1.0 NE2 C:HIS1200 4.1 7.6 1.0 CG C:HIS1187 4.1 8.9 1.0 ND1 C:HIS1172 4.2 7.2 1.0 CD2 C:HIS1200 4.2 8.7 1.0 CB C:ASP1174 4.2 6.8 1.0 O C:TYR1176 4.2 8.0 1.0 CZ C:PHE1189 4.6 13.6 1.0 CB C:TYR1176 4.6 8.8 1.0 CE2 C:PHE1178 4.8 8.6 1.0 CZ C:PHE1178 4.9 8.7 1.0 CE1 C:PHE1189 4.9 13.7 1.0 O C:HOH254 4.9 16.9 1.0 CA C:HIS1200 4.9 8.2 1.0 C C:TYR1176 5.0 7.7 1.0

Zinc binding site 6 out of 8 in the Mmp-13 in Complex with Selective Tetrazole Core Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Mmp-13 in Complex with Selective Tetrazole Core Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn1999 b:9.3 occ:1.00 NE2 C:HIS1222 2.0 7.4 1.0 NE2 C:HIS1232 2.0 9.9 1.0 O5 C:3O21801 2.1 14.0 1.0 NE2 C:HIS1226 2.1 8.2 1.0 O6 C:3O21801 2.2 12.1 1.0 C6 C:3O21801 2.9 15.0 1.0 CD2 C:HIS1232 3.0 9.3 1.0 CD2 C:HIS1222 3.0 7.9 1.0 CE1 C:HIS1222 3.0 8.1 1.0 CE1 C:HIS1232 3.1 9.5 1.0 N2 C:3O21801 3.1 13.4 1.0 CD2 C:HIS1226 3.1 8.2 1.0 CE1 C:HIS1226 3.1 8.5 1.0 O C:HOH46 4.0 10.2 1.0 OE2 C:GLU1223 4.1 11.3 1.0 ND1 C:HIS1222 4.1 7.5 1.0 CG C:HIS1232 4.1 9.2 1.0 ND1 C:HIS1232 4.1 9.5 1.0 CG C:HIS1222 4.2 7.7 1.0 ND1 C:HIS1226 4.2 7.6 1.0 CG C:HIS1226 4.3 7.6 1.0 C1 C:3O21801 4.4 16.2 1.0 C12 C:3O21801 4.7 14.1 1.0 CD C:GLU1223 4.8 10.8 1.0 OE1 C:GLU1223 4.8 10.7 1.0 CE C:MET1240 4.8 6.0 1.0 C5 C:3O21801 4.8 16.9 1.0 C2 C:3O21801 4.9 18.3 1.0 C10 C:3O21801 4.9 14.4 1.0 C15 C:3O21801 5.0 13.7 1.0

Zinc binding site 7 out of 8 in the Mmp-13 in Complex with Selective Tetrazole Core Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Mmp-13 in Complex with Selective Tetrazole Core Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn2998 b:12.0 occ:1.00 OD2 D:ASP2174 1.9 6.8 1.0 NE2 D:HIS2187 2.0 8.0 1.0 NE2 D:HIS2172 2.0 7.7 1.0 ND1 D:HIS2200 2.0 7.1 1.0 CG D:ASP2174 2.8 6.3 1.0 CD2 D:HIS2172 2.9 6.4 1.0 CE1 D:HIS2187 2.9 8.6 1.0 CE1 D:HIS2200 3.0 8.4 1.0 CD2 D:HIS2187 3.0 8.6 1.0 CG D:HIS2200 3.1 7.5 1.0 CE1 D:HIS2172 3.1 6.8 1.0 OD1 D:ASP2174 3.1 6.6 1.0 CB D:HIS2200 3.4 8.5 1.0 ND1 D:HIS2187 4.0 8.6 1.0 CG D:HIS2172 4.1 6.8 1.0 ND1 D:HIS2172 4.1 7.2 1.0 NE2 D:HIS2200 4.1 7.2 1.0 CG D:HIS2187 4.1 8.1 1.0 CD2 D:HIS2200 4.2 7.6 1.0 CB D:ASP2174 4.2 6.1 1.0 O D:TYR2176 4.2 7.0 1.0 CZ D:PHE2189 4.4 13.1 1.0 CB D:TYR2176 4.6 8.1 1.0 CE1 D:PHE2189 4.8 13.6 1.0 CE2 D:PHE2178 4.8 7.2 1.0 CZ D:PHE2178 4.9 7.8 1.0 CA D:HIS2200 4.9 8.0 1.0 C D:TYR2176 5.0 7.4 1.0

Zinc binding site 8 out of 8 in the Mmp-13 in Complex with Selective Tetrazole Core Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Mmp-13 in Complex with Selective Tetrazole Core Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn2999 b:11.4 occ:1.00 NE2 D:HIS2222 2.1 6.5 1.0 NE2 D:HIS2232 2.1 6.9 1.0 O5 D:3O21801 2.1 18.1 1.0 O6 D:3O21801 2.1 15.1 1.0 NE2 D:HIS2226 2.1 8.0 1.0 C6 D:3O21801 2.9 19.5 1.0 N2 D:3O21801 3.0 17.6 1.0 CD2 D:HIS2232 3.0 6.9 1.0 CD2 D:HIS2222 3.0 6.8 1.0 CE1 D:HIS2222 3.1 7.3 1.0 CE1 D:HIS2232 3.1 7.6 1.0 CD2 D:HIS2226 3.1 9.5 1.0 CE1 D:HIS2226 3.2 7.9 1.0 OE2 D:GLU2223 4.0 8.7 1.0 O D:HOH86 4.0 11.7 1.0 ND1 D:HIS2232 4.2 6.6 1.0 ND1 D:HIS2222 4.2 7.3 1.0 CG D:HIS2232 4.2 6.8 1.0 CG D:HIS2222 4.2 7.1 1.0 ND1 D:HIS2226 4.3 7.2 1.0 CG D:HIS2226 4.3 7.7 1.0 C1 D:3O21801 4.4 20.5 1.0 C12 D:3O21801 4.7 18.6 1.0 CD D:GLU2223 4.7 8.9 1.0 O D:HOH833 4.7 25.7 1.0 OE1 D:GLU2223 4.7 8.6 1.0 CE D:MET2240 4.8 5.6 1.0 C5 D:3O21801 4.9 21.8 1.0 C10 D:3O21801 4.9 19.3 1.0 C15 D:3O21801 4.9 18.7 1.0 C2 D:3O21801 4.9 22.9 1.0

T.E.Barta, D.P.Becker, L.J.Bedell, S.L.Hockerman, J.R.Kiefer, M.H.Li, C.I.Villamill, J.G.Rico, J.J.Mcdonald. Mmp-13 in Complex with Selective Tetrazole Core Inhibitor To Be Published.