Zinc in PDB 3i7g: Mmp-13 in Complex with A Non Zinc-Chelating Inhibitor

The structure of Mmp-13 in Complex with A Non Zinc-Chelating Inhibitor, PDB code: 3i7g was solved by N.A.Farrow, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	33.37 / 1.95
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	133.770, 36.100, 95.333, 90.00, 130.77, 90.00
R / Rfree (%)	17.3 / 22.8

The structure of Mmp-13 in Complex with A Non Zinc-Chelating Inhibitor also contains other interesting chemical elements:

Chlorine	(Cl)	1 atom
Calcium	(Ca)	6 atoms

The binding sites of Zinc atom in the Mmp-13 in Complex with A Non Zinc-Chelating Inhibitor (pdb code 3i7g). 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 in Complex with A Non Zinc-Chelating Inhibitor, PDB code: 3i7g:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Mmp-13 in Complex with A Non Zinc-Chelating 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 A Non Zinc-Chelating Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1261 b:17.2 occ:1.00 NE2 A:HIS226 2.0 14.1 1.0 NE2 A:HIS222 2.1 14.1 1.0 NE2 A:HIS232 2.1 18.7 1.0 O1 A:FMT2 2.3 23.0 1.0 O2 A:FMT2 2.3 30.6 1.0 C A:FMT2 2.6 21.9 1.0 CD2 A:HIS232 2.9 15.2 1.0 CE1 A:HIS226 3.0 18.1 1.0 CD2 A:HIS226 3.0 14.1 1.0 CD2 A:HIS222 3.1 15.7 1.0 CE1 A:HIS222 3.1 14.2 1.0 CE1 A:HIS232 3.2 21.1 1.0 CG A:HIS232 4.1 16.3 1.0 ND1 A:HIS226 4.1 14.9 1.0 ND1 A:HIS222 4.2 13.2 1.0 CG A:HIS226 4.2 14.6 1.0 CG A:HIS222 4.2 14.2 1.0 ND1 A:HIS232 4.2 21.3 1.0 OE2 A:GLU223 4.3 12.4 1.0 O A:HOH475 4.6 25.1 1.0 C10 A:732999 4.7 33.2 1.0 CE A:MET240 4.7 13.7 1.0 C9 A:732999 4.8 27.3 1.0 OE1 A:GLU223 4.8 18.2 1.0 CD A:GLU223 4.9 17.8 1.0 C7 A:732999 5.0 29.5 1.0 O A:HOH481 5.0 38.5 1.0

Zinc binding site 2 out of 4 in the Mmp-13 in Complex with A Non Zinc-Chelating 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 A Non Zinc-Chelating Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1262 b:15.8 occ:1.00 ND1 A:HIS200 2.0 12.6 1.0 OD2 A:ASP174 2.0 12.7 1.0 NE2 A:HIS172 2.0 12.0 1.0 NE2 A:HIS187 2.0 15.7 1.0 CE1 A:HIS200 2.9 17.1 1.0 CD2 A:HIS172 2.9 11.6 1.0 CG A:ASP174 2.9 14.3 1.0 CE1 A:HIS187 3.0 20.9 1.0 CG A:HIS200 3.0 16.6 1.0 CD2 A:HIS187 3.1 13.4 1.0 CE1 A:HIS172 3.1 12.5 1.0 OD1 A:ASP174 3.2 14.9 1.0 CB A:HIS200 3.4 12.1 1.0 NE2 A:HIS200 4.0 14.3 1.0 CG A:HIS172 4.1 13.0 1.0 CD2 A:HIS200 4.1 13.1 1.0 ND1 A:HIS187 4.1 19.1 1.0 ND1 A:HIS172 4.1 14.5 1.0 CG A:HIS187 4.2 13.9 1.0 O A:TYR176 4.2 13.9 1.0 CB A:ASP174 4.3 16.7 1.0 CE1 A:PHE189 4.4 17.5 1.0 CZ A:PHE178 4.7 13.3 1.0 CB A:TYR176 4.7 21.2 1.0 CE2 A:PHE178 4.8 12.3 1.0 CZ A:PHE189 4.8 20.5 1.0 CA A:HIS200 4.9 16.6 1.0 O A:HOH522 4.9 29.1 1.0 C A:TYR176 5.0 14.8 1.0

Zinc binding site 3 out of 4 in the Mmp-13 in Complex with A Non Zinc-Chelating 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 A Non Zinc-Chelating Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn2261 b:22.4 occ:1.00 NE2 B:HIS226 2.0 16.3 1.0 NE2 B:HIS222 2.1 20.5 1.0 NE2 B:HIS232 2.2 24.2 1.0 O1 B:FMT3 2.3 33.1 1.0 C B:FMT3 2.4 24.4 1.0 O2 B:FMT3 2.6 28.3 1.0 CD2 B:HIS232 3.0 25.8 1.0 CD2 B:HIS226 3.0 16.9 1.0 CD2 B:HIS222 3.0 20.0 1.0 CE1 B:HIS226 3.0 20.3 1.0 CE1 B:HIS222 3.1 24.5 1.0 CE1 B:HIS232 3.2 35.0 1.0 CG B:HIS232 4.1 25.0 1.0 ND1 B:HIS226 4.1 22.0 1.0 CG B:HIS226 4.2 21.4 1.0 CG B:HIS222 4.2 22.1 1.0 ND1 B:HIS222 4.2 19.5 1.0 ND1 B:HIS232 4.2 22.7 1.0 OE2 B:GLU223 4.5 18.6 1.0 O B:HOH553 4.6 41.5 1.0 O B:HOH490 4.6 20.9 1.0 CE B:MET240 4.7 18.5 1.0 OE1 B:GLU223 4.9 17.4 1.0

Zinc binding site 4 out of 4 in the Mmp-13 in Complex with A Non Zinc-Chelating 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 A Non Zinc-Chelating Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn2262 b:16.5 occ:1.00 OD2 B:ASP174 2.0 14.7 1.0 NE2 B:HIS172 2.0 13.6 1.0 NE2 B:HIS187 2.1 14.2 1.0 ND1 B:HIS200 2.2 15.1 1.0 CG B:ASP174 2.9 18.1 1.0 CD2 B:HIS172 2.9 12.1 1.0 CE1 B:HIS187 3.0 17.5 1.0 CE1 B:HIS172 3.1 12.8 1.0 OD1 B:ASP174 3.1 14.6 1.0 CE1 B:HIS200 3.1 14.3 1.0 CD2 B:HIS187 3.1 17.6 1.0 CG B:HIS200 3.2 13.6 1.0 CB B:HIS200 3.5 14.0 1.0 CG B:HIS172 4.1 14.2 1.0 ND1 B:HIS172 4.1 12.2 1.0 ND1 B:HIS187 4.2 14.9 1.0 CG B:HIS187 4.3 14.3 1.0 NE2 B:HIS200 4.3 16.5 1.0 O B:TYR176 4.3 15.7 1.0 CB B:ASP174 4.3 14.5 1.0 CD2 B:HIS200 4.3 13.5 1.0 CE1 B:PHE189 4.6 16.6 1.0 CZ B:PHE178 4.7 14.7 1.0 O B:HOH61 4.7 14.4 1.0 CE2 B:PHE178 4.8 13.6 1.0 CB B:TYR176 4.8 17.0 1.0 CZ B:PHE189 4.9 22.7 1.0 CA B:HIS200 5.0 12.8 1.0

A.Heim-Riether, S.J.Taylor, S.Liang, D.A.Gao, Z.Xiong, E.Michael August, B.K.Collins, B.T.Farmer, K.Haverty, M.Hill-Drzewi, H.D.Junker, S.Mariana Margarit, N.Moss, T.Neumann, J.R.Proudfoot, L.S.Keenan, R.Sekul, Q.Zhang, J.Li, N.A.Farrow. Improving Potency and Selectivity of A New Class of Non-Zn-Chelating Mmp-13 Inhibitors. Bioorg.Med.Chem.Lett. V. 19 5321 2009.
ISSN: ISSN 0960-894X
PubMed: 19692239
DOI: 10.1016/J.BMCL.2009.07.151