Zinc in PDB 3i7i: 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: 3i7i was solved by N.A.Farrow, S.M.Margarit, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.86 / 2.21
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	134.186, 35.777, 95.295, 90.00, 131.08, 90.00
R / Rfree (%)	23 / 31.4

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

Calcium

(Ca)

6 atoms

The binding sites of Zinc atom in the Mmp-13 in Complex with A Non Zinc-Chelating Inhibitor (pdb code 3i7i). 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: 3i7i:
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:24.4 occ:1.00 NE2 A:HIS226 2.1 18.1 1.0 NE2 A:HIS222 2.2 18.9 1.0 NE2 A:HIS232 2.3 25.1 1.0 CD2 A:HIS226 3.0 15.4 1.0 CD2 A:HIS222 3.0 21.1 1.0 CD2 A:HIS232 3.1 20.1 1.0 CE1 A:HIS226 3.2 18.1 1.0 CE1 A:HIS222 3.3 21.6 1.0 CE1 A:HIS232 3.4 24.7 1.0 OE2 A:GLU223 4.0 24.1 1.0 CG A:HIS226 4.2 22.1 1.0 ND1 A:HIS226 4.2 22.9 1.0 CG A:HIS222 4.2 20.2 1.0 CG A:HIS232 4.3 20.6 1.0 C8 A:518999 4.3 37.2 1.0 ND1 A:HIS222 4.4 21.3 1.0 C9 A:518999 4.4 30.2 1.0 ND1 A:HIS232 4.5 28.3 1.0 CD A:GLU223 4.7 21.6 1.0 OE1 A:GLU223 4.7 26.4 1.0 CA A:PRO242 4.9 23.1 1.0 C7 A:518999 4.9 37.2 1.0 O A:HOH354 5.0 30.3 1.0 C10 A:518999 5.0 32.9 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:22.9 occ:1.00 OD2 A:ASP174 2.1 20.4 1.0 ND1 A:HIS200 2.1 22.5 1.0 NE2 A:HIS187 2.2 19.9 1.0 NE2 A:HIS172 2.2 20.8 1.0 CG A:HIS200 3.0 23.1 1.0 CD2 A:HIS172 3.0 19.8 1.0 CG A:ASP174 3.0 22.0 1.0 CE1 A:HIS200 3.0 18.3 1.0 CE1 A:HIS187 3.1 17.6 1.0 CD2 A:HIS187 3.2 19.4 1.0 CB A:HIS200 3.3 19.6 1.0 CE1 A:HIS172 3.3 21.2 1.0 OD1 A:ASP174 3.3 20.4 1.0 CD2 A:HIS200 4.1 20.0 1.0 NE2 A:HIS200 4.1 22.2 1.0 O A:TYR176 4.2 29.4 1.0 CG A:HIS172 4.2 19.3 1.0 ND1 A:HIS187 4.3 22.2 1.0 CG A:HIS187 4.3 18.1 1.0 ND1 A:HIS172 4.3 22.4 1.0 CB A:ASP174 4.4 21.5 1.0 CE1 A:PHE189 4.4 29.1 1.0 CZ A:PHE178 4.6 18.8 1.0 CE2 A:PHE178 4.6 23.2 1.0 CZ A:PHE189 4.6 26.5 1.0 CA A:HIS200 4.8 19.1 1.0 CB A:TYR176 4.9 26.5 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:37.0 occ:1.00 NE2 B:HIS226 2.2 25.8 1.0 NE2 B:HIS232 2.3 44.4 1.0 NE2 B:HIS222 2.4 34.9 1.0 CD2 B:HIS222 3.0 25.0 1.0 CD2 B:HIS226 3.1 30.9 1.0 CD2 B:HIS232 3.2 36.5 1.0 CE1 B:HIS232 3.2 44.9 1.0 CE1 B:HIS226 3.3 33.8 1.0 CE1 B:HIS222 3.6 32.0 1.0 OE2 B:GLU223 4.0 30.1 1.0 CG B:HIS232 4.3 35.7 1.0 CG B:HIS226 4.3 30.1 1.0 ND1 B:HIS232 4.3 41.1 1.0 CG B:HIS222 4.3 25.5 1.0 ND1 B:HIS226 4.3 31.9 1.0 O B:HOH43 4.4 34.8 1.0 ND1 B:HIS222 4.5 28.5 1.0 OE1 B:GLU223 4.6 26.8 1.0 O B:HOH318 4.6 43.9 1.0 CD B:GLU223 4.6 29.4 1.0 O B:HOH70 4.7 32.6 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:27.8 occ:1.00 OD2 B:ASP174 2.1 20.5 1.0 NE2 B:HIS172 2.3 20.5 1.0 ND1 B:HIS200 2.3 26.6 1.0 NE2 B:HIS187 2.4 22.4 1.0 CG B:ASP174 2.9 22.9 1.0 CD2 B:HIS172 3.0 20.4 1.0 OD1 B:ASP174 3.0 21.6 1.0 CE1 B:HIS200 3.2 28.5 1.0 CG B:HIS200 3.3 27.1 1.0 CE1 B:HIS187 3.3 30.7 1.0 CE1 B:HIS172 3.3 20.9 1.0 CD2 B:HIS187 3.5 26.2 1.0 CB B:HIS200 3.7 24.2 1.0 CG B:HIS172 4.2 25.8 1.0 O B:TYR176 4.2 20.8 1.0 ND1 B:HIS172 4.3 25.9 1.0 NE2 B:HIS200 4.3 25.2 1.0 CB B:ASP174 4.3 26.2 1.0 CD2 B:HIS200 4.4 27.7 1.0 ND1 B:HIS187 4.5 25.6 1.0 CG B:HIS187 4.6 27.7 1.0 CE1 B:PHE189 4.6 29.9 1.0 CE2 B:PHE178 4.7 21.4 1.0 CZ B:PHE178 4.8 26.4 1.0 CZ B:PHE189 4.8 30.0 1.0 CB B:TYR176 4.8 23.3 1.0 O B:HOH305 4.9 29.9 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