Zinc in PDB 2yig: MMP13 in Complex with A Novel Selective Non Zinc Binding Inhibitor

The structure of MMP13 in Complex with A Novel Selective Non Zinc Binding Inhibitor, PDB code: 2yig was solved by S.Gerhardt, D.Hargreaves, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	67.12 / 1.70
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	134.417, 36.074, 95.206, 90.00, 131.49, 90.00
R / Rfree (%)	18.4 / 22.1

The structure of MMP13 in Complex with A Novel Selective Non Zinc Binding Inhibitor also contains other interesting chemical elements:

Calcium	(Ca)	4 atoms
Sodium	(Na)	3 atoms

The binding sites of Zinc atom in the MMP13 in Complex with A Novel Selective Non Zinc Binding Inhibitor (pdb code 2yig). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the MMP13 in Complex with A Novel Selective Non Zinc Binding Inhibitor, PDB code: 2yig:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the MMP13 in Complex with A Novel Selective Non Zinc Binding Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of MMP13 in Complex with A Novel Selective Non Zinc Binding Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:10.9 occ:1.00 NE2 A:HIS222 2.1 8.1 1.0 NE2 A:HIS226 2.1 7.9 1.0 NE2 A:HIS232 2.2 11.3 1.0 O A:HOH480 2.3 13.8 1.0 CD2 A:HIS222 2.9 8.5 1.0 CD2 A:HIS232 3.0 11.3 1.0 CD2 A:HIS226 3.0 7.8 1.0 CE1 A:HIS226 3.1 8.6 1.0 CE1 A:HIS222 3.2 8.5 1.0 CE1 A:HIS232 3.2 11.6 1.0 OE2 A:GLU223 4.0 8.7 1.0 CG A:HIS222 4.1 8.2 1.0 CG A:HIS232 4.2 10.4 1.0 CG A:HIS226 4.2 7.9 1.0 ND1 A:HIS226 4.2 8.4 1.0 ND1 A:HIS222 4.2 8.4 1.0 ND1 A:HIS232 4.3 10.8 1.0 OE1 A:GLU223 4.5 8.3 1.0 CD A:GLU223 4.6 7.9 1.0 C20 A:5EL301 4.6 12.6 1.0 CE A:MET240 4.7 8.6 1.0 O A:HOH504 4.7 16.8 1.0 C21 A:5EL301 4.8 11.6 1.0

Zinc binding site 2 out of 4 in the MMP13 in Complex with A Novel Selective Non Zinc Binding Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of MMP13 in Complex with A Novel Selective Non Zinc Binding Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn304 b:11.0 occ:1.00 OD2 A:ASP174 2.0 9.0 1.0 NE2 A:HIS172 2.0 7.8 1.0 ND1 A:HIS200 2.0 9.6 1.0 NE2 A:HIS187 2.1 11.1 1.0 CD2 A:HIS172 2.9 8.9 1.0 CG A:ASP174 2.9 10.6 1.0 CE1 A:HIS187 3.0 10.9 1.0 CE1 A:HIS200 3.0 10.5 1.0 CG A:HIS200 3.1 9.3 1.0 CE1 A:HIS172 3.1 9.0 1.0 CD2 A:HIS187 3.1 10.0 1.0 OD1 A:ASP174 3.1 10.5 1.0 CB A:HIS200 3.4 8.4 1.0 CG A:HIS172 4.1 8.9 1.0 O A:TYR176 4.1 10.6 1.0 ND1 A:HIS187 4.1 11.3 1.0 ND1 A:HIS172 4.1 8.8 1.0 NE2 A:HIS200 4.2 10.1 1.0 CG A:HIS187 4.2 9.6 1.0 CD2 A:HIS200 4.2 9.7 1.0 CB A:ASP174 4.3 10.5 1.0 CB A:TYR176 4.4 13.0 1.0 CE1 A:PHE189 4.5 11.7 1.0 CZ A:PHE178 4.7 9.2 1.0 CZ A:PHE189 4.8 12.3 1.0 CE2 A:PHE178 4.8 8.5 1.0 C A:TYR176 4.8 11.2 1.0 O A:HOH467 4.9 12.9 1.0 CA A:HIS200 4.9 8.0 1.0

Zinc binding site 3 out of 4 in the MMP13 in Complex with A Novel Selective Non Zinc Binding Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of MMP13 in Complex with A Novel Selective Non Zinc Binding Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn302 b:14.8 occ:1.00 NE2 B:HIS232 2.1 15.4 1.0 NE2 B:HIS222 2.1 11.2 1.0 NE2 B:HIS226 2.1 11.9 1.0 O B:HOH500 2.2 24.1 1.0 CD2 B:HIS232 2.9 14.9 1.0 CD2 B:HIS222 3.0 10.5 1.0 CD2 B:HIS226 3.0 11.3 1.0 CE1 B:HIS226 3.2 13.4 1.0 CE1 B:HIS232 3.2 15.8 1.0 CE1 B:HIS222 3.2 10.9 1.0 OE2 B:GLU223 4.1 10.1 1.0 CG B:HIS232 4.1 16.1 1.0 CG B:HIS222 4.2 10.5 1.0 ND1 B:HIS232 4.2 15.6 1.0 CG B:HIS226 4.2 11.2 1.0 ND1 B:HIS226 4.2 11.1 1.0 ND1 B:HIS222 4.3 11.2 1.0 O B:HOH493 4.5 17.3 1.0 C20 B:5EL301 4.6 15.6 1.0 OE1 B:GLU223 4.7 11.5 1.0 CD B:GLU223 4.7 9.8 1.0 C21 B:5EL301 4.8 14.9 1.0 CE B:MET240 4.8 11.7 1.0 O B:HOH513 4.9 36.5 1.0 O B:HOH483 4.9 33.2 1.0

Zinc binding site 4 out of 4 in the MMP13 in Complex with A Novel Selective Non Zinc Binding Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of MMP13 in Complex with A Novel Selective Non Zinc Binding Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn303 b:11.0 occ:1.00 OD2 B:ASP174 2.0 11.6 1.0 NE2 B:HIS187 2.0 11.0 1.0 NE2 B:HIS172 2.1 9.4 1.0 ND1 B:HIS200 2.1 11.2 1.0 CG B:ASP174 2.9 11.4 1.0 CE1 B:HIS187 2.9 10.2 1.0 CD2 B:HIS172 3.0 9.7 1.0 CE1 B:HIS200 3.0 10.3 1.0 CG B:HIS200 3.1 10.3 1.0 CD2 B:HIS187 3.1 11.0 1.0 OD1 B:ASP174 3.1 10.8 1.0 CE1 B:HIS172 3.2 10.7 1.0 CB B:HIS200 3.5 9.2 1.0 ND1 B:HIS187 4.1 10.9 1.0 NE2 B:HIS200 4.2 10.2 1.0 CG B:HIS172 4.2 9.6 1.0 CD2 B:HIS200 4.2 9.7 1.0 O B:TYR176 4.2 12.0 1.0 CG B:HIS187 4.3 10.1 1.0 ND1 B:HIS172 4.3 9.8 1.0 CB B:ASP174 4.3 11.2 1.0 CE1 B:PHE189 4.6 16.2 1.0 CZ B:PHE178 4.6 9.4 1.0 CE2 B:PHE178 4.7 9.3 1.0 O B:HOH436 4.8 10.1 1.0 CZ B:PHE189 4.8 18.2 1.0 CB B:TYR176 4.8 12.6 1.0 CA B:HIS200 5.0 9.2 1.0

C.D.Savi, A.D.Morley, A.Ting, I.Nash, K.Karabelas, C.M.Wood, M.James, S.J.Norris, G.Karoutchi, N.Rankine, G.Hamlin, P.A.Macfaul, D.Ryan, S.V.Baker, D.Hargreaves, S.Gerhardt. Selective Non Zinc Binding Inhibitors of MMP13. Bioorg.Med.Chem.Lett. V. 21 4215 2011.
ISSN: ISSN 0960-894X
PubMed: 21669521
DOI: 10.1016/J.BMCL.2011.05.075