Zinc in PDB 1xud: Matrix Metalloproteinase-13 Complexed with Non-Zinc Binding Inhibitor

The structure of Matrix Metalloproteinase-13 Complexed with Non-Zinc Binding Inhibitor, PDB code: 1xud was solved by C.K.Engel, K.U.Wendt, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 1.80
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	134.022, 36.475, 95.060, 90.00, 130.41, 90.00
R / Rfree (%)	16.8 / 20.3

The structure of Matrix Metalloproteinase-13 Complexed with Non-Zinc Binding Inhibitor also contains other interesting chemical elements:

Fluorine	(F)	4 atoms
Calcium	(Ca)	4 atoms

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

Zinc binding site 1 out of 4 in the Matrix Metalloproteinase-13 Complexed with 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 Matrix Metalloproteinase-13 Complexed with Non-Zinc Binding Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1261 b:7.9 occ:1.00 NE2 A:HIS232 2.1 8.6 1.0 NE2 A:HIS226 2.1 8.8 1.0 NE2 A:HIS222 2.2 8.2 1.0 O A:HOH2019 2.4 11.8 1.0 CD2 A:HIS222 3.0 9.2 1.0 CD2 A:HIS232 3.0 7.3 1.0 CD2 A:HIS226 3.1 7.9 1.0 CE1 A:HIS226 3.1 9.4 1.0 CE1 A:HIS232 3.2 10.7 1.0 CE1 A:HIS222 3.3 9.3 1.0 CG A:HIS232 4.2 9.2 1.0 O A:HOH2015 4.2 14.5 1.0 CG A:HIS222 4.2 6.9 1.0 ND1 A:HIS232 4.2 10.5 1.0 ND1 A:HIS226 4.2 8.7 1.0 CG A:HIS226 4.3 6.5 1.0 ND1 A:HIS222 4.3 6.8 1.0 O A:HOH2093 4.3 10.4 1.0 OE2 A:GLU223 4.6 11.2 1.0 O A:HOH2022 4.6 30.4 1.0 C7 A:PB42001 4.7 8.1 1.0 CE A:MET240 4.8 6.1 1.0 OE1 A:GLU223 5.0 9.6 1.0

Zinc binding site 2 out of 4 in the Matrix Metalloproteinase-13 Complexed with 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 Matrix Metalloproteinase-13 Complexed with Non-Zinc Binding Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1262 b:7.7 occ:1.00 OD2 A:ASP174 2.0 7.7 1.0 NE2 A:HIS172 2.1 7.1 1.0 NE2 A:HIS187 2.1 8.8 1.0 ND1 A:HIS200 2.1 6.6 1.0 CD2 A:HIS172 2.9 6.9 1.0 CG A:ASP174 2.9 8.3 1.0 CE1 A:HIS187 3.0 6.6 1.0 CE1 A:HIS200 3.1 7.7 1.0 CG A:HIS200 3.1 7.8 1.0 CE1 A:HIS172 3.2 7.3 1.0 OD1 A:ASP174 3.2 7.7 1.0 CD2 A:HIS187 3.2 6.5 1.0 CB A:HIS200 3.4 7.1 1.0 CG A:HIS172 4.1 7.0 1.0 O A:TYR176 4.1 7.0 1.0 ND1 A:HIS187 4.2 7.3 1.0 ND1 A:HIS172 4.2 5.1 1.0 NE2 A:HIS200 4.2 6.9 1.0 CD2 A:HIS200 4.3 7.2 1.0 CG A:HIS187 4.3 6.1 1.0 CB A:ASP174 4.3 6.6 1.0 CE1 A:PHE189 4.4 12.2 1.0 CZ A:PHE189 4.7 12.4 1.0 CZ A:PHE178 4.7 6.8 1.0 CB A:TYR176 4.8 10.2 1.0 CE2 A:PHE178 4.8 5.2 1.0 C A:TYR176 4.9 7.2 1.0 CA A:HIS200 4.9 5.4 1.0 O A:HOH2060 5.0 5.8 1.0

Zinc binding site 3 out of 4 in the Matrix Metalloproteinase-13 Complexed with 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 Matrix Metalloproteinase-13 Complexed with Non-Zinc Binding Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1261 b:14.2 occ:1.00 NE2 B:HIS222 2.2 11.3 1.0 NE2 B:HIS232 2.2 16.8 1.0 NE2 B:HIS226 2.2 13.7 1.0 O B:HOH3013 2.4 32.9 1.0 CD2 B:HIS232 2.9 15.9 1.0 CD2 B:HIS222 3.0 11.3 1.0 CD2 B:HIS226 3.1 12.8 1.0 CE1 B:HIS226 3.2 13.1 1.0 CE1 B:HIS222 3.2 12.2 1.0 CE1 B:HIS232 3.3 18.0 1.0 O B:HOH3010 3.7 28.3 1.0 CG B:HIS232 4.2 16.5 1.0 CG B:HIS222 4.2 11.0 1.0 ND1 B:HIS222 4.2 9.4 1.0 ND1 B:HIS232 4.3 18.3 1.0 CG B:HIS226 4.3 12.3 1.0 ND1 B:HIS226 4.3 14.2 1.0 OE2 B:GLU223 4.3 16.9 1.0 O B:HOH3031 4.6 14.8 1.0 C7 B:PB43001 4.7 15.9 1.0 CE B:MET240 4.9 10.8 1.0 CD B:GLU223 5.0 15.2 1.0 OE1 B:GLU223 5.0 14.6 1.0

Zinc binding site 4 out of 4 in the Matrix Metalloproteinase-13 Complexed with 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 Matrix Metalloproteinase-13 Complexed with Non-Zinc Binding Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1262 b:8.8 occ:1.00 OD2 B:ASP174 2.1 7.6 1.0 NE2 B:HIS172 2.1 7.4 1.0 NE2 B:HIS187 2.1 7.3 1.0 ND1 B:HIS200 2.2 7.1 1.0 CD2 B:HIS172 2.9 8.3 1.0 CG B:ASP174 2.9 8.9 1.0 CE1 B:HIS187 3.0 8.8 1.0 CE1 B:HIS200 3.1 9.6 1.0 OD1 B:ASP174 3.1 6.5 1.0 CE1 B:HIS172 3.2 8.0 1.0 CG B:HIS200 3.2 6.4 1.0 CD2 B:HIS187 3.2 9.2 1.0 CB B:HIS200 3.5 7.7 1.0 CG B:HIS172 4.1 6.6 1.0 ND1 B:HIS187 4.1 8.3 1.0 ND1 B:HIS172 4.2 6.6 1.0 O B:TYR176 4.2 8.8 1.0 NE2 B:HIS200 4.3 8.5 1.0 CG B:HIS187 4.3 8.8 1.0 CD2 B:HIS200 4.3 9.3 1.0 CB B:ASP174 4.3 6.2 1.0 CE1 B:PHE189 4.6 14.4 1.0 CB B:TYR176 4.7 10.0 1.0 CZ B:PHE178 4.7 7.0 1.0 O B:HOH3035 4.7 9.3 1.0 CE2 B:PHE178 4.7 6.4 1.0 CZ B:PHE189 4.8 13.6 1.0 CA B:HIS200 5.0 6.9 1.0

C.K.Engel, B.Pirard, S.Schimanski, R.Kirsch, J.Habermann, O.Klingler, V.Schlotte, K.U.Weithmann, K.U.Wendt. Structural Basis For the Highly Selective Inhibition of Mmp-13. Chem.Biol. V. 12 181 2005.
ISSN: ISSN 1074-5521
PubMed: 15734640
DOI: 10.1016/J.CHEMBIOL.2004.11.014