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

The structure of Matrix Metalloproteinase-13 Complexed with Non-Zinc Binding Inhibitor, PDB code: 1xur 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 / 1.85
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	134.508, 36.486, 95.586, 90.00, 130.52, 90.00
R / Rfree (%)	16.7 / 20.6

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

Calcium

(Ca)

4 atoms

The binding sites of Zinc atom in the Matrix Metalloproteinase-13 Complexed with Non-Zinc Binding Inhibitor (pdb code 1xur). 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: 1xur:
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:6.4 occ:1.00 NE2 A:HIS232 2.1 7.2 1.0 NE2 A:HIS222 2.2 7.1 1.0 NE2 A:HIS226 2.2 6.3 1.0 O A:HOH2023 2.2 10.0 1.0 O A:HOH2016 2.6 30.4 1.0 CD2 A:HIS232 3.0 6.5 1.0 CD2 A:HIS222 3.0 6.6 1.0 CE1 A:HIS232 3.1 9.7 1.0 CD2 A:HIS226 3.2 5.8 1.0 CE1 A:HIS226 3.2 7.6 1.0 CE1 A:HIS222 3.3 8.0 1.0 CG A:HIS232 4.2 7.3 1.0 ND1 A:HIS232 4.2 9.7 1.0 CG A:HIS222 4.2 5.5 1.0 ND1 A:HIS226 4.3 6.3 1.0 ND1 A:HIS222 4.3 5.0 1.0 CG A:HIS226 4.3 5.1 1.0 OE2 A:GLU223 4.3 13.0 1.0 O A:HOH2099 4.5 14.7 1.0 O A:HOH2017 4.6 18.5 1.0 O A:HOH2015 4.7 25.4 1.0 O A:HOH2026 4.8 25.4 1.0 OE1 A:GLU223 4.8 10.3 1.0 CE A:MET240 4.8 5.0 1.0 O A:HOH2182 4.9 40.0 1.0 CD A:GLU223 4.9 8.8 1.0 O A:HOH2018 5.0 15.7 1.0 O A:HOH2183 5.0 36.6 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:6.2 occ:1.00 OD2 A:ASP174 2.0 6.1 1.0 NE2 A:HIS172 2.1 5.0 1.0 ND1 A:HIS200 2.1 5.3 1.0 NE2 A:HIS187 2.2 10.0 1.0 CG A:ASP174 3.0 6.6 1.0 CD2 A:HIS172 3.0 5.9 1.0 CE1 A:HIS187 3.0 7.3 1.0 CE1 A:HIS200 3.1 7.2 1.0 CG A:HIS200 3.1 6.4 1.0 CE1 A:HIS172 3.2 6.2 1.0 OD1 A:ASP174 3.2 6.1 1.0 CD2 A:HIS187 3.3 6.9 1.0 CB A:HIS200 3.5 5.8 1.0 O A:TYR176 4.1 5.8 1.0 CG A:HIS172 4.2 6.0 1.0 ND1 A:HIS187 4.2 7.3 1.0 ND1 A:HIS172 4.2 5.0 1.0 NE2 A:HIS200 4.2 6.1 1.0 CD2 A:HIS200 4.3 5.0 1.0 CB A:ASP174 4.3 5.3 1.0 CG A:HIS187 4.3 6.3 1.0 CE1 A:PHE189 4.5 9.7 1.0 CZ A:PHE178 4.7 5.0 1.0 CB A:TYR176 4.7 8.7 1.0 CE2 A:PHE178 4.7 5.0 1.0 CZ A:PHE189 4.8 10.8 1.0 C A:TYR176 4.9 5.7 1.0 CA A:HIS200 5.0 5.0 1.0 O A:HOH2066 5.0 6.6 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:12.4 occ:1.00 NE2 B:HIS222 2.2 9.2 1.0 NE2 B:HIS232 2.2 14.1 1.0 O B:HOH3017 2.2 20.8 1.0 NE2 B:HIS226 2.3 12.8 1.0 O B:HOH3012 2.6 28.1 1.0 CD2 B:HIS232 2.9 13.6 1.0 CD2 B:HIS222 3.0 10.6 1.0 CD2 B:HIS226 3.2 11.6 1.0 CE1 B:HIS222 3.2 10.0 1.0 CE1 B:HIS226 3.3 12.5 1.0 CE1 B:HIS232 3.3 15.8 1.0 OE2 B:GLU223 4.1 11.9 1.0 CG B:HIS232 4.2 14.7 1.0 CG B:HIS222 4.2 9.3 1.0 ND1 B:HIS222 4.3 9.6 1.0 ND1 B:HIS232 4.3 16.0 1.0 CG B:HIS226 4.4 11.7 1.0 ND1 B:HIS226 4.4 12.7 1.0 O B:HOH3033 4.7 15.2 1.0 O B:HOH3014 4.8 19.8 1.0 CD B:GLU223 4.8 10.2 1.0 OE1 B:GLU223 4.9 11.7 1.0 CE B:MET240 4.9 10.2 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:7.9 occ:1.00 OD2 B:ASP174 2.1 6.5 1.0 NE2 B:HIS172 2.1 7.4 1.0 ND1 B:HIS200 2.2 5.8 1.0 NE2 B:HIS187 2.2 6.4 1.0 CD2 B:HIS172 2.9 6.8 1.0 CG B:ASP174 2.9 7.0 1.0 CE1 B:HIS187 3.0 7.5 1.0 CE1 B:HIS200 3.1 8.1 1.0 OD1 B:ASP174 3.2 5.0 1.0 CG B:HIS200 3.2 5.4 1.0 CE1 B:HIS172 3.2 6.3 1.0 CD2 B:HIS187 3.2 8.1 1.0 CB B:HIS200 3.5 6.3 1.0 CG B:HIS172 4.1 6.2 1.0 ND1 B:HIS187 4.2 7.0 1.0 NE2 B:HIS200 4.2 7.1 1.0 ND1 B:HIS172 4.3 5.1 1.0 CD2 B:HIS200 4.3 7.4 1.0 O B:TYR176 4.3 8.3 1.0 CG B:HIS187 4.3 7.4 1.0 CB B:ASP174 4.3 5.9 1.0 CE1 B:PHE189 4.6 11.9 1.0 CZ B:PHE178 4.7 5.0 1.0 CB B:TYR176 4.7 8.1 1.0 O B:HOH3037 4.7 9.1 1.0 CE2 B:PHE178 4.8 5.3 1.0 CZ B:PHE189 4.9 11.2 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