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

The structure of Matrix Metalloproteinase-13 Complexed with Non-Zinc Binding Inhibitor, PDB code: 1xuc 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 / 1.70
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	134.437, 36.476, 95.320, 90.00, 130.51, 90.00
R / Rfree (%)	17.5 / 20

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 1xuc). 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: 1xuc:
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:9.7 occ:1.00 NE2 A:HIS232 2.1 13.0 1.0 NE2 A:HIS222 2.1 9.8 1.0 NE2 A:HIS226 2.1 11.1 1.0 O A:HOH2020 2.4 17.4 1.0 CD2 A:HIS232 3.0 10.8 1.0 CD2 A:HIS222 3.0 9.8 1.0 CE1 A:HIS232 3.1 13.5 1.0 CD2 A:HIS226 3.1 10.5 1.0 CE1 A:HIS226 3.1 12.6 1.0 CE1 A:HIS222 3.2 10.1 1.0 O A:HOH2016 4.1 19.4 1.0 CG A:HIS232 4.1 11.5 1.0 ND1 A:HIS232 4.2 12.8 1.0 CG A:HIS222 4.2 7.5 1.0 ND1 A:HIS222 4.2 6.8 1.0 ND1 A:HIS226 4.2 10.7 1.0 CG A:HIS226 4.3 8.8 1.0 O A:HOH2093 4.4 14.3 1.0 OE2 A:GLU223 4.5 13.4 1.0 CE A:MET240 4.7 8.5 1.0 C7 A:PB32001 4.7 11.5 1.0 O A:HOH2178 4.8 42.8 1.0 O A:HOH2023 4.8 25.9 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:8.8 occ:1.00 OD2 A:ASP174 2.0 8.0 1.0 NE2 A:HIS172 2.1 8.6 1.0 NE2 A:HIS187 2.1 9.3 1.0 ND1 A:HIS200 2.1 9.3 1.0 CG A:ASP174 2.9 9.5 1.0 CD2 A:HIS172 2.9 8.1 1.0 CE1 A:HIS187 2.9 9.0 1.0 CE1 A:HIS200 3.1 10.2 1.0 CG A:HIS200 3.1 9.6 1.0 CE1 A:HIS172 3.1 8.6 1.0 CD2 A:HIS187 3.2 8.9 1.0 OD1 A:ASP174 3.2 9.4 1.0 CB A:HIS200 3.5 8.8 1.0 O A:TYR176 4.1 9.5 1.0 ND1 A:HIS187 4.1 8.6 1.0 CG A:HIS172 4.1 8.1 1.0 ND1 A:HIS172 4.2 8.1 1.0 NE2 A:HIS200 4.2 10.8 1.0 CG A:HIS187 4.3 6.4 1.0 CD2 A:HIS200 4.3 10.2 1.0 CB A:ASP174 4.3 8.2 1.0 CE1 A:PHE189 4.5 12.8 1.0 CB A:TYR176 4.7 10.7 1.0 CZ A:PHE178 4.7 7.0 1.0 CZ A:PHE189 4.7 14.1 1.0 CE2 A:PHE178 4.8 7.1 1.0 C A:TYR176 4.9 9.0 1.0 CA A:HIS200 5.0 6.7 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:14.5 occ:1.00 NE2 B:HIS222 2.1 11.8 1.0 NE2 B:HIS232 2.1 16.9 1.0 NE2 B:HIS226 2.2 15.6 1.0 O B:HOH3014 2.4 31.8 1.0 CD2 B:HIS232 3.0 17.2 1.0 CD2 B:HIS222 3.0 12.9 1.0 CD2 B:HIS226 3.1 14.6 1.0 CE1 B:HIS222 3.2 13.1 1.0 CE1 B:HIS226 3.2 15.3 1.0 CE1 B:HIS232 3.2 19.6 1.0 O B:HOH3011 3.7 35.4 1.0 CG B:HIS232 4.2 17.8 1.0 CG B:HIS222 4.2 11.0 1.0 ND1 B:HIS222 4.2 11.4 1.0 ND1 B:HIS232 4.2 19.1 1.0 ND1 B:HIS226 4.3 15.9 1.0 CG B:HIS226 4.3 13.6 1.0 OE2 B:GLU223 4.4 18.7 1.0 O B:HOH3032 4.6 18.3 1.0 C7 B:PB33001 4.8 16.6 1.0 CE B:MET240 4.8 10.9 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:10.1 occ:1.00 OD2 B:ASP174 2.0 10.2 1.0 NE2 B:HIS172 2.1 10.6 1.0 ND1 B:HIS200 2.1 9.3 1.0 NE2 B:HIS187 2.1 9.3 1.0 CG B:ASP174 2.9 10.1 1.0 CD2 B:HIS172 3.0 9.5 1.0 CE1 B:HIS187 3.0 11.2 1.0 CE1 B:HIS200 3.0 9.1 1.0 CE1 B:HIS172 3.2 8.3 1.0 CG B:HIS200 3.2 8.5 1.0 OD1 B:ASP174 3.2 8.4 1.0 CD2 B:HIS187 3.2 11.5 1.0 CB B:HIS200 3.5 9.8 1.0 CG B:HIS172 4.1 8.5 1.0 ND1 B:HIS187 4.2 9.1 1.0 NE2 B:HIS200 4.2 10.1 1.0 ND1 B:HIS172 4.2 8.3 1.0 O B:TYR176 4.3 10.7 1.0 CD2 B:HIS200 4.3 9.5 1.0 CG B:HIS187 4.3 9.5 1.0 CB B:ASP174 4.3 10.1 1.0 CE1 B:PHE189 4.6 14.7 1.0 CB B:TYR176 4.7 12.3 1.0 CZ B:PHE178 4.7 9.9 1.0 CE2 B:PHE178 4.8 10.4 1.0 O B:HOH3036 4.8 13.1 1.0 CZ B:PHE189 4.9 14.1 1.0 O B:HOH3045 4.9 30.4 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: 15734645
DOI: 10.1016/J.CHEMBIOL.2004.11.014