Calcium 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:

Zinc

(Zn)

4 atoms

The binding sites of Calcium 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 Calcium atom.
In total 4 binding sites of Calcium where determined in the Matrix Metalloproteinase-13 Complexed with Non-Zinc Binding Inhibitor, PDB code: 1xuc:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium 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 Calcium with other atoms in the Ca 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:Ca1264 b:9.1 occ:1.00 O A:LEU184 2.4 11.5 1.0 O A:GLY180 2.4 12.5 1.0 OD2 A:ASP202 2.4 10.7 1.0 OD1 A:ASP179 2.5 12.4 1.0 O A:SER182 2.5 13.0 1.0 OE2 A:GLU205 2.6 19.7 1.0 C A:LEU184 3.5 12.0 1.0 CD A:GLU205 3.5 16.6 1.0 CG A:ASP202 3.5 8.1 1.0 C A:SER182 3.5 16.1 1.0 CG A:ASP179 3.6 13.2 1.0 C A:GLY180 3.6 13.8 1.0 N A:LEU184 3.9 13.3 1.0 N A:SER182 3.9 17.2 1.0 CG A:GLU205 4.1 12.8 1.0 C A:GLY183 4.1 13.8 1.0 C A:PRO181 4.1 16.5 1.0 N A:GLY180 4.2 11.7 1.0 CA A:LEU184 4.2 12.9 1.0 OD2 A:ASP179 4.2 13.8 1.0 N A:ASP179 4.3 10.5 1.0 C A:ASP179 4.3 12.3 1.0 CB A:ASP202 4.3 7.5 1.0 CA A:SER182 4.3 18.2 1.0 OD1 A:ASP202 4.4 7.9 1.0 N A:GLY183 4.4 13.8 1.0 CA A:PRO181 4.5 16.7 1.0 OE1 A:GLU205 4.5 17.1 1.0 N A:PRO181 4.5 15.1 1.0 CA A:GLY183 4.5 13.6 1.0 CB A:LEU184 4.5 14.4 1.0 CA A:GLY180 4.5 12.5 1.0 O A:GLY183 4.5 13.6 1.0 N A:LEU185 4.6 9.3 1.0 CA A:ASP179 4.6 11.6 1.0 O A:PRO181 4.6 17.5 1.0 O A:HOH2159 4.6 22.3 1.0 O A:ASP179 4.7 12.8 1.0 CA A:LEU185 4.7 9.9 1.0 CB A:ASP179 4.7 12.5 1.0

Calcium 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 Calcium with other atoms in the Ca 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:Ca1265 b:18.9 occ:1.00 O A:ASN194 2.5 16.8 1.0 O A:GLY196 2.5 10.6 1.0 O A:ASP162 2.5 11.6 1.0 OD1 A:ASP198 2.6 10.4 1.0 O A:HOH2098 2.7 19.8 1.0 O A:HOH2110 2.8 16.1 1.0 CG A:ASP198 3.5 10.6 1.0 C A:GLY196 3.6 9.3 1.0 C A:ASP162 3.6 9.1 1.0 C A:ASN194 3.6 16.2 1.0 C A:TYR195 3.7 12.0 1.0 N A:GLY196 3.9 10.8 1.0 OD2 A:ASP198 4.0 11.7 1.0 O A:TYR195 4.0 10.3 1.0 O A:ALA161 4.0 11.1 1.0 O A:HOH2120 4.0 16.9 1.0 CA A:TYR195 4.0 14.3 1.0 N A:ASP198 4.1 7.5 1.0 CA A:GLY196 4.3 9.3 1.0 N A:TYR195 4.3 14.5 1.0 CA A:ASP162 4.3 9.1 1.0 N A:ILE163 4.5 8.7 1.0 N A:GLY197 4.5 8.9 1.0 C A:GLY197 4.6 9.0 1.0 CA A:GLY197 4.7 9.3 1.0 CB A:ASP198 4.7 9.8 1.0 N A:MET164 4.7 8.5 1.0 CA A:ILE163 4.7 9.0 1.0 CA A:ASN194 4.7 17.1 1.0 O A:HOH2072 4.7 18.0 1.0 CG A:MET164 4.8 10.4 1.0 CA A:ASP198 4.8 8.6 1.0 O A:GLY192 4.8 12.4 1.0 CH2 A:TRP113 4.8 9.9 1.0

Calcium 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 Calcium with other atoms in the Ca 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:Ca1264 b:12.7 occ:1.00 O B:LEU184 2.4 17.8 1.0 OD2 B:ASP202 2.5 9.8 1.0 O B:GLY180 2.5 16.1 1.0 OD1 B:ASP179 2.6 17.8 1.0 OE2 B:GLU205 2.6 26.9 1.0 O B:SER182 2.7 23.4 1.0 C B:SER182 3.5 23.1 1.0 CG B:ASP202 3.6 9.6 1.0 CD B:GLU205 3.6 19.1 1.0 C B:LEU184 3.6 15.7 1.0 C B:GLY180 3.7 18.2 1.0 CG B:ASP179 3.7 19.5 1.0 N B:LEU184 3.8 17.3 1.0 N B:SER182 3.9 22.4 1.0 CG B:GLU205 4.0 16.6 1.0 C B:GLY183 4.1 19.1 1.0 C B:PRO181 4.1 22.0 1.0 CA B:LEU184 4.2 17.5 1.0 N B:GLY180 4.2 17.1 1.0 CA B:SER182 4.2 23.8 1.0 CB B:ASP202 4.2 8.6 1.0 N B:ASP179 4.3 14.4 1.0 N B:GLY183 4.3 21.8 1.0 OD2 B:ASP179 4.3 21.4 1.0 C B:ASP179 4.3 17.4 1.0 OD1 B:ASP202 4.4 8.6 1.0 CA B:GLY183 4.5 20.2 1.0 CB B:LEU184 4.5 16.6 1.0 CA B:PRO181 4.5 20.7 1.0 OE1 B:GLU205 4.5 17.9 1.0 N B:PRO181 4.6 19.9 1.0 CA B:GLY180 4.6 18.0 1.0 O B:PRO181 4.6 23.6 1.0 CA B:ASP179 4.6 16.4 1.0 N B:LEU185 4.7 14.5 1.0 O B:GLY183 4.7 19.9 1.0 O B:ASP179 4.8 17.2 1.0 CB B:ASP179 4.8 17.8 1.0 CA B:LEU185 4.9 12.6 1.0

Calcium 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 Calcium with other atoms in the Ca 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:Ca1265 b:18.4 occ:1.00 O B:GLY196 2.5 14.7 1.0 O B:ASP162 2.5 13.6 1.0 OD1 B:ASP198 2.6 14.0 1.0 O B:ASN194 2.6 21.6 1.0 O B:HOH3077 2.7 20.6 1.0 O B:HOH3133 2.8 37.0 1.0 CG B:ASP198 3.5 11.4 1.0 C B:ASP162 3.5 11.9 1.0 C B:GLY196 3.6 13.2 1.0 C B:ASN194 3.7 21.6 1.0 C B:TYR195 3.9 16.7 1.0 OD2 B:ASP198 3.9 12.8 1.0 O B:TYR195 4.0 14.8 1.0 O B:ALA161 4.0 12.1 1.0 O B:HOH3182 4.0 36.6 1.0 N B:GLY196 4.1 15.4 1.0 N B:ASP198 4.1 10.7 1.0 O B:HOH3022 4.2 13.8 1.0 CA B:ASP162 4.3 12.7 1.0 CA B:TYR195 4.3 17.4 1.0 CA B:GLY196 4.4 12.7 1.0 N B:ILE163 4.4 10.4 1.0 O B:GLY192 4.5 21.0 1.0 N B:TYR195 4.5 20.1 1.0 N B:GLY197 4.5 12.9 1.0 CB B:ASP198 4.6 11.1 1.0 CA B:ILE163 4.6 10.3 1.0 C B:GLY197 4.6 12.4 1.0 CA B:GLY197 4.6 12.2 1.0 N B:MET164 4.7 9.3 1.0 CA B:ASP198 4.7 10.1 1.0 N B:ASN194 4.7 24.8 1.0 CA B:ASN194 4.7 23.8 1.0 O B:HOH3073 4.8 21.0 1.0 CG B:MET164 4.9 9.5 1.0 C B:PRO193 4.9 24.2 1.0 CH2 B:TRP113 5.0 17.4 1.0 C B:ALA161 5.0 12.9 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: 15734645
DOI: 10.1016/J.CHEMBIOL.2004.11.014