Calcium in PDB 3zxh: Mmp-13 Complexed with 2-Napthylsulfonamide Hydroxamic Acid Inhibitor

The structure of Mmp-13 Complexed with 2-Napthylsulfonamide Hydroxamic Acid Inhibitor, PDB code: 3zxh was solved by K.L.Clark, R.Kulathila, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	9.00 / 1.30
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	134.904, 36.141, 95.069, 90.00, 131.02, 90.00
R / Rfree (%)	14.5 / 15.9

The structure of Mmp-13 Complexed with 2-Napthylsulfonamide Hydroxamic Acid Inhibitor also contains other interesting chemical elements:

Zinc

(Zn)

4 atoms

The binding sites of Calcium atom in the Mmp-13 Complexed with 2-Napthylsulfonamide Hydroxamic Acid Inhibitor (pdb code 3zxh). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 7 binding sites of Calcium where determined in the Mmp-13 Complexed with 2-Napthylsulfonamide Hydroxamic Acid Inhibitor, PDB code: 3zxh:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7;

Calcium binding site 1 out of 7 in the Mmp-13 Complexed with 2-Napthylsulfonamide Hydroxamic Acid Inhibitor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Mmp-13 Complexed with 2-Napthylsulfonamide Hydroxamic Acid Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca302 b:9.4 occ:1.00 OE2 A:GLU205 2.2 15.2 1.0 OD2 A:ASP202 2.3 8.9 1.0 O A:GLY180 2.3 9.0 1.0 O A:LEU184 2.3 13.5 1.0 O A:SER182 2.3 14.2 1.0 OD1 A:ASP179 2.3 10.0 1.0 CG A:ASP202 3.4 8.1 1.0 C A:SER182 3.5 15.5 1.0 C A:LEU184 3.5 11.6 1.0 CD A:GLU205 3.5 12.3 1.0 CG A:ASP179 3.5 11.5 1.0 C A:GLY180 3.5 9.1 1.0 H A:ASP179 3.5 12.2 1.0 HB2 A:LEU184 3.8 16.7 1.0 N A:SER182 3.9 13.9 1.0 N A:LEU184 3.9 12.1 1.0 HB3 A:ASP202 3.9 8.6 1.0 C A:PRO181 4.0 13.1 1.0 H A:LEU184 4.0 14.5 1.0 H A:SER182 4.0 16.6 1.0 HG2 A:GLU205 4.1 12.3 1.0 OD2 A:ASP179 4.1 12.2 1.0 HA A:LEU185 4.1 11.8 1.0 N A:GLY180 4.1 9.2 1.0 CB A:ASP202 4.1 7.2 1.0 HA A:PRO181 4.1 14.0 1.0 CA A:LEU184 4.2 11.9 1.0 C A:GLY183 4.2 13.6 1.0 H A:GLY180 4.2 11.0 1.0 CA A:SER182 4.2 17.5 1.0 HB2 A:ASP202 4.2 8.6 1.0 HD21 A:LEU185 4.3 20.5 1.0 C A:ASP179 4.3 9.6 1.0 HB3 A:PHE178 4.3 9.9 1.0 OE1 A:GLU205 4.3 13.5 1.0 OD1 A:ASP202 4.3 8.1 1.0 N A:ASP179 4.3 10.2 1.0 HA3 A:GLY183 4.3 14.9 1.0 O A:PRO181 4.3 17.8 1.0 CG A:GLU205 4.3 10.2 1.0 CA A:PRO181 4.4 11.7 1.0 N A:PRO181 4.4 10.2 1.0 HB2 A:ASP204 4.4 10.2 1.0 CA A:GLY180 4.4 9.1 1.0 N A:GLY183 4.4 14.7 1.0 CB A:LEU184 4.5 13.9 1.0 HA A:SER182 4.5 21.0 1.0 O A:HOH2134 4.5 20.9 1.0 N A:LEU185 4.5 9.3 1.0 CA A:GLY183 4.6 12.5 1.0 CA A:ASP179 4.6 9.9 1.0 HG3 A:GLU205 4.6 12.3 1.0 O A:GLY183 4.6 15.5 1.0 CB A:ASP179 4.7 11.4 1.0 O A:ASP179 4.7 12.8 1.0 CA A:LEU185 4.8 9.8 1.0 HD1 A:PHE178 4.9 10.4 1.0 HA2 A:GLY180 4.9 11.0 1.0

Calcium binding site 2 out of 7 in the Mmp-13 Complexed with 2-Napthylsulfonamide Hydroxamic Acid Inhibitor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Mmp-13 Complexed with 2-Napthylsulfonamide Hydroxamic Acid Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca303 b:10.8 occ:0.74 O A:GLU205 2.3 9.8 1.0 O A:HOH2036 2.3 16.4 1.0 OD2 A:ASP128 2.4 10.0 1.0 O A:ASP203 2.4 9.9 1.0 OD1 A:ASP203 2.4 9.0 1.0 O A:HOH2038 2.7 21.0 1.0 CG A:ASP128 3.1 11.0 1.0 OD1 A:ASP128 3.1 18.0 1.0 HA A:ASP203 3.3 8.9 1.0 HA A:THR206 3.3 10.7 1.0 C A:ASP203 3.3 7.8 1.0 HG1 A:THR126 3.4 8.6 1.0 HD1 A:TRP207 3.4 8.6 1.0 C A:GLU205 3.5 8.1 1.0 CG A:ASP203 3.5 8.0 1.0 HD2 A:PRO127 3.7 8.2 1.0 CA A:ASP203 3.7 7.4 1.0 OG1 A:THR126 3.9 7.2 1.0 H A:TRP207 3.9 9.1 1.0 CB A:ASP203 4.0 8.2 1.0 CD1 A:TRP207 4.1 7.2 1.0 HB3 A:ASP203 4.1 9.9 1.0 CA A:THR206 4.1 8.9 1.0 N A:THR206 4.2 8.7 1.0 N A:GLU205 4.3 8.0 1.0 H A:GLU205 4.4 9.6 1.0 HA A:ASP204 4.4 8.6 1.0 HE1 A:TRP207 4.4 8.9 1.0 N A:ASP204 4.4 7.3 1.0 HG1 A:THR206 4.5 15.5 1.0 CB A:ASP128 4.5 8.8 1.0 CA A:GLU205 4.5 7.8 1.0 C A:ASP204 4.6 9.1 1.0 OD2 A:ASP203 4.6 9.8 1.0 NE1 A:TRP207 4.6 7.5 1.0 N A:TRP207 4.6 7.6 1.0 HB2 A:ASP128 4.6 10.5 1.0 CD A:PRO127 4.6 6.9 1.0 CA A:ASP204 4.7 7.2 1.0 H A:ASP128 4.8 9.2 1.0 HG2 A:PRO127 4.8 10.2 1.0 C A:THR206 4.9 8.7 1.0 HB2 A:ASP203 4.9 9.9 1.0 O A:ASP202 5.0 7.2 1.0 HB3 A:ASP128 5.0 10.5 1.0

Calcium binding site 3 out of 7 in the Mmp-13 Complexed with 2-Napthylsulfonamide Hydroxamic Acid Inhibitor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Mmp-13 Complexed with 2-Napthylsulfonamide Hydroxamic Acid Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca304 b:10.3 occ:1.00 O A:GLY196 2.3 7.8 1.0 O A:HOH2104 2.4 10.9 1.0 O A:ASP162 2.4 9.2 1.0 O A:ASN194 2.4 14.9 1.0 OD1 A:ASP198 2.4 7.6 1.0 O A:HOH2106 2.5 11.3 1.0 CG A:ASP198 3.4 7.5 1.0 C A:GLY196 3.4 7.0 1.0 C A:ASP162 3.5 8.3 1.0 C A:ASN194 3.6 11.4 1.0 HA A:TYR195 3.8 14.4 1.0 C A:TYR195 3.8 8.5 1.0 OD2 A:ASP198 3.9 8.1 1.0 HA A:ASP162 3.9 9.9 1.0 HH2 A:TRP113 3.9 14.3 1.0 H A:MET164 3.9 8.3 1.0 H A:ASP198 3.9 8.2 1.0 HA A:ILE163 4.0 8.9 1.0 N A:GLY196 4.0 9.3 1.0 O A:HOH2149 4.0 19.0 1.0 HG2 A:MET164 4.0 9.8 1.0 O A:TYR195 4.1 8.8 1.0 HA3 A:GLY197 4.1 8.6 1.0 O A:ALA161 4.1 9.9 1.0 N A:ASP198 4.2 6.9 1.0 CA A:TYR195 4.2 12.0 1.0 CA A:GLY196 4.2 7.9 1.0 H A:GLY196 4.3 11.2 1.0 CA A:ASP162 4.3 8.3 1.0 N A:TYR195 4.4 11.9 1.0 N A:GLY197 4.4 6.7 1.0 O A:HOH2150 4.5 32.4 1.0 N A:ILE163 4.5 7.4 1.0 O A:GLY192 4.5 12.1 1.0 HG3 A:MET164 4.5 9.8 1.0 CA A:GLY197 4.5 7.2 1.0 HA3 A:GLY196 4.6 9.4 1.0 CA A:ASN194 4.6 17.0 1.0 CB A:ASP198 4.6 7.1 1.0 N A:ASN194 4.6 14.9 1.0 C A:GLY197 4.6 6.0 1.0 N A:MET164 4.6 6.9 1.0 CA A:ILE163 4.6 7.4 1.0 HA A:ASN194 4.6 20.4 1.0 HA A:ASP198 4.7 8.3 1.0 CG A:MET164 4.7 8.2 1.0 H A:ASN194 4.7 17.9 1.0 O A:HOH2107 4.7 14.3 1.0 CA A:ASP198 4.7 6.9 1.0 HB2 A:MET164 4.8 8.4 1.0 CH2 A:TRP113 4.8 11.9 1.0 HB2 A:ASP198 4.9 8.5 1.0 C A:PRO193 4.9 14.4 1.0

Calcium binding site 4 out of 7 in the Mmp-13 Complexed with 2-Napthylsulfonamide Hydroxamic Acid Inhibitor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Mmp-13 Complexed with 2-Napthylsulfonamide Hydroxamic Acid Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca305 b:11.4 occ:0.61 O A:THR149 2.3 8.8 1.0 O A:SER146 2.4 9.2 1.0 O A:HOH2063 2.4 13.1 1.0 O A:HOH2061 2.4 21.5 1.0 O A:HOH2070 2.5 10.8 1.0 O A:HOH2073 2.5 11.9 1.0 H A:THR149 3.4 10.8 1.0 C A:THR149 3.5 8.2 1.0 O A:HOH2062 3.5 19.3 1.0 HA A:PRO150 3.6 11.2 1.0 C A:SER146 3.6 9.3 1.0 HA3 A:GLY269 3.7 11.1 1.0 H A:ASP270 3.8 10.8 1.0 HA A:ASP147 3.9 12.9 1.0 O A:HOH2083 3.9 22.8 1.0 N A:THR149 4.0 9.0 1.0 C A:ASP147 4.2 9.8 1.0 CA A:PRO150 4.3 9.3 1.0 N A:PRO150 4.4 8.0 1.0 CA A:ASP147 4.4 10.7 1.0 HA A:SER146 4.4 9.7 1.0 N A:ASP147 4.4 8.1 1.0 HB2 A:SER146 4.4 13.1 1.0 CA A:THR149 4.4 8.3 1.0 O A:ASP147 4.4 10.5 1.0 N A:VAL148 4.5 9.0 1.0 O A:HOH2080 4.5 23.8 1.0 N A:ASP270 4.5 9.1 1.0 CA A:SER146 4.6 8.1 1.0 H A:VAL148 4.6 10.8 1.0 O A:LEU151 4.6 10.6 1.0 HB3 A:ASP270 4.6 15.3 1.0 CA A:GLY269 4.7 9.2 1.0 C A:PRO150 4.7 10.4 1.0 H A:LEU151 4.7 10.0 1.0 O A:PRO268 4.8 9.6 1.0 HG1 A:THR149 4.8 11.6 1.0 O A:HOH2071 4.8 32.8 1.0 O A:HOH2069 4.8 18.4 1.0 N A:LEU151 4.9 8.3 1.0 O A:ASP270 4.9 11.1 1.0 O A:HOH2064 5.0 16.1 1.0 C A:VAL148 5.0 9.7 1.0

Calcium binding site 5 out of 7 in the Mmp-13 Complexed with 2-Napthylsulfonamide Hydroxamic Acid Inhibitor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Mmp-13 Complexed with 2-Napthylsulfonamide Hydroxamic Acid Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca302 b:9.9 occ:1.00 O B:LEU184 2.3 10.5 1.0 OD2 B:ASP202 2.3 8.2 1.0 O B:GLY180 2.3 12.9 1.0 OE2 B:GLU205 2.3 15.5 1.0 O B:SER182 2.3 14.2 1.0 OD1 B:ASP179 2.4 9.8 1.0 CG B:ASP202 3.4 8.7 1.0 C B:LEU184 3.5 9.3 1.0 C B:SER182 3.5 16.3 1.0 C B:GLY180 3.5 15.1 1.0 H B:ASP179 3.5 12.1 1.0 CD B:GLU205 3.5 12.2 1.0 CG B:ASP179 3.6 11.6 1.0 HB2 B:LEU184 3.7 11.9 1.0 H B:LEU184 3.8 12.1 1.0 N B:LEU184 3.8 10.1 1.0 N B:SER182 3.8 16.2 1.0 H B:SER182 3.9 19.4 1.0 HB3 B:ASP202 3.9 9.6 1.0 C B:PRO181 4.0 14.7 1.0 HG2 B:GLU205 4.1 14.1 1.0 HA B:PRO181 4.1 16.6 1.0 OD2 B:ASP179 4.1 13.9 1.0 N B:GLY180 4.1 11.8 1.0 CA B:LEU184 4.1 10.2 1.0 HA B:LEU185 4.1 10.4 1.0 CB B:ASP202 4.1 8.0 1.0 H B:GLY180 4.2 14.2 1.0 C B:GLY183 4.2 11.4 1.0 CA B:SER182 4.2 17.2 1.0 HB2 B:ASP202 4.2 9.6 1.0 HB3 B:PHE178 4.2 10.3 1.0 HD21 B:LEU185 4.3 15.2 1.0 C B:ASP179 4.3 13.2 1.0 N B:ASP179 4.3 10.1 1.0 OD1 B:ASP202 4.3 8.0 1.0 CA B:PRO181 4.3 13.8 1.0 OE1 B:GLU205 4.4 12.0 1.0 O B:PRO181 4.4 16.1 1.0 HA3 B:GLY183 4.4 16.9 1.0 CG B:GLU205 4.4 11.7 1.0 N B:PRO181 4.4 13.5 1.0 CB B:LEU184 4.4 9.9 1.0 CA B:GLY180 4.4 12.6 1.0 N B:GLY183 4.5 15.1 1.0 HB2 B:ASP204 4.5 11.1 1.0 N B:LEU185 4.5 8.3 1.0 HA B:SER182 4.6 20.7 1.0 CA B:GLY183 4.6 14.1 1.0 CA B:ASP179 4.7 11.7 1.0 O B:GLY183 4.7 13.2 1.0 CB B:ASP179 4.7 13.3 1.0 O B:ASP179 4.7 13.3 1.0 HG3 B:GLU205 4.7 14.1 1.0 CA B:LEU185 4.8 8.7 1.0 HB3 B:LEU184 4.9 11.9 1.0 HA2 B:GLY180 4.9 15.1 1.0

Calcium binding site 6 out of 7 in the Mmp-13 Complexed with 2-Napthylsulfonamide Hydroxamic Acid Inhibitor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Mmp-13 Complexed with 2-Napthylsulfonamide Hydroxamic Acid Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca303 b:11.8 occ:0.82 O B:GLU205 2.2 9.4 1.0 O B:HOH2036 2.3 17.9 1.0 OD2 B:ASP128 2.4 11.5 1.0 O B:ASP203 2.4 10.0 1.0 OD1 B:ASP203 2.5 9.5 1.0 O B:HOH2035 2.7 23.5 1.0 CG B:ASP128 3.0 12.0 1.0 OD1 B:ASP128 3.1 18.1 1.0 HA B:THR206 3.3 11.2 1.0 HA B:ASP203 3.3 9.5 1.0 C B:ASP203 3.3 9.0 1.0 C B:GLU205 3.4 8.7 1.0 HG1 B:THR126 3.4 8.8 1.0 HD1 B:TRP207 3.4 10.6 1.0 CG B:ASP203 3.6 8.4 1.0 HD2 B:PRO127 3.7 8.8 1.0 CA B:ASP203 3.7 7.9 1.0 H B:TRP207 3.9 9.8 1.0 OG1 B:THR126 3.9 7.4 1.0 CB B:ASP203 4.0 9.7 1.0 CA B:THR206 4.1 9.4 1.0 HB3 B:ASP203 4.1 11.6 1.0 CD1 B:TRP207 4.1 8.8 1.0 N B:THR206 4.2 9.1 1.0 N B:GLU205 4.3 8.8 1.0 HA B:ASP204 4.3 12.0 1.0 N B:ASP204 4.4 8.3 1.0 H B:GLU205 4.4 10.6 1.0 CB B:ASP128 4.5 10.7 1.0 CA B:GLU205 4.5 9.6 1.0 HE1 B:TRP207 4.5 10.8 1.0 C B:ASP204 4.5 11.2 1.0 OD2 B:ASP203 4.6 9.5 1.0 N B:TRP207 4.6 8.2 1.0 HB2 B:ASP128 4.6 12.8 1.0 NE1 B:TRP207 4.7 9.0 1.0 CA B:ASP204 4.7 10.0 1.0 CD B:PRO127 4.7 7.3 1.0 H B:ASP128 4.9 11.2 1.0 C B:THR206 4.9 9.3 1.0 HG2 B:PRO127 4.9 10.4 1.0 HB3 B:ASP128 4.9 12.8 1.0 HB2 B:ASP203 5.0 11.6 1.0 H B:THR206 5.0 10.9 1.0

Calcium binding site 7 out of 7 in the Mmp-13 Complexed with 2-Napthylsulfonamide Hydroxamic Acid Inhibitor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Mmp-13 Complexed with 2-Napthylsulfonamide Hydroxamic Acid Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca304 b:9.3 occ:1.00 O B:GLY196 2.3 8.3 1.0 O B:ASP162 2.3 7.8 1.0 O B:HOH2094 2.4 10.2 1.0 O B:ASN194 2.4 10.9 1.0 O B:HOH2095 2.4 11.2 1.0 OD1 B:ASP198 2.4 8.0 1.0 CG B:ASP198 3.4 7.8 1.0 C B:GLY196 3.4 7.9 1.0 C B:ASP162 3.5 7.4 1.0 C B:ASN194 3.6 11.3 1.0 C B:TYR195 3.8 10.2 1.0 HA B:ASP162 3.8 10.2 1.0 H B:ASP198 3.8 9.0 1.0 H B:MET164 3.9 7.7 1.0 OD2 B:ASP198 3.9 8.3 1.0 HA B:TYR195 3.9 12.1 1.0 N B:GLY196 3.9 9.5 1.0 HA B:ILE163 3.9 8.5 1.0 O B:TYR195 4.0 9.0 1.0 HG2 B:MET164 4.0 8.9 1.0 O B:HOH2143 4.0 15.5 1.0 HH2 B:TRP113 4.0 14.0 1.0 O B:ALA161 4.1 8.2 1.0 HA3 B:GLY197 4.2 9.1 1.0 N B:ASP198 4.2 7.5 1.0 H B:GLY196 4.2 11.4 1.0 CA B:GLY196 4.2 9.4 1.0 CA B:TYR195 4.2 10.1 1.0 CA B:ASP162 4.3 8.5 1.0 N B:TYR195 4.4 11.4 1.0 O B:GLY192 4.4 11.1 1.0 N B:GLY197 4.4 7.9 1.0 N B:ILE163 4.4 6.6 1.0 N B:ASN194 4.5 13.5 1.0 CA B:ASN194 4.5 13.2 1.0 HA3 B:GLY196 4.5 11.2 1.0 HA B:ASN194 4.5 15.9 1.0 H B:ASN194 4.6 16.2 1.0 CA B:GLY197 4.6 7.6 1.0 CB B:ASP198 4.6 7.0 1.0 N B:MET164 4.6 6.4 1.0 CA B:ILE163 4.6 7.1 1.0 C B:GLY197 4.7 8.3 1.0 HA B:ASP198 4.7 7.8 1.0 O B:HOH2096 4.7 19.2 1.0 HG3 B:MET164 4.7 8.9 1.0 CA B:ASP198 4.8 6.5 1.0 CG B:MET164 4.8 7.5 1.0 C B:PRO193 4.8 12.7 1.0 HB2 B:MET164 4.8 8.2 1.0 HB2 B:ASP198 4.9 8.4 1.0 HD12 B:ILE160 4.9 21.6 1.0 CH2 B:TRP113 4.9 11.6 1.0 O B:PRO193 4.9 11.7 1.0

R.A.Tommasi, S.Weiler, L.W.Mcquire, O.Rogel, M.Chambers, K.L.Clark, J.Doughty, J.Fang, V.Ganu, J.Grob, R.Goldberg, R.Goldstein, S.Lavoie, R.Kulathila, W.Macchia, R.Melton, C.Springer, M.Walker, J.Zhang, L.Zhu, M.Shultz. Potent and Selective 2-Naphthylsulfonamide Substituted Hydroxamic Acid Inhibitors of Matrix Metalloproteinase-13. Bioorg.Med.Chem.Lett. V. 21 6440 2011.
ISSN: ISSN 0960-894X
PubMed: 21937229
DOI: 10.1016/J.BMCL.2011.08.087