Calcium in PDB 3i7i: Mmp-13 in Complex with A Non Zinc-Chelating Inhibitor

The structure of Mmp-13 in Complex with A Non Zinc-Chelating Inhibitor, PDB code: 3i7i was solved by N.A.Farrow, S.M.Margarit, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.86 / 2.21
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	134.186, 35.777, 95.295, 90.00, 131.08, 90.00
R / Rfree (%)	23 / 31.4

The structure of Mmp-13 in Complex with A Non Zinc-Chelating Inhibitor also contains other interesting chemical elements:

Zinc

(Zn)

4 atoms

The binding sites of Calcium atom in the Mmp-13 in Complex with A Non Zinc-Chelating Inhibitor (pdb code 3i7i). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Mmp-13 in Complex with A Non Zinc-Chelating Inhibitor, PDB code: 3i7i:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in the Mmp-13 in Complex with A Non Zinc-Chelating 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 in Complex with A Non Zinc-Chelating Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1263 b:57.6 occ:1.00 OD2 A:ASP128 2.6 33.2 1.0 O A:GLU205 2.9 31.3 1.0 O A:ASP203 3.1 25.3 1.0 OD1 A:ASP128 3.1 25.0 1.0 CG A:ASP128 3.1 28.5 1.0 OG1 A:THR126 3.4 22.4 1.0 O A:HOH23 3.4 23.1 1.0 OD2 A:ASP203 3.7 27.4 1.0 C A:ASP203 3.9 25.1 1.0 CD A:PRO127 3.9 21.3 1.0 CG A:ASP203 3.9 29.4 1.0 C A:GLU205 4.1 27.7 1.0 OD1 A:ASP203 4.2 34.6 1.0 CA A:ASP203 4.3 19.4 1.0 CD1 A:TRP207 4.4 22.5 1.0 CB A:ASP128 4.5 22.8 1.0 CG A:PRO127 4.5 24.5 1.0 CB A:ASP203 4.6 23.9 1.0 N A:ASP128 4.6 28.3 1.0 CA A:THR206 4.7 23.6 1.0 CB A:THR126 4.8 22.6 1.0 N A:GLU205 4.8 23.8 1.0 N A:PRO127 4.8 24.6 1.0 N A:ASP204 4.9 20.3 1.0 N A:THR206 4.9 26.4 1.0 N A:TRP207 4.9 25.5 1.0

Calcium binding site 2 out of 6 in the Mmp-13 in Complex with A Non Zinc-Chelating 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 in Complex with A Non Zinc-Chelating Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1264 b:28.7 occ:1.00 OE2 A:GLU205 2.4 25.6 1.0 O A:GLY180 2.5 29.7 1.0 O A:LEU184 2.5 27.6 1.0 OD2 A:ASP202 2.6 26.7 1.0 OD1 A:ASP179 2.7 31.9 1.0 O A:SER182 2.9 45.3 1.0 C A:SER182 3.5 37.6 1.0 CD A:GLU205 3.6 28.9 1.0 CG A:ASP202 3.6 27.4 1.0 C A:LEU184 3.6 30.2 1.0 CG A:ASP179 3.7 36.8 1.0 C A:GLY180 3.7 31.4 1.0 N A:SER182 3.7 28.5 1.0 N A:LEU184 3.9 27.7 1.0 C A:PRO181 3.9 31.4 1.0 CA A:SER182 4.1 32.8 1.0 CB A:ASP202 4.1 19.3 1.0 OD2 A:ASP179 4.2 35.1 1.0 C A:GLY183 4.3 34.1 1.0 CG A:GLU205 4.3 18.7 1.0 N A:ASP179 4.3 28.9 1.0 N A:GLY183 4.3 38.1 1.0 CA A:PRO181 4.3 25.1 1.0 CA A:LEU184 4.3 29.7 1.0 N A:GLY180 4.4 31.0 1.0 O A:PRO181 4.5 33.2 1.0 N A:PRO181 4.5 34.1 1.0 C A:ASP179 4.5 25.9 1.0 CA A:GLY183 4.5 36.1 1.0 OE1 A:GLU205 4.6 40.5 1.0 OD1 A:ASP202 4.6 22.3 1.0 N A:LEU185 4.6 28.8 1.0 CA A:GLY180 4.7 30.7 1.0 CA A:ASP179 4.7 30.2 1.0 CB A:LEU184 4.8 32.9 1.0 CA A:LEU185 4.8 26.7 1.0 CB A:ASP179 4.8 32.1 1.0 O A:GLY183 4.8 30.5 1.0 O A:ASP179 5.0 31.1 1.0

Calcium binding site 3 out of 6 in the Mmp-13 in Complex with A Non Zinc-Chelating 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 in Complex with A Non Zinc-Chelating Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1265 b:41.5 occ:1.00 O A:ASN194 2.6 34.1 1.0 O A:GLY196 2.6 27.3 1.0 OD1 A:ASP198 2.7 24.7 1.0 O A:HOH46 2.7 28.3 1.0 O A:ASP162 2.8 24.6 1.0 O A:HOH2 2.9 25.2 1.0 CG A:ASP198 3.3 26.9 1.0 OD2 A:ASP198 3.6 27.2 1.0 C A:GLY196 3.6 31.5 1.0 C A:ASP162 3.7 20.2 1.0 C A:ASN194 3.7 33.6 1.0 N A:GLY196 3.8 29.9 1.0 C A:TYR195 3.8 31.2 1.0 CA A:TYR195 4.0 33.8 1.0 O A:ALA161 4.0 26.7 1.0 O A:HOH82 4.1 28.3 1.0 N A:ASP198 4.2 24.1 1.0 CA A:GLY196 4.2 28.5 1.0 O A:TYR195 4.3 26.1 1.0 N A:TYR195 4.3 37.7 1.0 CA A:ASP162 4.5 19.8 1.0 N A:ILE163 4.5 21.1 1.0 CB A:ASP198 4.5 24.3 1.0 N A:GLY197 4.6 25.6 1.0 CA A:ILE163 4.6 25.9 1.0 N A:MET164 4.6 20.4 1.0 CG A:MET164 4.7 21.8 1.0 C A:GLY197 4.7 26.5 1.0 CA A:ASP198 4.7 21.7 1.0 CA A:GLY197 4.8 23.6 1.0 O A:GLY192 4.8 29.2 1.0 CA A:ASN194 4.9 38.3 1.0

Calcium binding site 4 out of 6 in the Mmp-13 in Complex with A Non Zinc-Chelating 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 in Complex with A Non Zinc-Chelating Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca2263 b:63.4 occ:1.00 O B:HOH303 3.0 27.5 1.0 O B:GLU205 3.1 29.9 1.0 OD2 B:ASP128 3.2 30.5 1.0 O B:ASP203 3.5 30.0 1.0 OD1 B:ASP128 3.7 28.4 1.0 CG B:ASP128 3.8 29.1 1.0 C B:GLU205 3.8 26.9 1.0 OD2 B:ASP203 4.2 28.8 1.0 C B:ASP203 4.2 24.0 1.0 C B:ASP204 4.3 34.5 1.0 CA B:THR206 4.3 27.5 1.0 N B:THR206 4.4 30.4 1.0 CA B:ASP204 4.4 28.8 1.0 N B:GLU205 4.5 26.4 1.0 OG1 B:THR206 4.5 23.6 1.0 O B:ASP204 4.6 37.0 1.0 N B:ASP204 4.7 22.5 1.0 CA B:GLU205 4.8 26.9 1.0 CB B:THR206 5.0 25.6 1.0

Calcium binding site 5 out of 6 in the Mmp-13 in Complex with A Non Zinc-Chelating 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 in Complex with A Non Zinc-Chelating Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca2264 b:33.5 occ:1.00 OD1 B:ASP179 2.5 33.1 1.0 OE1 B:GLU205 2.6 32.9 1.0 OD2 B:ASP202 2.6 29.8 1.0 O B:LEU184 2.6 39.2 1.0 O B:GLY180 2.7 32.7 1.0 O B:SER182 2.8 37.3 1.0 CG B:ASP202 3.3 25.8 1.0 C B:LEU184 3.5 31.8 1.0 CD B:GLU205 3.6 28.2 1.0 CG B:ASP179 3.6 31.4 1.0 N B:LEU184 3.7 37.9 1.0 C B:SER182 3.7 36.1 1.0 CB B:ASP202 3.8 25.4 1.0 C B:GLY180 3.9 30.6 1.0 CG B:GLU205 4.0 24.7 1.0 N B:SER182 4.0 34.2 1.0 C B:PRO181 4.1 36.4 1.0 CA B:LEU184 4.1 35.1 1.0 OD1 B:ASP202 4.1 28.3 1.0 OD2 B:ASP179 4.1 31.1 1.0 C B:GLY183 4.2 37.7 1.0 N B:ASP179 4.3 29.7 1.0 C B:ASP179 4.4 30.8 1.0 O B:ASP179 4.4 28.6 1.0 CA B:PRO181 4.4 33.9 1.0 O B:PRO181 4.5 39.5 1.0 N B:LEU185 4.5 26.1 1.0 CA B:SER182 4.5 37.9 1.0 CB B:LEU184 4.5 41.1 1.0 N B:GLY183 4.6 34.3 1.0 N B:PRO181 4.6 28.1 1.0 CA B:GLY183 4.6 39.4 1.0 OE2 B:GLU205 4.6 30.9 1.0 N B:GLY180 4.7 30.2 1.0 CA B:LEU185 4.7 31.6 1.0 CA B:ASP179 4.7 26.0 1.0 CB B:ASP179 4.8 30.5 1.0 O B:GLY183 4.9 38.7 1.0 CA B:GLY180 4.9 33.5 1.0 CD2 B:LEU185 4.9 30.2 1.0 CB B:PHE178 4.9 24.9 1.0

Calcium binding site 6 out of 6 in the Mmp-13 in Complex with A Non Zinc-Chelating 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 in Complex with A Non Zinc-Chelating Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca2265 b:43.7 occ:1.00 O B:HOH29 2.6 35.0 1.0 O B:ASN194 2.7 38.6 1.0 O B:ASP162 2.8 23.9 1.0 OD1 B:ASP198 2.9 24.1 1.0 O B:GLY196 2.9 32.5 1.0 CG B:ASP198 3.5 30.2 1.0 OD2 B:ASP198 3.6 33.1 1.0 O B:HOH85 3.6 29.0 1.0 O B:ALA161 3.7 30.7 1.0 C B:ASN194 3.7 41.0 1.0 C B:ASP162 3.8 28.2 1.0 C B:TYR195 3.9 37.6 1.0 C B:GLY196 4.0 35.0 1.0 O B:TYR195 4.0 31.1 1.0 N B:GLY196 4.1 33.4 1.0 CA B:TYR195 4.2 38.6 1.0 N B:TYR195 4.4 40.8 1.0 CA B:ASP162 4.4 28.8 1.0 O B:HOH11 4.5 42.3 1.0 CG B:MET164 4.5 27.6 1.0 N B:MET164 4.6 29.3 1.0 CA B:GLY196 4.6 30.9 1.0 N B:ASP198 4.7 29.0 1.0 N B:ILE163 4.7 24.6 1.0 CA B:ASN194 4.7 45.9 1.0 C B:ALA161 4.8 32.2 1.0 O B:GLY192 4.8 37.3 1.0 CB B:ASP198 4.8 28.1 1.0 N B:ASN194 4.8 49.1 1.0 CA B:ILE163 4.9 26.1 1.0 N B:GLY197 5.0 33.1 1.0

A.Heim-Riether, S.J.Taylor, S.Liang, D.A.Gao, Z.Xiong, E.Michael August, B.K.Collins, B.T.Farmer, K.Haverty, M.Hill-Drzewi, H.D.Junker, S.Mariana Margarit, N.Moss, T.Neumann, J.R.Proudfoot, L.S.Keenan, R.Sekul, Q.Zhang, J.Li, N.A.Farrow. Improving Potency and Selectivity of A New Class of Non-Zn-Chelating Mmp-13 Inhibitors. Bioorg.Med.Chem.Lett. V. 19 5321 2009.
ISSN: ISSN 0960-894X
PubMed: 19692239
DOI: 10.1016/J.BMCL.2009.07.151