Calcium in PDB 4jpa: MMP13 in Complex with A Piperazine Hydantoin Ligand

The structure of MMP13 in Complex with A Piperazine Hydantoin Ligand, PDB code: 4jpa was solved by S.Gerhardt, D.Hargreaves, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.90 / 2.00
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	134.771, 35.986, 101.492, 90.00, 134.99, 90.00
R / Rfree (%)	17.7 / 23

The structure of MMP13 in Complex with A Piperazine Hydantoin Ligand also contains other interesting chemical elements:

Zinc	(Zn)	4 atoms
Sodium	(Na)	2 atoms

The binding sites of Calcium atom in the MMP13 in Complex with A Piperazine Hydantoin Ligand (pdb code 4jpa). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the MMP13 in Complex with A Piperazine Hydantoin Ligand, PDB code: 4jpa:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the MMP13 in Complex with A Piperazine Hydantoin Ligand


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of MMP13 in Complex with A Piperazine Hydantoin Ligand within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca302 b:13.1 occ:1.00 O A:ASN194 2.3 17.7 1.0 O A:GLY196 2.3 13.0 1.0 O A:HOH402 2.3 12.2 1.0 O A:HOH584 2.4 9.8 1.0 O A:ASP162 2.4 13.0 1.0 OD1 A:ASP198 2.5 11.0 1.0 CG A:ASP198 3.4 11.1 1.0 C A:ASN194 3.5 17.2 1.0 C A:GLY196 3.5 12.9 1.0 C A:ASP162 3.5 13.2 1.0 OD2 A:ASP198 3.8 11.8 1.0 C A:TYR195 4.0 15.7 1.0 N A:GLY196 4.1 14.4 1.0 O A:ALA161 4.2 14.3 1.0 N A:ASP198 4.2 11.0 1.0 CA A:ASP162 4.3 13.5 1.0 O A:TYR195 4.3 15.4 1.0 CA A:GLY196 4.3 13.7 1.0 N A:TYR195 4.3 17.0 1.0 CA A:TYR195 4.4 16.8 1.0 CA A:ASN194 4.4 17.6 1.0 O A:GLY192 4.4 15.0 1.0 N A:ASN194 4.4 17.2 1.0 N A:GLY197 4.5 12.1 1.0 O A:HOH530 4.5 18.2 1.0 O A:HOH553 4.5 11.1 1.0 N A:ILE163 4.5 12.9 1.0 CA A:GLY197 4.6 11.7 1.0 CB A:ASP198 4.6 10.6 1.0 C A:GLY197 4.6 11.3 1.0 CG A:MET164 4.6 11.8 1.0 N A:MET164 4.7 12.1 1.0 CA A:ILE163 4.7 12.5 1.0 CA A:ASP198 4.8 10.7 1.0 CH2 A:TRP113 4.8 19.5 1.0 C A:PRO193 4.8 16.7 1.0

Calcium binding site 2 out of 4 in the MMP13 in Complex with A Piperazine Hydantoin Ligand


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of MMP13 in Complex with A Piperazine Hydantoin Ligand within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca304 b:11.0 occ:1.00 OE2 A:GLU205 2.2 13.5 1.0 O A:GLY180 2.2 15.8 1.0 OD2 A:ASP202 2.2 10.5 1.0 O A:LEU184 2.3 13.6 1.0 O A:SER182 2.4 15.7 1.0 OD1 A:ASP179 2.5 12.8 1.0 CG A:ASP202 3.3 11.4 1.0 CD A:GLU205 3.4 12.0 1.0 C A:GLY180 3.4 15.6 1.0 C A:LEU184 3.5 13.6 1.0 C A:SER182 3.5 15.9 1.0 CG A:ASP179 3.6 14.0 1.0 N A:SER182 3.9 16.2 1.0 C A:PRO181 3.9 16.2 1.0 N A:LEU184 4.0 14.1 1.0 CB A:ASP202 4.0 11.4 1.0 N A:GLY180 4.1 14.7 1.0 OD2 A:ASP179 4.1 11.9 1.0 OE1 A:GLU205 4.1 11.6 1.0 CA A:LEU184 4.2 14.0 1.0 CA A:SER182 4.2 16.4 1.0 C A:ASP179 4.2 14.4 1.0 OD1 A:ASP202 4.2 10.2 1.0 N A:ASP179 4.3 14.3 1.0 C A:GLY183 4.3 14.7 1.0 CA A:PRO181 4.3 16.1 1.0 O A:PRO181 4.3 16.3 1.0 N A:PRO181 4.3 15.9 1.0 CG A:GLU205 4.4 12.0 1.0 CA A:GLY180 4.4 15.2 1.0 N A:LEU185 4.5 13.1 1.0 N A:GLY183 4.5 15.6 1.0 O A:ASP179 4.6 14.3 1.0 CB A:LEU184 4.6 14.0 1.0 CA A:ASP179 4.6 14.3 1.0 CA A:LEU185 4.7 12.8 1.0 CA A:GLY183 4.7 15.1 1.0 CB A:ASP179 4.7 14.2 1.0 O A:GLY183 4.8 15.2 1.0

Calcium binding site 3 out of 4 in the MMP13 in Complex with A Piperazine Hydantoin Ligand


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of MMP13 in Complex with A Piperazine Hydantoin Ligand within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca303 b:9.0 occ:1.00 O B:HOH428 2.2 11.1 1.0 O B:ASP162 2.3 8.7 1.0 O B:ASN194 2.3 15.7 1.0 O B:HOH427 2.4 5.6 1.0 O B:GLY196 2.4 13.4 1.0 OD1 B:ASP198 2.5 9.1 1.0 C B:ASP162 3.4 9.7 1.0 CG B:ASP198 3.5 10.3 1.0 C B:ASN194 3.5 16.3 1.0 C B:GLY196 3.5 13.6 1.0 OD2 B:ASP198 3.9 11.3 1.0 C B:TYR195 4.0 15.9 1.0 O B:ALA161 4.0 11.2 1.0 N B:GLY196 4.0 14.9 1.0 O B:TYR195 4.2 15.8 1.0 CA B:ASP162 4.2 10.2 1.0 O B:HOH512 4.2 18.0 1.0 N B:ASP198 4.3 11.6 1.0 CA B:GLY196 4.3 14.1 1.0 O B:GLY192 4.4 15.3 1.0 N B:TYR195 4.4 16.3 1.0 CA B:ASN194 4.4 16.5 1.0 N B:ASN194 4.4 16.4 1.0 CA B:TYR195 4.4 16.7 1.0 N B:ILE163 4.5 9.6 1.0 N B:GLY197 4.5 12.9 1.0 O B:HOH577 4.5 17.2 1.0 CA B:GLY197 4.6 12.7 1.0 CA B:ILE163 4.7 9.7 1.0 N B:MET164 4.7 9.6 1.0 CB B:ASP198 4.7 10.9 1.0 C B:GLY197 4.8 12.1 1.0 C B:PRO193 4.8 16.1 1.0 CG B:MET164 4.8 9.9 1.0 CA B:ASP198 4.9 10.9 1.0 C B:ALA161 4.9 10.7 1.0 CH2 B:TRP113 5.0 18.4 1.0

Calcium binding site 4 out of 4 in the MMP13 in Complex with A Piperazine Hydantoin Ligand


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of MMP13 in Complex with A Piperazine Hydantoin Ligand within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca304 b:13.8 occ:1.00 OE2 B:GLU205 2.2 13.3 1.0 O B:LEU184 2.3 15.4 1.0 OD2 B:ASP202 2.3 10.7 1.0 OD1 B:ASP179 2.3 14.6 1.0 O B:GLY180 2.4 17.9 1.0 O B:SER182 2.4 17.4 1.0 C B:LEU184 3.4 15.2 1.0 CG B:ASP202 3.4 11.3 1.0 CD B:GLU205 3.4 13.6 1.0 C B:SER182 3.5 17.9 1.0 CG B:ASP179 3.5 15.8 1.0 C B:GLY180 3.6 17.6 1.0 N B:SER182 3.9 18.4 1.0 N B:LEU184 3.9 16.3 1.0 C B:PRO181 4.0 18.5 1.0 CB B:ASP202 4.1 11.1 1.0 OD2 B:ASP179 4.1 15.9 1.0 N B:GLY180 4.2 16.9 1.0 CA B:LEU184 4.2 16.1 1.0 OE1 B:GLU205 4.2 14.2 1.0 CA B:SER182 4.3 18.6 1.0 N B:ASP179 4.3 15.4 1.0 C B:ASP179 4.3 16.4 1.0 C B:GLY183 4.3 16.7 1.0 CG B:GLU205 4.3 13.3 1.0 O B:PRO181 4.4 18.8 1.0 OD1 B:ASP202 4.4 9.2 1.0 N B:LEU185 4.4 14.3 1.0 CA B:PRO181 4.5 18.4 1.0 N B:PRO181 4.5 18.1 1.0 CA B:GLY180 4.5 17.4 1.0 CB B:LEU184 4.5 16.4 1.0 N B:GLY183 4.5 17.5 1.0 CA B:ASP179 4.6 16.0 1.0 CA B:LEU185 4.6 13.6 1.0 O B:ASP179 4.7 16.7 1.0 CB B:ASP179 4.7 16.1 1.0 CA B:GLY183 4.7 17.2 1.0 O B:GLY183 4.8 16.5 1.0 CD2 B:LEU185 5.0 13.4 1.0

C.De Savi, D.Waterson, A.Pape, S.Lamont, E.Hadley, M.Mills, K.M.Page, J.Bowyer, R.A.Maciewicz. Hydantoin Based Inhibitors of MMP13--Discovery of AZD6605. Bioorg.Med.Chem.Lett. V. 23 4705 2013.
ISSN: ISSN 0960-894X
PubMed: 23810497
DOI: 10.1016/J.BMCL.2013.05.089