Sodium 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:

Calcium	(Ca)	4 atoms
Zinc	(Zn)	4 atoms

The binding sites of Sodium 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 Sodium atom.
In total 2 binding sites of Sodium where determined in the MMP13 in Complex with A Piperazine Hydantoin Ligand, PDB code: 4jpa:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the MMP13 in Complex with A Piperazine Hydantoin Ligand


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na 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:Na305 b:15.4 occ:1.00 O A:GLU205 2.4 13.6 1.0 OD2 A:ASP128 2.5 18.7 1.0 O A:ASP203 2.6 13.6 1.0 OD2 A:ASP203 2.6 13.8 1.0 O A:HOH526 2.7 31.4 1.0 CG A:ASP128 3.4 15.3 1.0 C A:ASP203 3.4 12.7 1.0 O A:HOH473 3.4 28.1 1.0 OD1 A:ASP128 3.5 18.1 1.0 C A:GLU205 3.6 13.4 1.0 CG A:ASP203 3.7 13.1 1.0 CA A:ASP203 3.9 12.5 1.0 OG1 A:THR126 4.0 10.2 1.0 O A:HOH447 4.0 11.3 1.0 N A:GLU205 4.3 12.7 1.0 CB A:ASP203 4.3 12.7 1.0 CD1 A:TRP207 4.4 13.1 1.0 N A:ASP204 4.4 12.4 1.0 CA A:THR206 4.4 13.9 1.0 N A:THR206 4.4 13.7 1.0 C A:ASP204 4.5 12.7 1.0 CD A:PRO127 4.5 11.7 1.0 O A:HOH477 4.5 43.3 1.0 CA A:ASP204 4.6 12.5 1.0 CA A:GLU205 4.6 12.9 1.0 OD1 A:ASP203 4.7 12.8 1.0 CB A:ASP128 4.7 13.7 1.0 NE1 A:TRP207 4.8 13.7 1.0 N A:TRP207 4.9 14.5 1.0 CG A:PRO127 4.9 12.4 1.0

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


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of MMP13 in Complex with A Piperazine Hydantoin Ligand within 5.0Å range: probe atom residue distance (Å) B Occ B:Na305 b:10.6 occ:1.00 OD2 B:ASP128 2.3 15.2 1.0 O B:GLU205 2.4 13.1 1.0 OD2 B:ASP203 2.6 13.1 1.0 O B:ASP203 2.7 13.5 1.0 CG B:ASP128 3.1 14.2 1.0 OD1 B:ASP128 3.2 16.6 1.0 C B:ASP203 3.5 12.9 1.0 C B:GLU205 3.6 12.8 1.0 CG B:ASP203 3.7 12.5 1.0 OG1 B:THR126 3.8 10.0 1.0 CA B:ASP203 4.0 12.4 1.0 CD1 B:TRP207 4.2 12.1 1.0 CA B:THR206 4.3 12.2 1.0 CB B:ASP203 4.3 12.5 1.0 N B:GLU205 4.3 13.1 1.0 N B:THR206 4.3 12.5 1.0 N B:ASP204 4.5 13.0 1.0 CB B:ASP128 4.5 12.6 1.0 C B:ASP204 4.6 13.3 1.0 CD B:PRO127 4.6 12.1 1.0 CA B:GLU205 4.6 13.1 1.0 N B:TRP207 4.6 12.5 1.0 OD1 B:ASP203 4.7 12.4 1.0 NE1 B:TRP207 4.8 11.9 1.0 CA B:ASP204 4.8 13.2 1.0 C B:THR206 5.0 12.5 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