Sodium in PDB 4a7b: MMP13 in Complex with A Novel Selective Non Zinc Binding Inhibitor CMPD22

The structure of MMP13 in Complex with A Novel Selective Non Zinc Binding Inhibitor CMPD22, PDB code: 4a7b was solved by D.Hargreaves, S.Gerhardt, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	72.02 / 2.20
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	135.854, 36.220, 95.568, 90.00, 131.10, 90.00
R / Rfree (%)	19.3 / 25.3

The structure of MMP13 in Complex with A Novel Selective Non Zinc Binding Inhibitor CMPD22 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 Novel Selective Non Zinc Binding Inhibitor CMPD22 (pdb code 4a7b). 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 Novel Selective Non Zinc Binding Inhibitor CMPD22, PDB code: 4a7b:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the MMP13 in Complex with A Novel Selective Non Zinc Binding Inhibitor CMPD22


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 Novel Selective Non Zinc Binding Inhibitor CMPD22 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1280 b:26.4 occ:1.00 O A:GLU205 2.4 24.5 1.0 OD2 A:ASP128 2.6 24.3 1.0 O A:ASP203 2.8 25.6 1.0 OD1 A:ASP203 2.8 22.5 1.0 OD1 A:ASP128 2.9 26.7 1.0 CG A:ASP128 3.1 23.3 1.0 C A:ASP203 3.6 23.1 1.0 C A:GLU205 3.6 24.1 1.0 CG A:ASP203 3.9 21.1 1.0 OG1 A:THR126 4.0 20.2 1.0 O A:HOH2078 4.0 27.7 1.0 CA A:ASP203 4.1 20.9 1.0 CD1 A:TRP207 4.3 20.6 1.0 CA A:THR206 4.4 24.3 1.0 CB A:ASP203 4.4 21.4 1.0 N A:THR206 4.4 24.3 1.0 N A:GLU205 4.5 22.5 1.0 CD A:PRO127 4.5 19.3 1.0 CB A:ASP128 4.6 21.4 1.0 N A:ASP204 4.6 21.5 1.0 C A:ASP204 4.7 24.1 1.0 CA A:GLU205 4.7 24.6 1.0 N A:TRP207 4.7 23.0 1.0 CA A:ASP204 4.8 23.3 1.0 NE1 A:TRP207 4.9 21.3 1.0 OD2 A:ASP203 4.9 19.7 1.0 CG A:PRO127 5.0 22.2 1.0

Sodium binding site 2 out of 2 in the MMP13 in Complex with A Novel Selective Non Zinc Binding Inhibitor CMPD22


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 Novel Selective Non Zinc Binding Inhibitor CMPD22 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na1277 b:28.0 occ:1.00 O B:GLU205 2.4 28.8 1.0 OD2 B:ASP128 2.5 30.7 1.0 OD1 B:ASP203 2.8 26.9 1.0 O B:ASP203 2.9 29.5 1.0 OD1 B:ASP128 3.2 31.0 1.0 CG B:ASP128 3.2 29.7 1.0 C B:GLU205 3.6 26.9 1.0 C B:ASP203 3.6 25.9 1.0 CG B:ASP203 3.8 27.4 1.0 OG1 B:THR126 3.8 22.4 1.0 CA B:ASP203 4.0 25.3 1.0 CA B:THR206 4.2 26.1 1.0 N B:THR206 4.3 26.0 1.0 CD1 B:TRP207 4.3 23.8 1.0 CB B:ASP203 4.4 26.1 1.0 N B:GLU205 4.4 28.2 1.0 CD B:PRO127 4.5 22.3 1.0 N B:ASP204 4.6 25.3 1.0 N B:TRP207 4.6 25.5 1.0 CA B:GLU205 4.7 28.1 1.0 C B:ASP204 4.7 29.2 1.0 CB B:ASP128 4.7 28.6 1.0 OD2 B:ASP203 4.8 26.3 1.0 CA B:ASP204 4.8 26.7 1.0 NE1 B:TRP207 4.9 23.6 1.0 C B:THR206 4.9 25.8 1.0

C.De Savi, A.D.Morley, I.Nash, G.Karoutchi, K.Page, A.Ting, S.Gerhardt. Lead Optimisation of Selective Non-Zinc Binding Inhibitors of MMP13. Part 2. Bioorg.Med.Chem.Lett. V. 22 271 2012.
ISSN: ISSN 0960-894X
PubMed: 22153941
DOI: 10.1016/J.BMCL.2011.11.034