Sodium in PDB 4jp4: MMP13 in Complex with A Reverse Hydroxamate Zn-Binder

The structure of MMP13 in Complex with A Reverse Hydroxamate Zn-Binder, PDB code: 4jp4 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)	51.16 / 1.43
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	135.616, 36.130, 95.755, 90.00, 131.02, 90.00
R / Rfree (%)	15.1 / 17.5

The structure of MMP13 in Complex with A Reverse Hydroxamate Zn-Binder also contains other interesting chemical elements:

Fluorine	(F)	8 atoms
Zinc	(Zn)	4 atoms
Calcium	(Ca)	4 atoms

The binding sites of Sodium atom in the MMP13 in Complex with A Reverse Hydroxamate Zn-Binder (pdb code 4jp4). 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 Reverse Hydroxamate Zn-Binder, PDB code: 4jp4:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the MMP13 in Complex with A Reverse Hydroxamate Zn-Binder


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 Reverse Hydroxamate Zn-Binder within 5.0Å range: probe atom residue distance (Å) B Occ A:Na305 b:7.3 occ:1.00 O A:GLU205 2.4 10.7 1.0 O A:HOH496 2.5 19.4 1.0 O A:HOH531 2.5 25.2 1.0 OD2 A:ASP128 2.5 13.1 1.0 OD2 A:ASP203 2.6 8.0 1.0 O A:ASP203 2.8 11.7 1.0 OD1 A:ASP128 2.8 15.5 1.0 CG A:ASP128 3.0 12.4 1.0 C A:ASP203 3.5 7.9 1.0 C A:GLU205 3.6 8.6 1.0 CG A:ASP203 3.7 7.4 1.0 OG1 A:THR126 3.9 7.1 1.0 CA A:ASP203 3.9 6.8 1.0 O A:HOH567 4.1 33.5 1.0 O A:HOH438 4.2 10.3 1.0 CB A:ASP203 4.2 8.0 1.0 CA A:THR206 4.3 9.0 1.0 CD1 A:TRP207 4.3 7.8 1.0 N A:THR206 4.4 8.6 1.0 N A:GLU205 4.4 7.4 1.0 CB A:ASP128 4.5 8.5 1.0 O A:HOH655 4.5 34.3 1.0 CD A:PRO127 4.5 6.4 1.0 N A:ASP204 4.5 7.6 1.0 CA A:GLU205 4.6 8.0 1.0 C A:ASP204 4.6 7.7 1.0 OD1 A:ASP203 4.7 11.4 1.0 N A:TRP207 4.7 7.4 1.0 CA A:ASP204 4.8 7.0 1.0 NE1 A:TRP207 4.8 6.9 1.0

Sodium binding site 2 out of 2 in the MMP13 in Complex with A Reverse Hydroxamate Zn-Binder


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 Reverse Hydroxamate Zn-Binder within 5.0Å range: probe atom residue distance (Å) B Occ B:Na305 b:10.8 occ:1.00 O B:GLU205 2.3 10.7 1.0 OD2 B:ASP128 2.5 14.1 1.0 O B:HOH576 2.7 20.2 1.0 OD2 B:ASP203 2.7 9.8 1.0 O B:ASP203 2.7 10.3 1.0 CG B:ASP128 3.2 13.6 1.0 OD1 B:ASP128 3.2 20.6 1.0 O B:HOH640 3.2 56.0 1.0 C B:ASP203 3.5 8.8 1.0 C B:GLU205 3.5 8.7 1.0 CG B:ASP203 3.8 8.4 1.0 OG1 B:THR126 3.9 7.2 1.0 CA B:ASP203 4.0 7.6 1.0 O B:HOH547 4.1 26.0 1.0 CA B:THR206 4.2 8.8 1.0 CD1 B:TRP207 4.3 7.7 1.0 N B:THR206 4.3 8.3 1.0 CB B:ASP203 4.3 7.7 1.0 N B:GLU205 4.3 9.0 1.0 N B:ASP204 4.5 8.2 1.0 C B:ASP204 4.6 9.2 1.0 CB B:ASP128 4.6 10.1 1.0 CA B:GLU205 4.6 8.8 1.0 CD B:PRO127 4.6 7.2 1.0 CA B:ASP204 4.7 8.4 1.0 N B:TRP207 4.7 8.3 1.0 OD1 B:ASP203 4.8 9.8 1.0 NE1 B:TRP207 4.8 6.2 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