Sodium in PDB 7a3k: Crystal Structure of DPP8 in Complex with A B-Lactam Based Inhibitor, A296.1

All present enzymatic activity of Crystal Structure of DPP8 in Complex with A B-Lactam Based Inhibitor, A296.1:
3.4.14.5;

The structure of Crystal Structure of DPP8 in Complex with A B-Lactam Based Inhibitor, A296.1, PDB code: 7a3k was solved by B.H.Ross, R.Huber, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.05 / 2.65
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	163.264, 250.38, 261.202, 90, 90, 90
R / Rfree (%)	21.7 / 24.4

The structure of Crystal Structure of DPP8 in Complex with A B-Lactam Based Inhibitor, A296.1 also contains other interesting chemical elements:

Chlorine	(Cl)	8 atoms
Bromine	(Br)	3 atoms

The binding sites of Sodium atom in the Crystal Structure of DPP8 in Complex with A B-Lactam Based Inhibitor, A296.1 (pdb code 7a3k). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Crystal Structure of DPP8 in Complex with A B-Lactam Based Inhibitor, A296.1, PDB code: 7a3k:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Crystal Structure of DPP8 in Complex with A B-Lactam Based Inhibitor, A296.1


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of DPP8 in Complex with A B-Lactam Based Inhibitor, A296.1 within 5.0Å range: probe atom residue distance (Å) B Occ C:Na906 b:79.7 occ:1.00 OD1 C:ASP278 2.8 72.4 1.0 OH C:TYR280 3.3 70.5 1.0 O C:GLN274 3.4 66.1 1.0 O C:GLU275 3.7 63.7 1.0 CG C:ASP278 3.9 70.0 1.0 CA C:GLU275 4.2 65.4 1.0 C C:GLU275 4.2 64.3 1.0 CZ C:TYR280 4.4 67.7 1.0 C C:GLN274 4.5 64.8 1.0 OD2 C:ASP278 4.5 74.0 1.0 OE1 C:GLU275 4.6 76.1 1.0 CE1 C:TYR280 4.7 67.5 1.0 CD C:GLU275 4.8 74.1 1.0 N C:GLU275 4.8 64.9 1.0

Sodium binding site 2 out of 3 in the Crystal Structure of DPP8 in Complex with A B-Lactam Based Inhibitor, A296.1


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of DPP8 in Complex with A B-Lactam Based Inhibitor, A296.1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na904 b:77.2 occ:1.00 O A:HOH1022 2.7 60.4 1.0 OD1 A:ASP278 2.9 74.2 1.0 OH A:TYR280 2.9 66.5 1.0 O A:GLN274 3.1 62.2 1.0 O A:GLU275 3.7 60.8 1.0 CG A:ASP278 3.9 70.2 1.0 CZ A:TYR280 3.9 66.2 1.0 C A:GLN274 4.1 61.9 1.0 CA A:GLU275 4.1 65.2 1.0 C A:GLU275 4.2 62.8 1.0 CE1 A:TYR280 4.2 66.8 1.0 OD2 A:ASP278 4.6 73.1 1.0 N A:GLU275 4.6 63.4 1.0 OE1 A:GLU275 4.7 75.8 1.0 CA A:ASP278 4.7 63.5 1.0 CB A:ASP278 4.8 66.3 1.0 CD A:GLU275 5.0 74.2 1.0

Sodium binding site 3 out of 3 in the Crystal Structure of DPP8 in Complex with A B-Lactam Based Inhibitor, A296.1


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of DPP8 in Complex with A B-Lactam Based Inhibitor, A296.1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na904 b:89.3 occ:1.00 OH B:TYR280 2.9 67.7 1.0 OD1 B:ASP278 2.9 68.2 1.0 O B:GLN274 3.3 62.0 1.0 CG B:ASP278 3.9 63.6 1.0 O B:GLU275 3.9 61.1 1.0 CZ B:TYR280 4.0 67.8 1.0 CE1 B:TYR280 4.3 67.2 1.0 CA B:GLU275 4.3 63.4 1.0 C B:GLN274 4.4 61.3 1.0 C B:GLU275 4.4 61.0 1.0 OD2 B:ASP278 4.5 63.3 1.0 OE1 B:GLU275 4.6 75.9 1.0 CD B:GLU275 4.8 73.9 1.0 N B:GLU275 4.8 62.2 1.0 OE2 B:GLU275 5.0 73.7 1.0

L.Fehr, L.A.R.Carvalho, B.H.Ross, K.Lum, A.C.Vieira, R.Kiefersauer, R.Geiss-Friedlander, M.Kaiser, T.Rodrigues, S.D.Lucas, B.F.Cravatt, R.Huber, R.Moreira. Discovery and Development of 4-Oxo-Beta-Lactams As Novel Inhibitors of Dipeptidyl Peptidases 8 and 9 To Be Published.