Sodium in PDB 7a3i: Crystal Structure of DPP8 in Complex with A 4-Oxo-B-Lactam Based Inhibitor, LMC375

All present enzymatic activity of Crystal Structure of DPP8 in Complex with A 4-Oxo-B-Lactam Based Inhibitor, LMC375:
3.4.14.5;

The structure of Crystal Structure of DPP8 in Complex with A 4-Oxo-B-Lactam Based Inhibitor, LMC375, PDB code: 7a3i 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)	49.33 / 2.80
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	163.649, 252.318, 259.962, 90, 90, 90
R / Rfree (%)	21.7 / 24.1

The structure of Crystal Structure of DPP8 in Complex with A 4-Oxo-B-Lactam Based Inhibitor, LMC375 also contains other interesting chemical elements:

Bromine	(Br)	6 atoms
Chlorine	(Cl)	3 atoms

The binding sites of Sodium atom in the Crystal Structure of DPP8 in Complex with A 4-Oxo-B-Lactam Based Inhibitor, LMC375 (pdb code 7a3i). 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 4-Oxo-B-Lactam Based Inhibitor, LMC375, PDB code: 7a3i:
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 4-Oxo-B-Lactam Based Inhibitor, LMC375


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 4-Oxo-B-Lactam Based Inhibitor, LMC375 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na903 b:77.3 occ:1.00 OD1 A:ASP278 2.7 73.0 1.0 OH A:TYR280 3.4 66.8 1.0 O A:GLU275 3.4 55.4 1.0 O A:GLN274 3.4 54.8 1.0 CG A:ASP278 3.9 67.2 1.0 C A:GLU275 4.0 56.7 1.0 CA A:GLU275 4.1 59.8 1.0 C A:GLN274 4.4 54.1 1.0 OE1 A:GLU275 4.4 81.1 1.0 CZ A:TYR280 4.5 63.6 1.0 OD2 A:ASP278 4.5 70.3 1.0 CE1 A:TYR280 4.7 62.5 1.0 CD A:GLU275 4.7 77.0 1.0 N A:GLU275 4.8 56.2 1.0 CA A:ASP278 5.0 58.0 1.0

Sodium binding site 2 out of 3 in the Crystal Structure of DPP8 in Complex with A 4-Oxo-B-Lactam Based Inhibitor, LMC375


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 4-Oxo-B-Lactam Based Inhibitor, LMC375 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na903 b:70.2 occ:1.00 OH B:TYR280 2.8 57.7 1.0 OD1 B:ASP278 2.9 70.7 1.0 O B:GLN274 2.9 57.9 1.0 CZ B:TYR280 3.8 57.7 1.0 CG B:ASP278 3.9 66.1 1.0 O B:GLU275 3.9 55.1 1.0 C B:GLN274 4.0 55.3 1.0 CE1 B:TYR280 4.0 56.7 1.0 CA B:GLU275 4.1 56.1 1.0 C B:GLU275 4.3 53.9 1.0 OD2 B:ASP278 4.5 69.0 1.0 N B:GLU275 4.5 54.9 1.0 OE2 B:GLU275 4.7 70.2 1.0 CA B:ASP278 4.8 56.8 1.0 CB B:ASP278 4.8 60.7 1.0 CD B:GLU275 4.9 70.1 1.0

Sodium binding site 3 out of 3 in the Crystal Structure of DPP8 in Complex with A 4-Oxo-B-Lactam Based Inhibitor, LMC375


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 4-Oxo-B-Lactam Based Inhibitor, LMC375 within 5.0Å range: probe atom residue distance (Å) B Occ C:Na903 b:77.3 occ:1.00 OH C:TYR280 2.9 66.2 1.0 OD1 C:ASP278 2.9 70.1 1.0 O C:GLN274 3.3 62.8 1.0 O C:GLU275 3.9 60.1 1.0 CZ C:TYR280 4.1 63.7 1.0 CG C:ASP278 4.1 67.8 1.0 CA C:GLU275 4.2 63.7 1.0 C C:GLN274 4.3 62.4 1.0 C C:GLU275 4.3 60.1 1.0 CE1 C:TYR280 4.5 62.9 1.0 OE2 C:GLU275 4.7 73.2 1.0 N C:GLU275 4.7 62.9 1.0 OD2 C:ASP278 4.9 74.0 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.