Sodium in PDB 6hp8: Crystal Structure of DPP8 in Complex with Val-Boropro

All present enzymatic activity of Crystal Structure of DPP8 in Complex with Val-Boropro:
3.4.14.5;

The structure of Crystal Structure of DPP8 in Complex with Val-Boropro, PDB code: 6hp8 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)	44.62 / 2.50
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	163.163, 245.317, 261.588, 90.00, 90.00, 90.00
R / Rfree (%)	20.3 / 22.8

The binding sites of Sodium atom in the Crystal Structure of DPP8 in Complex with Val-Boropro (pdb code 6hp8). 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 Val-Boropro, PDB code: 6hp8:
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 Val-Boropro


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 Val-Boropro within 5.0Å range: probe atom residue distance (Å) B Occ A:Na902 b:51.5 occ:1.00 O A:ARG158 2.5 49.2 1.0 OD1 A:ASP278 2.5 42.8 1.0 O A:GLN274 2.8 37.4 1.0 OH A:TYR280 2.9 37.4 1.0 O A:HOH1234 3.1 55.5 1.0 O A:HOH1247 3.3 56.6 1.0 O A:HOH1111 3.6 41.8 1.0 O A:GLU275 3.6 37.8 1.0 C A:ARG158 3.6 47.2 1.0 CG A:ASP278 3.7 42.9 1.0 C A:GLN274 3.9 36.8 1.0 CZ A:TYR280 3.9 35.9 1.0 CA A:GLU275 4.0 36.8 1.0 C A:GLU275 4.0 37.2 1.0 CE1 A:TYR280 4.2 36.4 1.0 N A:GLU275 4.4 36.7 1.0 CA A:ARG158 4.4 45.6 1.0 CA A:ASP278 4.4 40.1 1.0 NH1 A:ARG160 4.5 42.8 1.0 OD2 A:ASP278 4.5 45.1 1.0 OE2 A:GLU275 4.5 36.6 1.0 N A:LYS159 4.6 49.3 1.0 CB A:ASP278 4.6 41.2 1.0 N A:ASP278 4.7 39.1 1.0 O A:HOH1067 4.7 44.3 1.0 CA A:LYS159 4.8 50.0 1.0 CB A:ARG158 4.8 44.6 1.0 CD A:GLU275 4.9 37.4 1.0 N A:GLU276 5.0 36.9 1.0

Sodium binding site 2 out of 3 in the Crystal Structure of DPP8 in Complex with Val-Boropro


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 Val-Boropro within 5.0Å range: probe atom residue distance (Å) B Occ B:Na902 b:42.8 occ:1.00 OD1 B:ASP278 2.4 40.8 1.0 O B:ARG158 2.4 48.2 1.0 O B:HOH1131 2.4 38.0 1.0 OH B:TYR280 2.6 36.0 1.0 O B:GLN274 2.6 38.0 1.0 O B:HOH1192 3.1 50.5 1.0 O B:HOH1046 3.5 52.7 1.0 C B:ARG158 3.5 47.7 1.0 CG B:ASP278 3.6 40.7 1.0 CZ B:TYR280 3.6 36.8 1.0 C B:GLN274 3.8 37.7 1.0 CE1 B:TYR280 3.9 36.9 1.0 O B:GLU275 4.0 37.4 1.0 O B:HOH1208 4.0 49.8 1.0 CA B:GLU275 4.1 37.2 1.0 CA B:ASP278 4.2 38.5 1.0 C B:GLU275 4.2 37.2 1.0 CA B:ARG158 4.3 46.1 1.0 CB B:ASP278 4.4 39.0 1.0 OD2 B:ASP278 4.4 42.5 1.0 N B:GLU275 4.4 37.5 1.0 N B:LYS159 4.4 49.1 1.0 N B:ASP278 4.5 38.4 1.0 O B:HOH1110 4.5 40.3 1.0 CA B:LYS159 4.6 50.1 1.0 CB B:ARG158 4.7 45.6 1.0 NH1 B:ARG160 4.7 49.5 1.0 CE2 B:TYR280 4.8 36.7 1.0 OE2 B:GLU275 4.8 37.7 1.0 CA B:GLN274 4.9 38.8 1.0

Sodium binding site 3 out of 3 in the Crystal Structure of DPP8 in Complex with Val-Boropro


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 Val-Boropro within 5.0Å range: probe atom residue distance (Å) B Occ C:Na902 b:39.5 occ:1.00 O C:ARG158 2.3 46.1 1.0 OD1 C:ASP278 2.3 36.0 1.0 O C:HOH1007 2.3 40.2 1.0 O C:GLN274 2.6 36.2 1.0 OH C:TYR280 2.7 37.3 1.0 CG C:ASP278 3.5 36.1 1.0 C C:ARG158 3.5 45.9 1.0 CZ C:TYR280 3.7 36.8 1.0 O C:HOH1034 3.7 35.6 1.0 C C:GLN274 3.8 36.1 1.0 CE1 C:TYR280 3.9 36.5 1.0 O C:GLU275 3.9 34.8 1.0 CA C:GLU275 4.1 35.8 1.0 C C:GLU275 4.2 35.2 1.0 CA C:ASP278 4.2 35.7 1.0 OD2 C:ASP278 4.3 36.0 1.0 CA C:ARG158 4.3 44.5 1.0 CB C:ASP278 4.4 35.6 1.0 N C:LYS159 4.4 48.5 1.0 N C:GLU275 4.4 36.0 1.0 CA C:LYS159 4.5 49.5 1.0 O C:HOH1072 4.5 44.1 1.0 N C:ASP278 4.6 35.2 1.0 NH1 C:ARG160 4.6 47.4 1.0 CB C:ARG158 4.7 44.5 1.0 OE2 C:GLU275 4.8 38.3 1.0 CE2 C:TYR280 4.9 36.3 1.0 CA C:GLN274 5.0 37.0 1.0

B.H.Ross, B.H.Ross, R.Huber. N/A N/A.