Sodium in PDB 6trw: Crystal Structure of DPP8 in Complex with the Eil Peptide (Slrflfegqriadnh)

All present enzymatic activity of Crystal Structure of DPP8 in Complex with the Eil Peptide (Slrflfegqriadnh):
3.4.14.5;

The structure of Crystal Structure of DPP8 in Complex with the Eil Peptide (Slrflfegqriadnh), PDB code: 6trw was solved by B.Ross, R.Huber, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.17 / 3.00
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	163.045, 245.283, 261.439, 90, 90, 90
R / Rfree (%)	19.1 / 22.6

The binding sites of Sodium atom in the Crystal Structure of DPP8 in Complex with the Eil Peptide (Slrflfegqriadnh) (pdb code 6trw). 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 the Eil Peptide (Slrflfegqriadnh), PDB code: 6trw:
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 the Eil Peptide (Slrflfegqriadnh)


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 the Eil Peptide (Slrflfegqriadnh) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na901 b:75.6 occ:1.00 O A:ARG158 2.6 84.7 1.0 OD1 A:ASP278 2.7 92.7 1.0 O A:GLN274 2.9 63.5 1.0 OH A:TYR280 3.0 70.0 1.0 O A:GLU275 3.5 69.9 1.0 C A:ARG158 3.8 83.2 1.0 NH1 A:ARG160 3.9 92.5 1.0 CG A:ASP278 3.9 90.3 1.0 C A:GLU275 4.0 68.9 1.0 CZ A:TYR280 4.0 70.2 1.0 CA A:GLU275 4.0 69.6 1.0 C A:GLN274 4.0 65.5 1.0 CE1 A:TYR280 4.1 69.6 1.0 OE2 A:GLU275 4.3 84.3 1.0 N A:GLU275 4.5 66.1 1.0 CA A:ASP278 4.6 77.3 1.0 CA A:ARG158 4.6 81.3 1.0 CB A:ASP278 4.8 82.4 1.0 CZ A:ARG160 4.8 91.5 1.0 OD2 A:ASP278 4.8 96.6 1.0 N A:LYS159 4.8 85.5 1.0 N A:ASP278 4.8 74.2 1.0 CD A:GLU275 4.9 79.6 1.0 CA A:LYS159 4.9 86.4 1.0 N A:GLU276 5.0 68.5 1.0

Sodium binding site 2 out of 3 in the Crystal Structure of DPP8 in Complex with the Eil Peptide (Slrflfegqriadnh)


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 the Eil Peptide (Slrflfegqriadnh) within 5.0Å range: probe atom residue distance (Å) B Occ B:Na901 b:66.9 occ:1.00 O B:ARG158 2.6 84.2 1.0 OH B:TYR280 2.8 70.4 1.0 OD1 B:ASP278 2.8 89.0 1.0 O B:GLN274 2.9 63.7 1.0 O B:GLU275 3.5 67.1 1.0 CG B:ASP278 3.7 85.8 1.0 C B:ARG158 3.8 82.8 1.0 CZ B:TYR280 3.8 72.5 1.0 C B:GLU275 4.0 68.7 1.0 C B:GLN274 4.0 66.9 1.0 CA B:GLU275 4.0 71.8 1.0 CE1 B:TYR280 4.1 74.1 1.0 OD2 B:ASP278 4.3 93.1 1.0 CA B:ASP278 4.4 74.5 1.0 OE2 B:GLU275 4.4 89.6 1.0 N B:GLU275 4.5 69.0 1.0 CB B:ASP278 4.6 79.6 1.0 N B:ASP278 4.7 70.7 1.0 N B:LYS159 4.7 87.9 1.0 CA B:LYS159 4.7 90.4 1.0 NH2 B:ARG160 4.7 106.0 1.0 CA B:ARG158 4.7 80.7 1.0 CD B:GLU275 4.9 87.4 1.0 N B:GLU276 5.0 68.0 1.0

Sodium binding site 3 out of 3 in the Crystal Structure of DPP8 in Complex with the Eil Peptide (Slrflfegqriadnh)


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 the Eil Peptide (Slrflfegqriadnh) within 5.0Å range: probe atom residue distance (Å) B Occ C:Na901 b:72.9 occ:1.00 O C:ARG158 2.5 85.9 1.0 OD1 C:ASP278 2.7 87.2 1.0 OH C:TYR280 2.8 72.4 1.0 O C:GLN274 3.1 69.2 1.0 O C:GLU275 3.4 71.2 1.0 C C:ARG158 3.7 82.9 1.0 CG C:ASP278 3.9 87.5 1.0 CZ C:TYR280 4.0 73.0 1.0 C C:GLU275 4.0 75.2 1.0 CA C:GLU275 4.0 75.3 1.0 NH1 C:ARG160 4.1 103.3 1.0 C C:GLN274 4.2 71.8 1.0 CE1 C:TYR280 4.2 74.0 1.0 OE2 C:GLU275 4.3 95.0 1.0 CA C:ARG158 4.5 82.9 1.0 N C:GLU275 4.6 74.0 1.0 N C:LYS159 4.6 85.2 1.0 OD2 C:ASP278 4.7 96.4 1.0 CA C:LYS159 4.8 87.6 1.0 CA C:ASP278 4.8 75.5 1.0 CD C:GLU275 4.8 89.4 1.0 CB C:ASP278 4.8 79.2 1.0 CZ C:ARG160 4.8 103.1 1.0 CG C:ARG160 4.9 99.2 1.0

B.Ross, R.Huber. The Aerosol-Generator: Direct Soaking of Naked Protein Crystals For Protein-Ligand Complexation To Be Published.