Sodium in PDB 6trx: Crystal Structure of DPP8 in Complex with 1G244

All present enzymatic activity of Crystal Structure of DPP8 in Complex with 1G244:
3.4.14.5;

The structure of Crystal Structure of DPP8 in Complex with 1G244, PDB code: 6trx 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)	44.38 / 3.20
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	163.963, 246.288, 261.805, 90, 90, 90
R / Rfree (%)	19.7 / 23.8

The structure of Crystal Structure of DPP8 in Complex with 1G244 also contains other interesting chemical elements:

Fluorine

(F)

6 atoms

The binding sites of Sodium atom in the Crystal Structure of DPP8 in Complex with 1G244 (pdb code 6trx). 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 1G244, PDB code: 6trx:
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 1G244


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 1G244 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na1003 b:66.9 occ:1.00 O B:ARG158 2.5 87.6 1.0 OD1 B:ASP278 2.6 88.1 1.0 OH B:TYR280 2.9 83.1 1.0 O B:GLN274 2.9 81.1 1.0 O B:GLU275 3.4 79.4 1.0 CG B:ASP278 3.7 87.5 1.0 C B:ARG158 3.7 84.9 1.0 CZ B:TYR280 3.9 86.1 1.0 C B:GLU275 3.9 75.2 1.0 CA B:GLU275 3.9 77.6 1.0 C B:GLN274 4.0 82.1 1.0 CE1 B:TYR280 4.1 85.1 1.0 NH1 B:ARG160 4.2 104.3 1.0 OE2 B:GLU275 4.3 88.7 1.0 CA B:ASP278 4.4 82.5 1.0 O B:HOH1101 4.4 68.8 1.0 OD2 B:ASP278 4.4 85.0 1.0 N B:GLU275 4.5 80.2 1.0 CB B:ASP278 4.5 86.2 1.0 CA B:ARG158 4.6 83.9 1.0 N B:ASP278 4.6 81.1 1.0 N B:LYS159 4.7 85.9 1.0 CD B:GLU275 4.8 84.0 1.0 CA B:LYS159 4.8 89.2 1.0 N B:GLU276 5.0 73.6 1.0 CB B:ARG158 5.0 84.4 1.0

Sodium binding site 2 out of 3 in the Crystal Structure of DPP8 in Complex with 1G244


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 1G244 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na903 b:73.2 occ:1.00 O A:ARG158 2.5 87.8 1.0 OD1 A:ASP278 2.5 85.2 1.0 OH A:TYR280 2.9 88.5 1.0 O A:GLN274 2.9 83.6 1.0 O A:GLU275 3.3 83.9 1.0 C A:ARG158 3.6 89.1 1.0 CG A:ASP278 3.7 86.3 1.0 OE2 A:GLU275 3.7 85.7 1.0 CZ A:TYR280 3.8 85.7 1.0 NH1 A:ARG160 3.9 114.8 1.0 C A:GLU275 3.9 81.7 1.0 CA A:GLU275 3.9 81.1 1.0 CE1 A:TYR280 4.0 84.9 1.0 C A:GLN274 4.0 80.6 1.0 CA A:ARG158 4.4 88.8 1.0 OD2 A:ASP278 4.5 88.7 1.0 N A:GLU275 4.5 78.5 1.0 CA A:ASP278 4.6 81.4 1.0 CB A:ASP278 4.6 84.5 1.0 CD A:GLU275 4.6 86.2 1.0 N A:LYS159 4.7 91.3 1.0 CZ A:ARG160 4.8 111.7 1.0 CA A:LYS159 4.8 95.0 1.0 N A:ASP278 4.9 78.4 1.0 CB A:ARG158 4.9 89.5 1.0

Sodium binding site 3 out of 3 in the Crystal Structure of DPP8 in Complex with 1G244


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 1G244 within 5.0Å range: probe atom residue distance (Å) B Occ C:Na903 b:79.1 occ:1.00 O C:ARG158 2.7 97.1 1.0 OD1 C:ASP278 2.8 92.3 1.0 OH C:TYR280 3.1 83.2 1.0 O C:GLN274 3.1 84.0 1.0 O C:GLU275 3.2 85.9 1.0 NH1 C:ARG160 3.8 113.2 1.0 C C:ARG158 3.8 94.1 1.0 C C:GLU275 3.8 84.6 1.0 CA C:GLU275 3.9 82.5 1.0 CG C:ASP278 4.0 91.6 1.0 CZ C:TYR280 4.0 86.9 1.0 CE1 C:TYR280 4.1 87.7 1.0 C C:GLN274 4.1 84.6 1.0 OE1 C:GLU275 4.2 97.6 1.0 CZ C:ARG160 4.4 110.4 1.0 CD C:GLU275 4.5 94.9 1.0 CA C:ARG158 4.5 91.9 1.0 N C:GLU275 4.5 82.4 1.0 OE2 C:GLU275 4.5 101.2 1.0 OD2 C:ASP278 4.7 92.5 1.0 CA C:ASP278 4.8 89.6 1.0 NH2 C:ARG160 4.8 112.2 1.0 N C:LYS159 4.9 94.8 1.0 CB C:ASP278 4.9 90.1 1.0 CG C:ARG160 4.9 97.3 1.0 N C:GLU276 4.9 84.1 1.0 N C:ASP278 5.0 87.6 1.0

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