Sodium in PDB 6hsx: Thrombin in Complex with A D-Phe-Pro-Diaminopyridine Derivative

All present enzymatic activity of Thrombin in Complex with A D-Phe-Pro-Diaminopyridine Derivative:
3.4.21.5;

The structure of Thrombin in Complex with A D-Phe-Pro-Diaminopyridine Derivative, PDB code: 6hsx was solved by K.Ngo, A.Heine, G.Klebe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.51 / 1.56
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	69.997, 71.726, 72.634, 90.00, 100.35, 90.00
R / Rfree (%)	16.2 / 18.4

The binding sites of Sodium atom in the Thrombin in Complex with A D-Phe-Pro-Diaminopyridine Derivative (pdb code 6hsx). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Thrombin in Complex with A D-Phe-Pro-Diaminopyridine Derivative, PDB code: 6hsx:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Thrombin in Complex with A D-Phe-Pro-Diaminopyridine Derivative


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Thrombin in Complex with A D-Phe-Pro-Diaminopyridine Derivative within 5.0Å range: probe atom residue distance (Å) B Occ H:Na305 b:18.4 occ:1.00 O H:LYS169 2.4 17.6 1.0 O H:THR172 2.4 19.1 1.0 O H:HOH435 2.9 28.3 1.0 HA H:ASP170 3.3 24.6 1.0 HG2 H:LYS169 3.4 28.5 1.0 C H:LYS169 3.5 18.7 1.0 H H:THR172 3.5 22.8 1.0 C H:THR172 3.6 18.1 1.0 HA H:ARG173 3.7 24.6 1.0 CA H:ASP170 4.0 20.5 1.0 HG3 H:LYS169 4.1 28.5 1.0 CG H:LYS169 4.2 23.8 1.0 N H:ASP170 4.2 17.3 1.0 N H:THR172 4.3 19.0 1.0 O H:HOH495 4.4 44.5 1.0 C H:ASP170 4.4 19.0 1.0 HG23 H:THR172 4.4 23.8 1.0 CA H:ARG173 4.5 20.5 1.0 N H:ARG173 4.5 16.8 1.0 HA H:LYS169 4.5 20.2 1.0 CA H:LYS169 4.5 16.8 1.0 CA H:THR172 4.6 19.3 1.0 HE2 H:LYS169 4.6 38.9 1.0 HG22 H:THR172 4.7 23.8 1.0 OD1 H:ASP170 4.7 23.4 1.0 O H:ASP170 4.8 19.8 1.0 HE3 H:LYS169 4.8 38.9 1.0 N H:SER171 4.9 17.1 1.0 H H:SER171 4.9 20.5 1.0 CB H:LYS169 4.9 17.0 1.0 CG2 H:THR172 5.0 19.8 1.0

Sodium binding site 2 out of 2 in the Thrombin in Complex with A D-Phe-Pro-Diaminopyridine Derivative


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Thrombin in Complex with A D-Phe-Pro-Diaminopyridine Derivative within 5.0Å range: probe atom residue distance (Å) B Occ H:Na306 b:22.3 occ:1.00 O H:ARG221A 2.3 22.7 1.0 O H:LYS224 2.3 21.0 1.0 O H:HOH552 2.4 24.9 1.0 O H:HOH463 2.4 20.4 1.0 O H:HOH500 2.4 22.2 1.0 O H:HOH449 2.9 24.6 1.0 H H:LYS224 3.2 25.1 1.0 C H:ARG221A 3.4 28.5 1.0 C H:LYS224 3.4 18.1 1.0 HA H:ASP221 3.7 27.6 1.0 HA H:ASP222 3.8 35.7 1.0 HB2 H:LYS224 3.8 26.4 1.0 N H:LYS224 3.8 20.9 1.0 O H:HOH503 3.8 22.2 1.0 N H:ARG221A 3.9 27.9 1.0 H H:ARG221A 3.9 33.4 1.0 HA H:TYR225 4.0 21.4 1.0 H H:GLY223 4.0 31.2 1.0 CA H:LYS224 4.1 20.1 1.0 C H:ASP221 4.1 27.5 1.0 O H:HOH470 4.1 26.7 1.0 O H:TYR184A 4.2 24.1 1.0 CA H:ARG221A 4.2 24.7 1.0 N H:ASP222 4.2 28.7 1.0 O H:HOH454 4.3 20.5 1.0 N H:GLY223 4.3 26.1 1.0 CA H:ASP222 4.4 29.8 1.0 CA H:ASP221 4.4 23.0 1.0 N H:TYR225 4.4 18.5 1.0 CB H:LYS224 4.5 22.1 1.0 C H:ASP222 4.6 26.1 1.0 O H:ASP221 4.7 27.1 1.0 OD1 H:ASP221 4.7 24.8 1.0 CA H:TYR225 4.7 17.9 1.0 HB2 H:ARG221A 4.8 28.2 1.0 HB2 H:ASP189 4.9 24.3 1.0 C H:GLY223 4.9 21.4 1.0 O H:HOH537 4.9 24.0 1.0 HA H:ARG221A 5.0 29.6 1.0 H H:ASP221 5.0 24.8 1.0 HA3 H:GLY184 5.0 26.0 1.0

K.Ngo, A.Heine, G.Klebe. Thrombin in Complex with A D-Phe-Pro-Diaminopyridine Derivative To Be Published.