Sodium in PDB 6t52: Thrombin in Complex with A D-Phe-Pro-Imidazole Derivative

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

The structure of Thrombin in Complex with A D-Phe-Pro-Imidazole Derivative, PDB code: 6t52 was solved by K.Ngo, N.Abazi, A.Heine, G.Klebe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.50 / 1.45
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	69.998, 71.239, 72.866, 90.00, 100.50, 90.00
R / Rfree (%)	13 / 16.1

The binding sites of Sodium atom in the Thrombin in Complex with A D-Phe-Pro-Imidazole Derivative (pdb code 6t52). 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-Imidazole Derivative, PDB code: 6t52:
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-Imidazole 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-Imidazole Derivative within 5.0Å range: probe atom residue distance (Å) B Occ H:Na301 b:22.5 occ:1.00 O H:ARG221A 2.3 23.2 1.0 O H:LYS224 2.4 19.8 1.0 O H:HOH554 2.4 25.6 1.0 O H:HOH474 2.4 23.6 1.0 O H:HOH486 2.4 21.0 1.0 O H:HOH509 2.7 26.8 1.0 H H:LYS224 3.3 25.6 1.0 C H:ARG221A 3.4 24.6 1.0 C H:LYS224 3.4 19.0 1.0 HA H:ASP221 3.7 29.6 1.0 HA H:ASP222 3.7 32.2 1.0 O H:HOH504 3.9 24.3 1.0 HB2 H:LYS224 3.9 25.8 1.0 H H:GLY223 3.9 29.6 1.0 N H:LYS224 3.9 21.4 1.0 N H:ARG221A 3.9 24.7 1.0 H H:ARG221A 3.9 29.6 1.0 O H:HOH448 4.0 28.2 1.0 HA H:TYR225 4.0 20.8 1.0 C H:ASP221 4.1 25.1 1.0 O H:TYR184A 4.1 21.6 1.0 CA H:LYS224 4.2 19.6 1.0 N H:ASP222 4.2 26.3 1.0 N H:GLY223 4.2 24.6 1.0 CA H:ARG221A 4.2 24.8 1.0 O H:HOH483 4.3 20.9 1.0 CA H:ASP222 4.3 26.8 1.0 CA H:ASP221 4.4 24.6 1.0 N H:TYR225 4.4 17.8 1.0 C H:ASP222 4.5 25.4 1.0 CB H:LYS224 4.5 21.5 1.0 O H:ASP221 4.6 27.7 1.0 OD1 H:ASP221 4.7 25.2 1.0 CA H:TYR225 4.7 17.4 1.0 HB2 H:ARG221A 4.8 32.1 1.0 C H:GLY223 4.8 21.9 1.0 O H:HOH520 4.9 27.7 1.0 HA H:ARG221A 4.9 29.7 1.0 H H:ASP221 5.0 27.8 1.0 H H:ASP222 5.0 31.6 1.0 HA3 H:GLY184 5.0 19.9 1.0

Sodium binding site 2 out of 2 in the Thrombin in Complex with A D-Phe-Pro-Imidazole 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-Imidazole Derivative within 5.0Å range: probe atom residue distance (Å) B Occ H:Na302 b:17.8 occ:1.00 O H:LYS169 2.3 17.8 1.0 O H:THR172 2.3 17.9 1.0 O H:HOH564 2.3 21.3 1.0 O H:HOH562 2.4 31.5 1.0 O H:HOH458 2.8 28.9 1.0 HA H:ASP170 3.3 22.3 1.0 C H:LYS169 3.5 17.1 1.0 H H:THR172 3.5 20.8 1.0 HG3 H:LYS169 3.5 32.3 1.0 C H:THR172 3.6 16.5 1.0 HA H:ARG173 3.7 20.9 1.0 HG2 H:LYS169 4.0 32.3 1.0 CA H:ASP170 4.0 18.6 1.0 N H:ASP170 4.2 17.4 1.0 CG H:LYS169 4.2 26.9 1.0 N H:THR172 4.2 17.4 1.0 HG23 H:THR172 4.3 22.0 1.0 C H:ASP170 4.4 18.4 1.0 CA H:ARG173 4.4 17.4 1.0 N H:ARG173 4.4 17.7 1.0 HA H:LYS169 4.5 21.0 1.0 CA H:LYS169 4.5 17.5 1.0 HG22 H:THR172 4.5 22.0 1.0 CA H:THR172 4.5 17.4 1.0 O H:HOH425 4.7 51.4 1.0 OD1 H:ASP170 4.7 25.4 1.0 O H:ASP170 4.8 18.5 1.0 N H:SER171 4.8 18.0 1.0 H H:SER171 4.9 21.6 1.0 CG2 H:THR172 4.9 18.4 1.0 CB H:LYS169 4.9 19.1 1.0 H H:ASP170 5.0 20.9 1.0

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