Sodium in PDB 2bdy: Thrombin in Complex with Inhibitor

All present enzymatic activity of Thrombin in Complex with Inhibitor:
3.4.21.5;

The structure of Thrombin in Complex with Inhibitor, PDB code: 2bdy was solved by Y.Xue, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	70.71 / 1.61
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	69.918, 71.649, 71.234, 90.00, 99.56, 90.00
R / Rfree (%)	19.3 / 22.5

The binding sites of Sodium atom in the Thrombin in Complex with Inhibitor (pdb code 2bdy). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Thrombin in Complex with Inhibitor, PDB code: 2bdy:

Sodium binding site 1 out of 1 in the Thrombin in Complex with Inhibitor


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 Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Na402 b:24.1 occ:1.00 O A:HOH436 2.3 20.7 1.0 O A:HOH435 2.3 25.9 1.0 O A:ARG263 2.4 27.5 1.0 O A:LYS266 2.4 23.9 1.0 O A:HOH442 2.7 24.2 1.0 O A:HOH454 2.7 24.5 1.0 C A:ARG263 3.4 27.9 1.0 C A:LYS266 3.6 24.2 1.0 O A:HOH437 3.8 19.4 1.0 N A:LYS266 3.9 26.4 1.0 N A:ARG263 4.0 27.7 1.0 O A:HOH476 4.0 33.4 1.0 C A:ASP262 4.0 27.6 1.0 O A:TYR220 4.1 27.3 1.0 O A:HOH424 4.1 21.1 1.0 N A:ASP264 4.2 28.4 1.0 CA A:LYS266 4.2 25.5 1.0 CA A:ASP264 4.3 28.8 1.0 CA A:ASP262 4.3 27.0 1.0 CA A:ARG263 4.3 28.2 1.0 N A:GLY265 4.4 28.1 1.0 O A:ASP262 4.4 27.7 1.0 C A:ASP264 4.5 28.8 1.0 OD1 A:ASP262 4.6 25.3 1.0 N A:TYR267 4.6 23.2 1.0 O A:HOH740 4.6 30.8 1.0 CB A:LYS266 4.6 26.0 1.0 CA A:TYR267 4.9 22.4 1.0 C A:GLY265 4.9 26.9 1.0 O A:HOH748 5.0 30.8 1.0

S.Hanessian, E.Therrien, W.A.Van Otterlo, M.Bayrakdarian, I.Nilsson, Y.Xue. Phenolic P2/P3 Core Motif As Thrombin Inhibitors--Design, Synthesis, and X-Ray Co-Crystal Structure. Bioorg.Med.Chem.Lett. V. 16 1032 2006.
ISSN: ISSN 0960-894X
PubMed: 16290930
DOI: 10.1016/J.BMCL.2005.10.082