Sodium in PDB 3dhk: Bisphenylic Thrombin Inhibitors

All present enzymatic activity of Bisphenylic Thrombin Inhibitors:
3.4.21.5;

The structure of Bisphenylic Thrombin Inhibitors, PDB code: 3dhk was solved by B.Baum, A.Heine, G.Klebe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	10.00 / 1.73
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	69.950, 71.340, 72.440, 90.00, 100.32, 90.00
R / Rfree (%)	19.1 / 29.6

The structure of Bisphenylic Thrombin Inhibitors also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Sodium atom in the Bisphenylic Thrombin Inhibitors (pdb code 3dhk). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Bisphenylic Thrombin Inhibitors, PDB code: 3dhk:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Bisphenylic Thrombin Inhibitors


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Bisphenylic Thrombin Inhibitors within 5.0Å range: probe atom residue distance (Å) B Occ H:Na1701 b:24.2 occ:1.00 O H:LYS224 2.2 24.7 1.0 O H:HOH2034 2.2 25.0 1.0 O H:ARG221A 2.3 19.8 1.0 O H:HOH2047 2.5 14.9 1.0 O H:HOH2078 2.6 18.7 1.0 O H:HOH2087 3.0 24.8 1.0 C H:LYS224 3.3 23.4 1.0 C H:ARG221A 3.4 26.4 1.0 N H:LYS224 3.8 17.8 1.0 N H:ARG221A 3.8 20.9 1.0 O H:HOH2014 3.8 22.6 1.0 CA H:LYS224 4.0 16.9 0.5 CA H:LYS224 4.0 16.9 0.5 O H:HOH2058 4.0 18.6 1.0 C H:ASP221 4.0 26.9 1.0 CA H:ARG221A 4.2 22.4 1.0 N H:ASP222 4.2 17.4 1.0 N H:TYR225 4.2 21.4 1.0 CA H:ASP221 4.3 21.0 1.0 N H:GLY223 4.3 21.1 1.0 O H:TYR184A 4.3 22.8 1.0 CA H:ASP222 4.3 16.0 1.0 O H:HOH2049 4.3 17.8 1.0 C H:ASP222 4.4 21.5 1.0 CB H:LYS224 4.5 16.8 0.5 CB H:LYS224 4.5 16.8 0.5 CA H:TYR225 4.6 16.7 1.0 O H:ASP221 4.6 24.5 1.0 O H:HOH2036 4.6 20.4 1.0 OD1 H:ASP221 4.6 22.7 1.0 C H:GLY223 4.8 22.1 1.0 N H:ASP221 4.9 14.3 1.0 CB H:ARG221A 5.0 17.9 1.0

Sodium binding site 2 out of 2 in the Bisphenylic Thrombin Inhibitors


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Bisphenylic Thrombin Inhibitors within 5.0Å range: probe atom residue distance (Å) B Occ H:Na1702 b:14.5 occ:1.00 O H:THR172 2.1 12.7 1.0 O H:LYS169 2.3 19.2 1.0 O H:HOH2059 2.4 15.2 1.0 O H:HOH2051 2.5 20.6 1.0 C H:THR172 3.4 13.0 1.0 C H:LYS169 3.5 14.5 1.0 N H:THR172 4.1 10.5 1.0 CA H:ASP170 4.1 20.1 1.0 N H:ASP170 4.2 17.4 1.0 CA H:THR172 4.3 13.5 1.0 N H:ARG173 4.3 13.5 1.0 CA H:ARG173 4.4 18.2 1.0 C H:ASP170 4.4 17.5 1.0 CG2 H:THR172 4.4 11.7 1.0 CA H:LYS169 4.5 14.4 1.0 O H:ASP170 4.8 18.1 1.0 CB H:LYS169 4.9 15.0 1.0 O H:ILE174 4.9 14.0 1.0 C H:ARG173 4.9 19.5 1.0 N H:SER171 4.9 9.4 1.0

B.Baum, L.Muley, A.Heine, M.Smolinski, D.Hangauer, G.Klebe. Think Twice: Understanding the High Potency of Bis(Phenyl)Methane Inhibitors of Thrombin J.Mol.Biol. V. 391 552 2009.
ISSN: ISSN 0022-2836
PubMed: 19520086
DOI: 10.1016/J.JMB.2009.06.016