Sodium in PDB 2zo3: Bisphenylic Thrombin Inhibitors

All present enzymatic activity of Bisphenylic Thrombin Inhibitors:
3.4.21.5;

The structure of Bisphenylic Thrombin Inhibitors, PDB code: 2zo3 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 / 1.70
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	69.950, 71.640, 71.910, 90.00, 100.10, 90.00
R / Rfree (%)	18.7 / 25

The binding sites of Sodium atom in the Bisphenylic Thrombin Inhibitors (pdb code 2zo3). 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: 2zo3:
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:Na2502 b:18.9 occ:1.00 O H:ARG221A 2.2 18.0 1.0 O H:LYS224 2.2 19.4 1.0 O H:HOH3177 2.3 25.3 1.0 O H:HOH3034 2.4 14.1 1.0 O H:HOH3061 2.6 15.9 1.0 O H:HOH3079 2.8 23.4 1.0 C H:ARG221A 3.3 25.6 1.0 C H:LYS224 3.3 20.7 1.0 N H:LYS224 3.8 16.4 1.0 O H:HOH3032 3.8 18.3 1.0 O H:HOH3080 3.9 22.4 1.0 N H:ARG221A 4.0 20.1 1.0 C H:ASP221 4.0 24.1 1.0 CA H:LYS224 4.1 14.6 1.0 N H:ASP222 4.1 24.8 1.0 O H:TYR184A 4.2 27.9 1.0 CA H:ARG221A 4.2 26.2 1.0 N H:GLY223 4.2 29.3 1.0 CA H:ASP222 4.2 22.9 1.0 CA H:ASP221 4.3 17.6 1.0 O H:HOH3030 4.3 16.0 1.0 N H:TYR225 4.4 15.8 1.0 C H:ASP222 4.4 25.8 1.0 O H:ASP221 4.5 20.4 1.0 CB H:LYS224 4.5 13.6 1.0 OD1 H:ASP221 4.7 21.8 1.0 O H:HOH3065 4.7 22.6 1.0 CA H:TYR225 4.7 17.9 1.0 C H:GLY223 4.7 26.7 1.0 O H:HOH3029 4.9 23.6 1.0 CA H:GLY223 5.0 30.0 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:Na2503 b:12.9 occ:1.00 O H:HOH3047 2.2 23.8 1.0 O H:LYS169 2.3 18.9 1.0 O H:THR172 2.3 12.7 1.0 O H:HOH3023 2.4 15.1 1.0 O H:HOH3042 2.6 20.3 1.0 C H:LYS169 3.4 14.6 1.0 C H:THR172 3.6 9.3 1.0 CA H:ASP170 4.1 16.2 1.0 N H:ASP170 4.2 16.4 1.0 N H:THR172 4.3 12.8 1.0 CA H:LYS169 4.4 12.0 1.0 C H:ASP170 4.4 13.7 1.0 N H:ARG173 4.5 11.2 1.0 CA H:ARG173 4.5 17.3 1.0 CA H:THR172 4.5 14.0 1.0 O H:HOH3091 4.5 40.3 1.0 CG2 H:THR172 4.7 13.7 1.0 OD1 H:ASP170 4.7 18.2 1.0 CB H:LYS169 4.8 16.1 1.0 N H:SER171 4.9 13.7 1.0 O H:ASP170 4.9 17.0 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