Sodium in PDB 1d3t: Crystal Structure of Human Alpha Thrombin in Complex with Benzo[B]Thiophene Inhibitor 1

All present enzymatic activity of Crystal Structure of Human Alpha Thrombin in Complex with Benzo[B]Thiophene Inhibitor 1:
3.4.21.5;

The structure of Crystal Structure of Human Alpha Thrombin in Complex with Benzo[B]Thiophene Inhibitor 1, PDB code: 1d3t was solved by N.Y.Chirgadze, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 3.00
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	71.140, 71.850, 72.960, 90.00, 100.50, 90.00
R / Rfree (%)	17.2 / 23.5

The binding sites of Sodium atom in the Crystal Structure of Human Alpha Thrombin in Complex with Benzo[B]Thiophene Inhibitor 1 (pdb code 1d3t). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of Human Alpha Thrombin in Complex with Benzo[B]Thiophene Inhibitor 1, PDB code: 1d3t:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Human Alpha Thrombin in Complex with Benzo[B]Thiophene Inhibitor 1


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Human Alpha Thrombin in Complex with Benzo[B]Thiophene Inhibitor 1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na398 b:18.0 occ:1.00 O B:THR213 2.4 16.3 1.0 O B:LYS210 2.6 27.4 1.0 C B:THR213 3.6 16.4 1.0 C B:LYS210 3.7 8.5 1.0 CA B:ASP211 4.3 24.1 1.0 N B:ASP211 4.4 24.1 1.0 CA B:ARG214 4.4 10.0 1.0 N B:ARG214 4.5 10.0 1.0 N B:THR213 4.5 16.4 1.0 CA B:THR213 4.7 16.4 1.0 CA B:LYS210 4.7 8.5 1.0 C B:ASP211 4.7 24.1 1.0 C B:ARG214 4.8 10.0 1.0 CG2 B:THR213 5.0 16.3 1.0 CB B:LYS210 5.0 27.4 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Human Alpha Thrombin in Complex with Benzo[B]Thiophene Inhibitor 1


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Human Alpha Thrombin in Complex with Benzo[B]Thiophene Inhibitor 1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na399 b:18.0 occ:1.00 O B:LYS272 2.4 29.9 1.0 O B:ARG269 2.9 30.2 1.0 C B:LYS272 3.4 23.6 1.0 N B:ARG269 3.8 23.2 1.0 C B:ARG269 4.0 23.2 1.0 CA B:ASP268 4.0 15.1 1.0 C B:ASP268 4.1 15.1 1.0 N B:TYR273 4.3 12.0 1.0 N B:LYS272 4.3 23.6 1.0 CA B:TYR273 4.3 12.0 1.0 CA B:LYS272 4.3 23.6 1.0 CB B:LYS272 4.5 29.9 1.0 CA B:ARG269 4.5 23.2 1.0 N B:ASP268 4.5 15.1 1.0 OD1 B:ASP268 4.6 39.3 1.0 OD2 B:ASP235 4.7 16.1 1.0 O B:TYR226 4.7 22.9 1.0 CB B:ASP235 4.9 16.1 1.0 CD2 B:TYR273 4.9 18.7 1.0 CG B:ASP235 4.9 16.1 1.0 N B:ASP270 5.0 23.9 1.0

N.Y.Chirgadze, D.J.Sall, S.L.Briggs, D.K.Clawson, M.Zhang, G.F.Smith, R.W.Schevitz. The Crystal Structures of Human Alpha-Thrombin Complexed with Active Site-Directed Diamino Benzo[B]Thiophene Derivatives: A Binding Mode For A Structurally Novel Class of Inhibitors. Protein Sci. V. 9 29 2000.
ISSN: ISSN 0961-8368
PubMed: 10739244