Sodium in PDB 1d3q: Crystal Structure of Human Alpha Thrombin in Complex with Benzo[B]Thiophene Inhibitor 2

All present enzymatic activity of Crystal Structure of Human Alpha Thrombin in Complex with Benzo[B]Thiophene Inhibitor 2:
3.4.21.5;

The structure of Crystal Structure of Human Alpha Thrombin in Complex with Benzo[B]Thiophene Inhibitor 2, PDB code: 1d3q 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 / 2.90
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	71.150, 71.730, 73.100, 90.00, 100.56, 90.00
R / Rfree (%)	16.7 / 22.8

The binding sites of Sodium atom in the Crystal Structure of Human Alpha Thrombin in Complex with Benzo[B]Thiophene Inhibitor 2 (pdb code 1d3q). 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 2, PDB code: 1d3q:
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 2


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 2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na398 b:20.0 occ:1.00 O B:THR213 2.5 16.9 1.0 O B:LYS210 2.7 31.9 1.0 C B:THR213 3.7 9.4 1.0 C B:LYS210 3.8 11.2 1.0 CA B:ARG214 4.3 8.2 1.0 CA B:ASP211 4.4 26.8 1.0 N B:ARG214 4.4 8.2 1.0 N B:ASP211 4.5 26.8 1.0 C B:ARG214 4.6 8.2 1.0 O B:ARG214 4.7 30.3 1.0 N B:THR213 4.7 9.4 1.0 CA B:THR213 4.8 9.4 1.0 C B:ASP211 4.8 26.8 1.0 CA B:LYS210 4.8 11.2 1.0 O B:ILE215 4.9 14.5 1.0 OD1 B:ASP211 5.0 20.5 1.0

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


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 2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na399 b:20.0 occ:1.00 O B:LYS272 2.4 13.1 1.0 O B:ARG269 2.5 30.6 1.0 C B:LYS272 3.4 30.4 1.0 C B:ARG269 3.5 13.2 1.0 N B:ARG269 3.6 13.2 1.0 N B:LYS272 4.0 30.4 1.0 C B:ASP268 4.0 30.2 1.0 CA B:LYS272 4.1 30.4 1.0 CA B:ASP268 4.2 30.2 1.0 CA B:ARG269 4.2 13.2 1.0 N B:TYR273 4.3 12.5 1.0 CB B:LYS272 4.4 13.1 1.0 O B:TYR226 4.4 28.3 1.0 CA B:TYR273 4.5 12.5 1.0 N B:ASP270 4.5 32.6 1.0 CA B:ASP270 4.7 32.6 1.0 OD1 B:ASP268 4.7 34.1 1.0 CD2 B:TYR273 4.7 16.0 1.0 N B:GLY271 4.8 20.2 1.0 C B:ASP270 4.8 32.6 1.0 O B:ASP268 4.8 34.1 1.0 N B:ASP268 4.8 30.2 1.0 OD2 B:ASP235 4.8 19.3 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