Sodium in PDB 1d3p: Crystal Structure of Human Aplha-Thrombin in Complex with Benzo[B]Thiophene Inhibitor 3

All present enzymatic activity of Crystal Structure of Human Aplha-Thrombin in Complex with Benzo[B]Thiophene Inhibitor 3:
3.4.21.5;

The structure of Crystal Structure of Human Aplha-Thrombin in Complex with Benzo[B]Thiophene Inhibitor 3, PDB code: 1d3p 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 / 2.10
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	71.370, 72.010, 73.440, 90.00, 100.36, 90.00
R / Rfree (%)	17.9 / 21.4

The binding sites of Sodium atom in the Crystal Structure of Human Aplha-Thrombin in Complex with Benzo[B]Thiophene Inhibitor 3 (pdb code 1d3p). 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 Aplha-Thrombin in Complex with Benzo[B]Thiophene Inhibitor 3, PDB code: 1d3p:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Human Aplha-Thrombin in Complex with Benzo[B]Thiophene Inhibitor 3


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 Aplha-Thrombin in Complex with Benzo[B]Thiophene Inhibitor 3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na398 b:24.9 occ:1.00 O B:HOH550 2.3 22.6 1.0 O B:THR213 2.3 18.5 1.0 O B:LYS210 2.5 24.9 1.0 O B:HOH547 2.6 30.8 1.0 C B:THR213 3.6 17.9 1.0 C B:LYS210 3.6 24.6 1.0 CA B:ASP211 4.1 24.4 1.0 N B:ASP211 4.3 23.9 1.0 N B:THR213 4.3 18.3 1.0 CA B:ARG214 4.4 25.3 1.0 N B:ARG214 4.4 19.9 1.0 C B:ASP211 4.5 23.0 1.0 CA B:THR213 4.6 18.4 1.0 OD1 B:ASP211 4.6 23.0 1.0 CA B:LYS210 4.7 27.0 1.0 C B:ARG214 4.8 24.2 1.0 N B:SER212 4.9 22.1 1.0 CG2 B:THR213 4.9 11.3 1.0 O B:ASP211 4.9 25.8 1.0 O B:ILE215 4.9 23.7 1.0 O B:ARG214 5.0 26.2 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Human Aplha-Thrombin in Complex with Benzo[B]Thiophene Inhibitor 3


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 Aplha-Thrombin in Complex with Benzo[B]Thiophene Inhibitor 3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na399 b:34.4 occ:1.00 O B:LYS272 2.5 21.1 1.0 O B:ARG269 2.5 28.9 1.0 O B:HOH513 2.6 20.2 1.0 O B:HOH526 2.6 34.3 1.0 O B:HOH552 2.6 32.4 1.0 O B:HOH558 3.3 26.9 1.0 O B:HOH524 3.4 37.1 1.0 C B:LYS272 3.5 24.1 1.0 C B:ARG269 3.6 29.9 1.0 N B:ARG269 3.8 25.3 1.0 N B:LYS272 3.9 24.0 1.0 C B:ASP268 4.1 26.8 1.0 CA B:LYS272 4.2 23.2 1.0 CA B:ASP268 4.2 24.1 1.0 O B:HOH522 4.3 20.9 1.0 O B:HOH541 4.3 33.0 1.0 CA B:ARG269 4.4 27.8 1.0 O B:TYR226 4.4 28.5 1.0 O B:HOH516 4.5 32.9 1.0 N B:ASP270 4.5 30.9 1.0 N B:TYR273 4.5 22.6 1.0 CB B:LYS272 4.5 26.5 1.0 CA B:ASP270 4.5 31.7 1.0 OD1 B:ASP268 4.5 28.8 1.0 N B:GLY271 4.5 29.1 1.0 CA B:TYR273 4.7 23.1 1.0 O B:ASP268 4.7 24.2 1.0 C B:ASP270 4.7 31.6 1.0 N B:ASP268 4.8 23.6 1.0 CD2 B:TYR273 5.0 23.6 1.0 C B:GLY271 5.0 26.7 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