Sodium in PDB 1d3d: Crystal Structure of Human Alpha Thrombin in Complex with Benzothiophene Inhibitor 4

All present enzymatic activity of Crystal Structure of Human Alpha Thrombin in Complex with Benzothiophene Inhibitor 4:
3.4.21.5;

The structure of Crystal Structure of Human Alpha Thrombin in Complex with Benzothiophene Inhibitor 4, PDB code: 1d3d 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 / 2.04
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	71.110, 71.888, 73.321, 90.00, 100.60, 90.00
R / Rfree (%)	17.5 / 22.3

The structure of Crystal Structure of Human Alpha Thrombin in Complex with Benzothiophene Inhibitor 4 also contains other interesting chemical elements:

Bromine

(Br)

1 atom

The binding sites of Sodium atom in the Crystal Structure of Human Alpha Thrombin in Complex with Benzothiophene Inhibitor 4 (pdb code 1d3d). 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 Benzothiophene Inhibitor 4, PDB code: 1d3d:
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 Benzothiophene Inhibitor 4


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 Benzothiophene Inhibitor 4 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na398 b:23.7 occ:1.00 O B:HOH550 2.4 22.5 1.0 O B:THR213 2.4 18.4 1.0 O B:LYS210 2.5 22.7 1.0 O B:HOH547 2.6 25.5 1.0 O B:HOH605 2.9 36.2 1.0 C B:LYS210 3.6 21.1 1.0 C B:THR213 3.6 18.0 1.0 CA B:ASP211 4.1 21.3 1.0 N B:ASP211 4.2 19.9 1.0 N B:THR213 4.4 15.8 1.0 C B:ASP211 4.4 20.9 1.0 CA B:ARG214 4.5 21.2 1.0 N B:ARG214 4.5 16.3 1.0 CA B:THR213 4.6 16.2 1.0 CA B:LYS210 4.7 24.3 1.0 OD1 B:ASP211 4.7 19.2 1.0 N B:SER212 4.9 20.1 1.0 O B:ASP211 4.9 21.2 1.0 CG2 B:THR213 4.9 10.8 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Human Alpha Thrombin in Complex with Benzothiophene Inhibitor 4


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 Benzothiophene Inhibitor 4 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na399 b:26.9 occ:1.00 O B:HOH526 2.4 26.9 1.0 O B:HOH552 2.4 23.0 1.0 O B:ARG269 2.5 27.3 1.0 O B:LYS272 2.5 18.4 1.0 O B:HOH513 2.6 21.1 1.0 O B:HOH557 3.2 22.9 1.0 C B:ARG269 3.5 25.8 1.0 C B:LYS272 3.5 21.6 1.0 N B:ARG269 3.7 22.7 1.0 O B:HOH524 3.9 24.3 1.0 N B:LYS272 3.9 23.6 1.0 C B:ASP268 4.0 22.2 1.0 O B:HOH541 4.1 24.4 1.0 CA B:LYS272 4.2 20.8 1.0 CA B:ASP268 4.2 18.3 1.0 CA B:ARG269 4.2 24.9 1.0 O B:HOH522 4.3 16.3 1.0 N B:ASP270 4.3 26.1 1.0 CB B:LYS272 4.4 24.1 1.0 O B:TYR226 4.4 24.7 1.0 CA B:ASP270 4.5 27.3 1.0 N B:TYR273 4.5 19.1 1.0 O B:HOH516 4.5 27.6 1.0 O B:ASP268 4.5 21.3 1.0 OD1 B:ASP268 4.6 26.0 1.0 N B:GLY271 4.6 25.3 1.0 C B:ASP270 4.7 27.4 1.0 CA B:TYR273 4.7 20.0 1.0 N B:ASP268 4.8 16.7 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