Sodium in PDB 1d4p: Crystal Structure of Human Alpha Thrombin in Complex with 5- Amidinoindole-4-Benzylpiperidine Inhibitor

All present enzymatic activity of Crystal Structure of Human Alpha Thrombin in Complex with 5- Amidinoindole-4-Benzylpiperidine Inhibitor:
3.4.21.5;

The structure of Crystal Structure of Human Alpha Thrombin in Complex with 5- Amidinoindole-4-Benzylpiperidine Inhibitor, PDB code: 1d4p 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 / 2.07
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	71.560, 72.060, 73.220, 90.00, 101.20, 90.00
R / Rfree (%)	18.4 / 23.1

The binding sites of Sodium atom in the Crystal Structure of Human Alpha Thrombin in Complex with 5- Amidinoindole-4-Benzylpiperidine Inhibitor (pdb code 1d4p). 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 5- Amidinoindole-4-Benzylpiperidine Inhibitor, PDB code: 1d4p:
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 5- Amidinoindole-4-Benzylpiperidine Inhibitor


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 5- Amidinoindole-4-Benzylpiperidine Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:Na398 b:24.3 occ:1.00 O B:HOH553 2.4 23.6 1.0 O B:THR213 2.4 20.2 1.0 O B:LYS210 2.6 24.0 1.0 O B:HOH549 2.6 29.8 1.0 O B:HOH617 2.8 34.8 1.0 C B:LYS210 3.6 23.0 1.0 C B:THR213 3.6 20.5 1.0 CA B:ASP211 4.1 22.2 1.0 N B:ASP211 4.3 22.3 1.0 N B:THR213 4.4 18.6 1.0 CA B:ARG214 4.5 25.1 1.0 N B:ARG214 4.5 21.0 1.0 C B:ASP211 4.5 22.2 1.0 OD1 B:ASP211 4.6 20.9 1.0 CA B:THR213 4.6 18.8 1.0 CA B:LYS210 4.7 25.2 1.0 N B:SER212 4.9 21.4 1.0 CG2 B:THR213 4.9 16.9 1.0 C B:ARG214 4.9 23.9 1.0 O B:ASP211 5.0 23.9 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Human Alpha Thrombin in Complex with 5- Amidinoindole-4-Benzylpiperidine Inhibitor


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 5- Amidinoindole-4-Benzylpiperidine Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:Na399 b:26.3 occ:1.00 O B:HOH527 2.4 30.1 1.0 O B:LYS272 2.4 20.3 1.0 O B:ARG269 2.5 26.1 1.0 O B:HOH555 2.5 22.9 1.0 O B:HOH513 2.7 19.8 1.0 O B:HOH563 3.3 31.9 1.0 C B:LYS272 3.5 22.8 1.0 C B:ARG269 3.6 25.9 1.0 O B:HOH524 3.6 25.2 1.0 N B:ARG269 3.8 23.3 1.0 C B:ASP268 3.9 24.2 1.0 N B:LYS272 4.0 22.6 1.0 CA B:ASP268 4.1 22.4 1.0 CA B:LYS272 4.2 21.5 1.0 O B:HOH522 4.2 17.2 1.0 O B:HOH543 4.3 26.4 1.0 CA B:ARG269 4.4 24.4 1.0 O B:ASP268 4.4 22.8 1.0 O B:TYR226 4.4 22.6 1.0 N B:ASP270 4.4 25.5 1.0 N B:TYR273 4.4 20.7 1.0 OD1 B:ASP268 4.5 24.5 1.0 CA B:ASP270 4.5 26.9 1.0 CB B:LYS272 4.5 23.3 1.0 O B:HOH516 4.5 27.9 1.0 N B:GLY271 4.6 27.3 1.0 CA B:TYR273 4.6 19.5 1.0 C B:ASP270 4.7 28.1 1.0 N B:ASP268 4.7 21.6 1.0

N.Y.Chirgadze, D.J.Sall, V.J.Klimkowski, D.K.Clawson, S.L.Briggs, R.Hermann, G.F.Smith, D.S.Gifford-Moore, J.P.Wery. The Crystal Structure of Human Alpha-Thrombin Complexed with LY178550, A Nonpeptidyl, Active Site-Directed Inhibitor. Protein Sci. V. 6 1412 1997.
ISSN: ISSN 0961-8368
PubMed: 9232642