Sodium in PDB 4bak: Thrombin in Complex with Inhibitor

All present enzymatic activity of Thrombin in Complex with Inhibitor:
3.4.21.5;

The structure of Thrombin in Complex with Inhibitor, PDB code: 4bak was solved by Y.Xue, D.Musil, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	21.36 / 1.94
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	69.410, 71.510, 72.160, 90.00, 100.34, 90.00
R / Rfree (%)	16.7 / 20.3

The binding sites of Sodium atom in the Thrombin in Complex with Inhibitor (pdb code 4bak). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Thrombin in Complex with Inhibitor, PDB code: 4bak:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Thrombin in Complex with Inhibitor


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Thrombin in Complex with Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:Na1288 b:15.4 occ:1.00 O B:HOH2206 2.2 16.9 1.0 O B:HOH2201 2.2 26.1 1.0 O B:THR207 2.3 20.1 1.0 O B:LYS204 2.4 20.7 1.0 O B:HOH2200 2.8 24.3 1.0 C B:LYS204 3.5 21.3 1.0 C B:THR207 3.5 18.8 1.0 CA B:ASP205 4.1 16.8 1.0 N B:ASP205 4.2 17.5 1.0 N B:THR207 4.3 14.1 1.0 CA B:ARG208 4.4 18.7 1.0 N B:ARG208 4.4 17.7 1.0 CG B:LYS204 4.4 36.9 1.0 CA B:THR207 4.5 14.3 1.0 C B:ASP205 4.5 18.4 1.0 CA B:LYS204 4.6 17.6 1.0 OD1 B:ASP205 4.7 20.0 1.0 C B:ARG208 4.8 23.6 1.0 O B:ASP205 4.9 17.0 1.0 N B:SER206 5.0 14.0 1.0 CG2 B:THR207 5.0 16.8 1.0 O B:ILE209 5.0 24.2 1.0

Sodium binding site 2 out of 2 in the Thrombin in Complex with Inhibitor


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Thrombin in Complex with Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:Na1289 b:22.8 occ:1.00 O B:LYS266 2.2 17.4 1.0 O B:ARG263 2.3 22.6 1.0 O B:HOH2235 2.4 24.2 1.0 O B:HOH2255 2.4 18.1 1.0 O B:HOH2222 2.6 22.1 1.0 O B:HOH2221 2.6 18.9 1.0 C B:ARG263 3.3 24.2 1.0 C B:LYS266 3.4 19.0 1.0 O B:HOH2233 3.8 21.6 1.0 N B:LYS266 3.8 18.3 1.0 N B:ARG263 3.9 19.9 1.0 O B:HOH2217 4.0 14.2 1.0 C B:ASP262 4.1 23.6 1.0 O B:TYR220 4.1 21.5 1.0 CA B:LYS266 4.1 17.0 1.0 N B:ASP264 4.1 21.9 1.0 CA B:ASP264 4.2 22.1 1.0 CA B:ARG263 4.3 20.4 1.0 O B:HOH2220 4.3 13.0 1.0 N B:GLY265 4.4 21.4 1.0 CA B:ASP262 4.4 18.3 1.0 N B:TYR267 4.4 14.7 1.0 C B:ASP264 4.5 24.6 1.0 O B:ASP262 4.5 23.4 1.0 CB B:LYS266 4.5 19.9 1.0 O B:HOH2234 4.6 24.9 1.0 OD1 B:ASP262 4.6 21.0 1.0 CA B:TYR267 4.7 14.6 1.0 C B:GLY265 4.9 24.1 1.0

J.Winquist, S.Geschwindner, Y.Xue, L.Gustavsson, D.Musil, J.Deinum, U.H.Danielson. Identification of Structure-Kinetic and Structure-Thermodynamic Relationships For Thrombin Inhibitors. Biochemistry V. 52 613 2013.
ISSN: ISSN 0006-2960
PubMed: 23290007
DOI: 10.1021/BI301333Z