Sodium in PDB 4bao: 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: 4bao 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)	21.50 / 1.87
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 (%)	18.6 / 21.8

The binding sites of Sodium atom in the Thrombin in Complex with Inhibitor (pdb code 4bao). 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: 4bao:
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:24.2 occ:1.00 O B:HOH2122 2.2 27.3 1.0 O B:THR207 2.3 29.6 1.0 O B:HOH2116 2.3 34.3 1.0 O B:LYS204 2.3 30.9 1.0 O B:HOH2115 2.6 34.2 1.0 C B:LYS204 3.4 30.2 1.0 C B:THR207 3.5 28.9 1.0 CA B:ASP205 4.1 25.5 1.0 N B:ASP205 4.2 25.4 1.0 N B:THR207 4.3 22.7 1.0 CG B:LYS204 4.3 59.8 1.0 O B:HOH2124 4.3 49.5 1.0 N B:ARG208 4.3 28.8 1.0 CA B:ARG208 4.4 30.4 1.0 CA B:THR207 4.5 23.8 1.0 C B:ASP205 4.5 28.1 1.0 CA B:LYS204 4.5 25.0 1.0 OD1 B:ASP205 4.7 30.3 1.0 O B:ASP205 4.8 26.9 1.0 C B:ARG208 4.8 34.1 1.0 CG2 B:THR207 4.8 28.0 1.0 O B:ILE209 4.9 32.5 1.0 NZ B:LYS204 4.9 93.9 1.0 N B:SER206 5.0 23.5 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:34.4 occ:1.00 O B:LYS266 2.3 29.9 1.0 O B:ARG263 2.3 37.6 1.0 O B:HOH2146 2.3 35.5 1.0 O B:HOH2159 2.5 36.1 1.0 O B:HOH2136 2.6 27.2 1.0 O B:HOH2137 2.6 36.6 1.0 C B:ARG263 3.4 39.7 1.0 C B:LYS266 3.4 31.2 1.0 N B:LYS266 3.9 31.1 1.0 N B:ARG263 3.9 34.9 1.0 O B:HOH2132 3.9 30.1 1.0 O B:HOH2144 4.0 35.7 1.0 O B:TYR220 4.1 38.3 1.0 C B:ASP262 4.1 37.1 1.0 CA B:LYS266 4.1 28.5 1.0 N B:ASP264 4.2 38.4 1.0 O B:HOH2135 4.2 30.0 1.0 CA B:ASP264 4.3 38.7 1.0 CA B:ARG263 4.3 35.2 1.0 CA B:ASP262 4.4 29.7 1.0 N B:GLY265 4.4 38.3 1.0 N B:TYR267 4.4 26.3 1.0 C B:ASP264 4.5 42.0 1.0 O B:ASP262 4.5 36.7 1.0 CB B:LYS266 4.6 30.4 1.0 OD1 B:ASP262 4.6 35.4 1.0 CA B:TYR267 4.7 26.0 1.0 O B:HOH2145 4.8 36.9 1.0 C B:GLY265 4.9 37.8 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