Sodium in PDB 4bam: 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: 4bam 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)	23.11 / 1.88
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 (%)	16.9 / 19.5

The binding sites of Sodium atom in the Thrombin in Complex with Inhibitor (pdb code 4bam). 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: 4bam:
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:16.1 occ:1.00 O B:HOH2261 2.2 16.6 1.0 O B:THR207 2.3 19.5 1.0 O B:LYS204 2.4 21.6 1.0 O B:HOH2254 2.4 24.5 1.0 O B:HOH2253 2.7 23.1 1.0 C B:LYS204 3.4 21.9 1.0 C B:THR207 3.5 19.1 1.0 CA B:ASP205 4.1 17.6 1.0 N B:ASP205 4.2 18.3 1.0 O B:HOH2264 4.3 33.2 1.0 N B:THR207 4.3 15.2 1.0 CG B:LYS204 4.3 38.8 1.0 CA B:ARG208 4.4 20.7 1.0 N B:ARG208 4.4 19.0 1.0 C B:ASP205 4.4 19.9 1.0 CA B:LYS204 4.5 17.7 1.0 CA B:THR207 4.5 16.2 1.0 OD1 B:ASP205 4.7 24.3 1.0 O B:ASP205 4.8 18.5 1.0 CG2 B:THR207 4.8 18.1 1.0 NZ B:LYS204 4.8 61.7 1.0 C B:ARG208 4.9 23.9 1.0 N B:SER206 4.9 15.4 1.0 CB B:LYS204 5.0 20.3 1.0 O B:ILE209 5.0 22.6 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:25.1 occ:1.00 O B:HOH2291 2.3 24.3 1.0 O B:ARG263 2.4 22.1 1.0 O B:LYS266 2.4 20.7 1.0 O B:HOH2311 2.4 22.1 1.0 O B:HOH2277 2.6 17.6 1.0 O B:HOH2278 2.8 23.7 1.0 C B:ARG263 3.4 24.3 1.0 C B:LYS266 3.5 20.1 1.0 N B:ARG263 3.8 19.7 1.0 O B:HOH2273 3.9 20.7 1.0 O B:HOH2290 3.9 25.6 1.0 N B:LYS266 3.9 17.4 1.0 C B:ASP262 3.9 23.4 1.0 O B:TYR220 4.1 22.8 1.0 CA B:LYS266 4.2 17.0 1.0 N B:ASP264 4.2 22.4 1.0 O B:HOH2276 4.2 15.2 1.0 CA B:ARG263 4.2 20.2 1.0 CA B:ASP262 4.3 19.0 1.0 CA B:ASP264 4.3 23.1 1.0 O B:HOH2292 4.4 25.4 1.0 O B:ASP262 4.4 22.4 1.0 N B:GLY265 4.4 22.8 1.0 N B:TYR267 4.5 16.4 1.0 CB B:LYS266 4.6 18.6 1.0 C B:ASP264 4.6 26.3 1.0 OD1 B:ASP262 4.6 22.2 1.0 CA B:TYR267 4.8 15.8 1.0 C B:GLY265 4.9 23.8 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