Sodium in PDB 4ueh: Thrombin in Complex with Benzamidine

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

The structure of Thrombin in Complex with Benzamidine, PDB code: 4ueh was solved by E.Ruehmann, A.Heine, G.Klebe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.76 / 1.16
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	70.421, 71.512, 72.465, 90.00, 100.47, 90.00
R / Rfree (%)	12.1 / 13.8

The binding sites of Sodium atom in the Thrombin in Complex with Benzamidine (pdb code 4ueh). 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 Benzamidine, PDB code: 4ueh:
Jump to Sodium binding site number: 1; 2;

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


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 Benzamidine within 5.0Å range: probe atom residue distance (Å) B Occ H:Na1247 b:14.8 occ:1.00 O H:THR172 2.3 15.9 1.0 O H:LYS169 2.4 15.9 1.0 O H:HOH2223 2.4 22.2 1.0 O H:HOH2222 2.6 22.7 1.0 HA H:ASP170 3.2 18.4 1.0 C H:LYS169 3.4 15.0 1.0 HG2 H:LYS169 3.4 21.1 0.4 H H:THR172 3.5 17.8 1.0 C H:THR172 3.6 15.0 1.0 HZ1 H:LYS169 3.6 30.8 0.4 HA H:ARG173 3.7 18.4 1.0 CA H:ASP170 4.0 15.3 1.0 N H:ASP170 4.1 15.0 1.0 HB3 H:LYS169 4.1 19.6 0.6 HG21 H:THR172 4.2 20.0 1.0 N H:THR172 4.3 14.8 1.0 CG H:LYS169 4.3 17.6 0.4 C H:ASP170 4.4 15.8 1.0 N H:ARG173 4.4 14.9 1.0 NZ H:LYS169 4.4 25.6 0.4 CA H:ARG173 4.4 15.3 1.0 HA H:LYS169 4.4 17.6 0.6 HA H:LYS169 4.4 18.1 0.4 O H:HOH2230 4.5 37.8 1.0 CA H:LYS169 4.5 14.7 0.6 HG3 H:LYS169 4.5 21.1 0.4 CA H:LYS169 4.5 15.1 0.4 HZ3 H:LYS169 4.5 30.8 0.4 CA H:THR172 4.5 15.4 1.0 HG23 H:THR172 4.6 20.0 1.0 OD1 H:ASP170 4.6 19.6 1.0 O H:ASP170 4.7 16.7 1.0 HZ2 H:LYS169 4.8 30.8 0.4 CG2 H:THR172 4.8 16.7 1.0 CB H:LYS169 4.8 16.4 0.6 N H:SER171 4.8 15.3 1.0 CB H:LYS169 4.9 16.5 0.4 H H:SER171 4.9 18.4 1.0 C H:ARG173 4.9 15.5 1.0 H H:ASP170 5.0 18.0 1.0 O H:ILE174 5.0 15.9 1.0

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


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 Benzamidine within 5.0Å range: probe atom residue distance (Å) B Occ H:Na1248 b:18.1 occ:1.00 O H:ARG221A 2.3 19.7 1.0 O H:HOH2255 2.4 18.1 1.0 O H:LYS224 2.4 16.7 1.0 O H:HOH2279 2.4 18.5 1.0 O H:HOH2241 2.5 16.4 1.0 O H:HOH2242 2.6 20.7 1.0 H H:LYS224 3.3 21.7 1.0 C H:ARG221A 3.4 19.2 1.0 C H:LYS224 3.5 16.1 1.0 HA H:ASP222 3.7 25.4 1.0 HA H:ASP221 3.7 21.5 1.0 H H:GLY223 3.8 25.3 1.0 N H:LYS224 3.9 18.1 1.0 HB2 H:LYS224 3.9 21.5 1.0 O H:HOH2237 3.9 16.4 1.0 O H:HOH2254 3.9 22.8 1.0 N H:ARG221A 3.9 18.9 1.0 H H:ARG221A 4.0 22.6 1.0 HA H:TYR225 4.1 17.1 1.0 O H:TYR184A 4.1 18.1 1.0 C H:ASP221 4.1 18.4 1.0 CA H:LYS224 4.2 17.1 1.0 N H:GLY223 4.2 21.1 1.0 N H:ASP222 4.2 21.5 1.0 CA H:ASP222 4.3 21.1 1.0 O H:HOH2240 4.3 17.3 1.0 CA H:ARG221A 4.3 19.7 1.0 CA H:ASP221 4.4 17.9 1.0 N H:TYR225 4.5 14.9 1.0 C H:ASP222 4.5 20.7 1.0 O H:ASP221 4.5 21.1 1.0 CB H:LYS224 4.5 17.9 1.0 OD1 H:ASP221 4.6 20.1 1.0 CA H:TYR225 4.8 14.3 1.0 C H:GLY223 4.8 19.1 1.0 O H:HOH2256 4.8 22.3 1.0 HB2 H:ARG221A 4.8 24.4 1.0 H H:ASP222 5.0 25.8 1.0 CA H:GLY223 5.0 20.3 1.0

E.Ruehmann, M.Betz, A.Heine, G.Klebe. Fragments Can Bind Either More Enthalpy or Entropy-Driven: Crystal Structures and Residual Hydration Pattern Suggest Why. J.Med.Chem. V. 58 6960 2015.
ISSN: ISSN 0022-2623
PubMed: 26270568
DOI: 10.1021/ACS.JMEDCHEM.5B00812