Sodium in PDB 5ahg: Thrombin in Complex with ((4-Chlorophenyl)Sulfamoyl))Diemethylamine

All present enzymatic activity of Thrombin in Complex with ((4-Chlorophenyl)Sulfamoyl))Diemethylamine:
3.4.21.5;

The structure of Thrombin in Complex with ((4-Chlorophenyl)Sulfamoyl))Diemethylamine, PDB code: 5ahg 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)	43.41 / 1.24
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	70.222, 71.263, 72.216, 90.00, 100.48, 90.00
R / Rfree (%)	12.3 / 14.4

The structure of Thrombin in Complex with ((4-Chlorophenyl)Sulfamoyl))Diemethylamine also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Sodium atom in the Thrombin in Complex with ((4-Chlorophenyl)Sulfamoyl))Diemethylamine (pdb code 5ahg). 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 ((4-Chlorophenyl)Sulfamoyl))Diemethylamine, PDB code: 5ahg:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Thrombin in Complex with ((4-Chlorophenyl)Sulfamoyl))Diemethylamine


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 ((4-Chlorophenyl)Sulfamoyl))Diemethylamine within 5.0Å range: probe atom residue distance (Å) B Occ H:Na1247 b:13.0 occ:1.00 O H:THR172 2.3 13.4 1.0 O H:LYS169 2.4 13.8 1.0 O H:HOH2200 2.4 21.3 1.0 O H:HOH2199 2.6 19.9 1.0 HA H:ASP170 3.3 15.1 1.0 C H:LYS169 3.5 12.7 1.0 H H:THR172 3.5 15.1 1.0 C H:THR172 3.5 12.8 1.0 HA H:ARG173 3.6 16.4 1.0 CA H:ASP170 4.0 12.6 1.0 N H:ASP170 4.2 12.6 1.0 HG21 H:THR172 4.2 16.7 1.0 N H:THR172 4.3 12.6 1.0 C H:ASP170 4.4 13.5 1.0 CA H:ARG173 4.4 13.6 1.0 N H:ARG173 4.4 12.8 1.0 O H:HOH2206 4.4 39.1 1.0 CA H:THR172 4.5 13.1 1.0 CA H:LYS169 4.5 13.1 1.0 HG23 H:THR172 4.6 16.7 1.0 OD1 H:ASP170 4.7 17.5 1.0 O H:ASP170 4.8 14.1 1.0 CG2 H:THR172 4.8 13.9 1.0 N H:SER171 4.8 12.8 1.0 CB H:LYS169 4.9 15.5 1.0 H H:SER171 4.9 15.4 1.0 C H:ARG173 4.9 13.5 1.0 O H:ILE174 5.0 14.1 1.0 H H:ASP170 5.0 15.1 1.0

Sodium binding site 2 out of 2 in the Thrombin in Complex with ((4-Chlorophenyl)Sulfamoyl))Diemethylamine


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 ((4-Chlorophenyl)Sulfamoyl))Diemethylamine within 5.0Å range: probe atom residue distance (Å) B Occ H:Na1248 b:16.1 occ:1.00 O H:ARG221A 2.3 16.1 1.0 O H:HOH2228 2.3 16.2 1.0 O H:LYS224 2.4 13.9 1.0 O H:HOH2251 2.4 15.9 1.0 O H:HOH2218 2.4 14.0 1.0 O H:HOH2219 2.7 17.4 1.0 H H:LYS224 3.2 17.7 1.0 C H:ARG221A 3.4 16.4 1.0 C H:LYS224 3.4 13.4 1.0 HA H:ASP221 3.7 20.3 1.0 HA H:ASP222 3.7 21.9 1.0 HB2 H:LYS224 3.8 18.3 1.0 N H:LYS224 3.8 14.8 1.0 H H:GLY223 3.9 19.7 1.0 O H:HOH2214 3.9 14.4 1.0 N H:ARG221A 3.9 17.3 1.0 H H:ARG221A 3.9 20.7 1.0 O H:HOH2226 4.0 20.9 1.0 HA H:TYR225 4.0 14.6 1.0 C H:ASP221 4.1 16.9 1.0 O H:TYR184A 4.1 15.5 1.0 CA H:LYS224 4.1 14.1 1.0 O H:HOH2217 4.2 14.6 1.0 N H:ASP222 4.2 17.9 1.0 N H:GLY223 4.2 16.4 1.0 CA H:ARG221A 4.3 17.6 1.0 CA H:ASP222 4.3 18.2 1.0 CA H:ASP221 4.4 16.9 1.0 N H:TYR225 4.4 12.9 1.0 CB H:LYS224 4.5 15.3 1.0 C H:ASP222 4.5 17.2 1.0 O H:ASP221 4.5 18.8 1.0 OD1 H:ASP221 4.6 17.6 1.0 CA H:TYR225 4.7 12.1 1.0 HB2 H:ARG221A 4.8 21.4 1.0 C H:GLY223 4.8 15.4 1.0 O H:HOH2227 4.9 17.8 1.0 HA3 H:GLY184 4.9 14.0 1.0 HA H:ARG221A 5.0 21.1 1.0 HB3 H:LYS224 5.0 18.3 1.0 H H:ASP221 5.0 18.5 1.0 HB2 H:ASP189 5.0 16.3 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