Sodium in PDB 4ud9: Thrombin in Complex with 5-Chlorothiophene-2-Carboxamide

All present enzymatic activity of Thrombin in Complex with 5-Chlorothiophene-2-Carboxamide:
3.4.21.5;

The structure of Thrombin in Complex with 5-Chlorothiophene-2-Carboxamide, PDB code: 4ud9 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)	35.68 / 1.12
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	70.113, 71.362, 72.103, 90.00, 100.38, 90.00
R / Rfree (%)	12.5 / 14.1

The structure of Thrombin in Complex with 5-Chlorothiophene-2-Carboxamide also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Sodium atom in the Thrombin in Complex with 5-Chlorothiophene-2-Carboxamide (pdb code 4ud9). 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 5-Chlorothiophene-2-Carboxamide, PDB code: 4ud9:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Thrombin in Complex with 5-Chlorothiophene-2-Carboxamide


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 5-Chlorothiophene-2-Carboxamide within 5.0Å range: probe atom residue distance (Å) B Occ H:Na1247 b:14.6 occ:1.00 O H:ARG221A 2.3 15.8 1.0 O H:HOH2212 2.3 15.2 1.0 O H:HOH2235 2.4 15.2 1.0 O H:LYS224 2.4 13.6 1.0 O H:HOH2202 2.5 13.3 1.0 O H:HOH2203 2.7 17.1 1.0 C H:ARG221A 3.4 16.3 1.0 C H:LYS224 3.4 13.0 1.0 HA H:ASP221 3.7 18.4 1.0 HA H:ASP222 3.7 21.4 1.0 N H:LYS224 3.8 14.4 1.0 H H:GLY223 3.8 20.1 1.0 O H:HOH2198 3.8 13.9 1.0 N H:ARG221A 3.9 15.3 1.0 H H:ARG221A 4.0 18.3 1.0 O H:HOH2211 4.0 19.1 1.0 HA H:TYR225 4.0 14.4 1.0 C H:ASP221 4.1 15.3 1.0 O H:TYR184A 4.1 15.5 1.0 CA H:LYS224 4.1 13.9 0.4 CA H:LYS224 4.1 14.2 0.6 N H:GLY223 4.2 16.7 1.0 N H:ASP222 4.2 17.7 1.0 O H:HOH2201 4.2 14.3 1.0 CA H:ARG221A 4.3 16.3 1.0 CA H:ASP222 4.3 17.8 1.0 CA H:ASP221 4.4 15.4 1.0 N H:TYR225 4.4 12.2 1.0 CB H:LYS224 4.5 15.1 0.6 CB H:LYS224 4.5 14.2 0.4 C H:ASP222 4.5 17.1 1.0 O H:ASP221 4.5 16.6 1.0 OD1 H:ASP221 4.6 16.8 1.0 CA H:TYR225 4.7 12.0 1.0 HB2 H:ARG221A 4.8 20.3 1.0 C H:GLY223 4.8 14.9 1.0 H H:ASP221 4.9 17.3 1.0 O H:HOH2232 4.9 16.3 1.0 HA3 H:GLY184 5.0 14.5 1.0 HB2 H:ASP189 5.0 15.7 1.0 HA H:ARG221A 5.0 19.6 1.0 H H:ASP222 5.0 21.2 1.0

Sodium binding site 2 out of 2 in the Thrombin in Complex with 5-Chlorothiophene-2-Carboxamide


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 5-Chlorothiophene-2-Carboxamide within 5.0Å range: probe atom residue distance (Å) B Occ H:Na1248 b:12.8 occ:1.00 O H:THR172 2.3 13.1 1.0 O H:LYS169 2.4 13.3 1.0 O H:HOH2185 2.6 17.6 1.0 HA H:ASP170 3.2 15.3 1.0 C H:LYS169 3.4 12.6 1.0 HG2 H:LYS169 3.4 21.0 0.5 H H:THR172 3.5 15.0 1.0 C H:THR172 3.5 12.4 1.0 HA H:ARG173 3.7 15.7 1.0 CA H:ASP170 4.0 12.8 1.0 N H:ASP170 4.1 12.4 1.0 HB3 H:LYS169 4.2 15.6 0.5 HG21 H:THR172 4.2 15.7 1.0 N H:THR172 4.2 12.5 1.0 HG3 H:LYS169 4.3 21.0 0.5 CG H:LYS169 4.3 17.5 0.5 C H:ASP170 4.4 12.6 1.0 N H:ARG173 4.4 12.5 1.0 CA H:ARG173 4.4 13.1 1.0 HA H:LYS169 4.4 15.8 0.5 CA H:LYS169 4.5 12.1 0.5 CA H:LYS169 4.5 13.2 0.5 O H:HOH2191 4.5 30.9 1.0 CA H:THR172 4.5 12.8 1.0 HG23 H:THR172 4.6 15.7 1.0 OD1 H:ASP170 4.6 17.3 1.0 O H:ASP170 4.7 13.6 1.0 N H:SER171 4.8 12.4 1.0 CG2 H:THR172 4.8 13.1 1.0 CB H:LYS169 4.8 13.0 0.5 H H:SER171 4.9 14.9 1.0 C H:ARG173 4.9 13.5 1.0 CB H:LYS169 4.9 15.5 0.5 O H:ILE174 5.0 13.6 1.0 H H:ASP170 5.0 14.9 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