Sodium in PDB 5af9: Thrombin in Complex with 4-Methoxy-N-(2-Pyridinyl)Benzamide

All present enzymatic activity of Thrombin in Complex with 4-Methoxy-N-(2-Pyridinyl)Benzamide:
3.4.21.5;

The structure of Thrombin in Complex with 4-Methoxy-N-(2-Pyridinyl)Benzamide, PDB code: 5af9 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)	70.96 / 1.18
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	70.034, 71.246, 72.138, 90.00, 100.38, 90.00
R / Rfree (%)	12.1 / 13.7

The binding sites of Sodium atom in the Thrombin in Complex with 4-Methoxy-N-(2-Pyridinyl)Benzamide (pdb code 5af9). 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-Methoxy-N-(2-Pyridinyl)Benzamide, PDB code: 5af9:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Thrombin in Complex with 4-Methoxy-N-(2-Pyridinyl)Benzamide


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-Methoxy-N-(2-Pyridinyl)Benzamide within 5.0Å range: probe atom residue distance (Å) B Occ H:Na1246 b:13.1 occ:1.00 O H:THR172 2.3 13.4 1.0 O H:LYS169 2.4 13.9 1.0 O H:HOH2186 2.4 21.6 1.0 O H:HOH2185 2.6 19.2 1.0 HA H:ASP170 3.2 16.1 1.0 C H:LYS169 3.4 12.9 1.0 H H:THR172 3.5 15.0 1.0 C H:THR172 3.5 12.9 1.0 HA H:ARG173 3.6 16.2 1.0 CA H:ASP170 4.0 13.4 1.0 N H:ASP170 4.1 12.8 1.0 HG21 H:THR172 4.2 17.3 1.0 N H:THR172 4.2 12.5 1.0 C H:ASP170 4.4 13.8 1.0 CA H:ARG173 4.4 13.5 1.0 N H:ARG173 4.4 13.0 1.0 HA H:LYS169 4.5 14.8 1.0 O H:HOH2190 4.5 35.9 1.0 CA H:THR172 4.5 12.9 1.0 CA H:LYS169 4.5 12.4 1.0 HG23 H:THR172 4.6 17.3 1.0 OD1 H:ASP170 4.6 17.5 1.0 O H:ASP170 4.7 14.1 1.0 N H:SER171 4.8 13.3 1.0 CG2 H:THR172 4.8 14.4 1.0 CB H:LYS169 4.9 15.4 1.0 H H:SER171 4.9 15.9 1.0 C H:ARG173 4.9 13.5 1.0 O H:ILE174 5.0 13.6 1.0 H H:ASP170 5.0 15.4 1.0

Sodium binding site 2 out of 2 in the Thrombin in Complex with 4-Methoxy-N-(2-Pyridinyl)Benzamide


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-Methoxy-N-(2-Pyridinyl)Benzamide within 5.0Å range: probe atom residue distance (Å) B Occ H:Na1247 b:15.7 occ:1.00 O H:ARG221A 2.3 16.4 1.0 O H:HOH2211 2.3 16.8 1.0 O H:LYS224 2.4 14.6 1.0 O H:HOH2234 2.4 16.7 1.0 O H:HOH2202 2.5 14.0 1.0 O H:HOH2203 2.7 18.2 1.0 H H:LYS224 3.3 18.1 0.6 H H:LYS224 3.3 18.1 0.4 C H:ARG221A 3.4 16.6 1.0 C H:LYS224 3.4 13.9 1.0 HA H:ASP221 3.7 19.5 1.0 HA H:ASP222 3.7 22.6 1.0 HB2 H:LYS224 3.7 16.2 0.4 HB2 H:LYS224 3.8 19.8 0.6 N H:LYS224 3.8 15.1 1.0 O H:HOH2198 3.9 15.6 1.0 N H:ARG221A 3.9 16.4 1.0 H H:GLY223 3.9 21.1 1.0 H H:ARG221A 4.0 19.7 1.0 HA H:TYR225 4.0 15.7 1.0 O H:HOH2210 4.0 20.8 1.0 C H:ASP221 4.1 16.5 1.0 CA H:LYS224 4.1 14.2 0.4 O H:TYR184A 4.1 16.2 1.0 CA H:LYS224 4.1 15.1 0.6 N H:ASP222 4.2 17.9 1.0 O H:HOH2201 4.2 15.4 1.0 CA H:ARG221A 4.2 17.2 1.0 N H:GLY223 4.3 17.6 1.0 CA H:ASP222 4.3 18.8 1.0 CA H:ASP221 4.3 16.2 1.0 N H:TYR225 4.4 13.7 1.0 CB H:LYS224 4.4 13.6 0.4 CB H:LYS224 4.4 16.5 0.6 O H:ASP221 4.5 18.4 1.0 C H:ASP222 4.5 17.8 1.0 OD1 H:ASP221 4.6 17.5 1.0 CA H:TYR225 4.7 13.1 1.0 HB2 H:ARG221A 4.8 21.8 1.0 C H:GLY223 4.8 15.1 1.0 HB3 H:LYS224 4.9 19.8 0.6 O H:HOH2232 4.9 17.9 1.0 H H:ASP221 4.9 18.0 1.0 HA3 H:GLY184 4.9 14.7 1.0 HA H:ARG221A 5.0 20.6 1.0 H H:ASP222 5.0 21.5 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