Sodium in PDB 5afy: Thrombin in Complex with 3-Chloro-Benzamide

All present enzymatic activity of Thrombin in Complex with 3-Chloro-Benzamide:
3.4.21.5;

The structure of Thrombin in Complex with 3-Chloro-Benzamide, PDB code: 5afy 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)	18.45 / 1.12
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	70.373, 71.500, 72.636, 90.00, 100.53, 90.00
R / Rfree (%)	12.2 / 13.8

The structure of Thrombin in Complex with 3-Chloro-Benzamide also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Sodium atom in the Thrombin in Complex with 3-Chloro-Benzamide (pdb code 5afy). 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 3-Chloro-Benzamide, PDB code: 5afy:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Thrombin in Complex with 3-Chloro-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 3-Chloro-Benzamide within 5.0Å range: probe atom residue distance (Å) B Occ H:Na1246 b:13.9 occ:1.00 O H:ARG221A 2.3 14.8 1.0 O H:HOH2240 2.4 15.1 1.0 O H:LYS224 2.4 12.5 1.0 O H:HOH2265 2.4 15.1 1.0 O H:HOH2230 2.5 12.8 1.0 O H:HOH2231 2.6 16.6 1.0 H H:LYS224 3.3 16.3 1.0 C H:ARG221A 3.4 15.7 1.0 C H:LYS224 3.4 12.1 1.0 HA H:ASP221 3.7 18.0 1.0 HA H:ASP222 3.7 20.4 1.0 HB2 H:LYS224 3.9 16.3 1.0 H H:GLY223 3.9 18.4 1.0 N H:LYS224 3.9 13.6 1.0 O H:HOH2226 3.9 13.2 1.0 N H:ARG221A 3.9 15.5 1.0 O H:HOH2239 4.0 18.9 1.0 HA H:TYR225 4.0 13.0 1.0 H H:ARG221A 4.0 18.6 1.0 C H:ASP221 4.1 15.1 1.0 O H:TYR184A 4.1 13.9 1.0 CA H:LYS224 4.2 12.8 1.0 N H:GLY223 4.2 15.3 1.0 N H:ASP222 4.2 17.2 1.0 O H:HOH2229 4.3 14.0 1.0 CA H:ARG221A 4.3 16.2 1.0 CA H:ASP222 4.3 17.0 1.0 CA H:ASP221 4.4 15.0 1.0 N H:TYR225 4.4 11.3 1.0 O H:ASP221 4.5 17.2 1.0 CB H:LYS224 4.5 13.6 1.0 C H:ASP222 4.5 16.4 1.0 OD1 H:ASP221 4.6 16.2 1.0 CA H:TYR225 4.7 10.9 1.0 HB2 H:ARG221A 4.8 20.0 1.0 C H:GLY223 4.8 13.7 1.0 H H:ASP221 5.0 17.0 1.0 HA3 H:GLY184 5.0 12.5 1.0 HA H:ARG221A 5.0 19.4 1.0 HB3 H:LYS224 5.0 16.3 1.0 O H:HOH2263 5.0 16.4 1.0

Sodium binding site 2 out of 2 in the Thrombin in Complex with 3-Chloro-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 3-Chloro-Benzamide within 5.0Å range: probe atom residue distance (Å) B Occ H:Na1247 b:11.2 occ:1.00 O H:THR172 2.3 11.7 1.0 O H:LYS169 2.4 11.8 1.0 O H:HOH2216 2.4 14.2 1.0 O H:HOH2212 2.4 18.0 1.0 O H:HOH2211 2.6 17.0 1.0 HA H:ASP170 3.2 13.5 1.0 C H:LYS169 3.4 10.9 1.0 HG2 H:LYS169 3.4 17.1 0.4 H H:THR172 3.5 13.1 1.0 C H:THR172 3.5 11.1 1.0 HA H:ARG173 3.7 14.3 1.0 HZ1 H:LYS169 3.7 25.4 0.4 CA H:ASP170 4.0 11.2 1.0 N H:ASP170 4.1 10.9 1.0 HB3 H:LYS169 4.2 14.5 0.6 HG21 H:THR172 4.2 15.1 1.0 N H:THR172 4.2 10.9 1.0 CG H:LYS169 4.3 14.3 0.4 C H:ASP170 4.4 11.3 1.0 N H:ARG173 4.4 11.2 1.0 CA H:ARG173 4.4 11.9 1.0 HA H:LYS169 4.5 13.1 0.6 HA H:LYS169 4.5 13.3 0.4 CA H:LYS169 4.5 10.9 0.6 CA H:LYS169 4.5 11.1 0.4 CA H:THR172 4.5 11.3 1.0 HG3 H:LYS169 4.5 17.1 0.4 O H:HOH2219 4.6 32.0 1.0 NZ H:LYS169 4.6 21.2 0.4 HG23 H:THR172 4.6 15.1 1.0 OD1 H:ASP170 4.6 15.8 1.0 O H:ASP170 4.8 12.1 1.0 HZ3 H:LYS169 4.8 25.4 0.4 N H:SER171 4.8 11.0 1.0 CG2 H:THR172 4.8 12.5 1.0 CB H:LYS169 4.8 12.1 0.6 H H:SER171 4.9 13.2 1.0 CB H:LYS169 4.9 12.3 0.4 C H:ARG173 5.0 11.7 1.0 H H:ASP170 5.0 13.1 1.0 HZ2 H:LYS169 5.0 25.4 0.4

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