Sodium in PDB 4ue7: Thrombin in Complex with 1-Amidinopiperidine

All present enzymatic activity of Thrombin in Complex with 1-Amidinopiperidine:
3.4.21.5;

The structure of Thrombin in Complex with 1-Amidinopiperidine, PDB code: 4ue7 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)	19.56 / 1.13
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	70.262, 71.483, 72.440, 90.00, 100.30, 90.00
R / Rfree (%)	12.4 / 13.9

The structure of Thrombin in Complex with 1-Amidinopiperidine also contains other interesting chemical elements:

Iodine

(I)

1 atom

The binding sites of Sodium atom in the Thrombin in Complex with 1-Amidinopiperidine (pdb code 4ue7). 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 1-Amidinopiperidine, PDB code: 4ue7:
Jump to Sodium binding site number: 1; 2;

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


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 1-Amidinopiperidine within 5.0Å range: probe atom residue distance (Å) B Occ H:Na1251 b:10.8 occ:1.00 O H:THR172 2.3 11.0 1.0 O H:LYS169 2.3 11.0 0.5 O H:LYS169 2.3 11.0 0.5 O H:HOH2209 2.7 17.6 1.0 HA H:ASP170 3.3 12.7 1.0 HG2 H:LYS169 3.4 20.1 0.5 C H:LYS169 3.4 11.0 0.5 C H:LYS169 3.4 11.0 0.5 HG2 H:LYS169 3.5 20.1 0.5 H H:THR172 3.5 12.0 1.0 C H:THR172 3.5 10.2 1.0 HA H:ARG173 3.7 12.8 1.0 HZ1 H:LYS169 3.7 34.6 0.5 CA H:ASP170 4.0 10.5 1.0 N H:ASP170 4.2 10.3 1.0 N H:THR172 4.2 10.0 1.0 CG H:LYS169 4.3 16.8 0.5 HG21 H:THR172 4.3 13.4 1.0 HG3 H:LYS169 4.3 20.1 0.5 CG H:LYS169 4.3 16.8 0.5 HG3 H:LYS169 4.3 20.1 0.5 C H:ASP170 4.4 10.9 1.0 N H:ARG173 4.4 10.3 1.0 CA H:ARG173 4.4 10.7 1.0 O H:HOH2215 4.4 32.3 1.0 HA H:LYS169 4.5 12.6 0.5 HA H:LYS169 4.5 12.6 0.5 CA H:LYS169 4.5 10.5 0.5 CA H:LYS169 4.5 10.5 0.5 CA H:THR172 4.5 10.4 1.0 NZ H:LYS169 4.6 28.8 0.5 HG23 H:THR172 4.7 13.4 1.0 OD1 H:ASP170 4.7 15.2 1.0 HE2 H:LYS169 4.7 28.8 0.5 O H:ASP170 4.7 11.7 1.0 N H:SER171 4.8 10.4 1.0 H H:SER171 4.9 12.5 1.0 HZ3 H:LYS169 4.9 34.6 0.5 CG2 H:THR172 4.9 11.2 1.0 CB H:LYS169 4.9 12.7 0.5 CB H:LYS169 4.9 12.7 0.5 HZ2 H:LYS169 5.0 34.6 0.5 C H:ARG173 5.0 11.2 1.0 H H:ASP170 5.0 12.4 1.0

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


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 1-Amidinopiperidine within 5.0Å range: probe atom residue distance (Å) B Occ H:Na1252 b:13.1 occ:1.00 O H:ARG221A 2.3 13.9 1.0 O H:HOH2239 2.4 13.4 1.0 O H:HOH2268 2.4 14.2 1.0 O H:LYS224 2.4 11.9 1.0 O H:HOH2227 2.5 11.7 1.0 O H:HOH2228 2.6 15.3 1.0 H H:LYS224 3.3 14.8 1.0 C H:ARG221A 3.4 14.5 1.0 C H:LYS224 3.5 11.4 1.0 HA H:ASP222 3.7 18.9 1.0 HA H:ASP221 3.7 16.3 1.0 H H:GLY223 3.8 17.8 1.0 N H:LYS224 3.9 12.3 1.0 O H:HOH2223 3.9 12.3 1.0 HB2 H:LYS224 3.9 14.6 1.0 O H:HOH2237 4.0 17.9 1.0 N H:ARG221A 4.0 14.1 1.0 O H:TYR184A 4.0 13.4 1.0 HA H:TYR225 4.1 12.6 1.0 H H:ARG221A 4.1 16.9 1.0 C H:ASP221 4.1 14.1 1.0 CA H:LYS224 4.2 11.8 1.0 N H:GLY223 4.2 14.8 1.0 N H:ASP222 4.2 15.4 1.0 O H:HOH2226 4.2 12.8 1.0 CA H:ASP222 4.3 15.8 1.0 CA H:ARG221A 4.3 14.9 1.0 CA H:ASP221 4.4 13.6 1.0 C H:ASP222 4.5 15.5 1.0 O H:ASP221 4.5 16.1 1.0 N H:TYR225 4.5 10.7 1.0 CB H:LYS224 4.6 12.2 1.0 OD1 H:ASP221 4.6 15.2 1.0 O H:HOH2238 4.7 14.9 1.0 CA H:TYR225 4.8 10.5 1.0 C H:GLY223 4.8 13.2 1.0 HB2 H:ARG221A 4.9 19.0 1.0 H H:ASP222 5.0 18.4 1.0 HA3 H:GLY184 5.0 11.7 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