Sodium in PDB 3qx5: Thrombin Inhibition By Pyridin Derivatives

All present enzymatic activity of Thrombin Inhibition By Pyridin Derivatives:
3.4.21.5;

The structure of Thrombin Inhibition By Pyridin Derivatives, PDB code: 3qx5 was solved by A.Biela, A.Heine, G.Klebe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.76 / 1.35
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	70.200, 71.100, 72.800, 90.00, 100.60, 90.00
R / Rfree (%)	13.2 / 15.6

The structure of Thrombin Inhibition By Pyridin Derivatives also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Sodium atom in the Thrombin Inhibition By Pyridin Derivatives (pdb code 3qx5). 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 Inhibition By Pyridin Derivatives, PDB code: 3qx5:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Thrombin Inhibition By Pyridin Derivatives


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Thrombin Inhibition By Pyridin Derivatives within 5.0Å range: probe atom residue distance (Å) B Occ H:Na1 b:12.2 occ:1.00 O H:THR172 2.4 12.1 1.0 O H:LYS169 2.4 11.6 1.0 O H:HOH1188 2.4 14.7 1.0 O H:HOH1295 2.5 18.2 1.0 O H:HOH1297 3.0 24.2 1.0 C H:LYS169 3.5 10.6 1.0 C H:THR172 3.6 11.1 1.0 CA H:ASP170 4.0 11.4 1.0 N H:ASP170 4.2 10.7 1.0 CG H:LYS169 4.3 16.8 1.0 N H:THR172 4.3 10.4 1.0 C H:ASP170 4.4 10.7 1.0 CA H:ARG173 4.4 11.7 1.0 N H:ARG173 4.4 11.0 1.0 O H:HOH1369 4.5 36.8 1.0 NZ H:LYS169 4.5 25.9 1.0 CA H:LYS169 4.6 10.9 1.0 CA H:THR172 4.6 11.6 1.0 OD1 H:ASP170 4.7 16.7 1.0 O H:ASP170 4.7 12.0 1.0 N H:SER171 4.8 10.8 1.0 CB H:LYS169 4.9 12.6 1.0 CG2 H:THR172 5.0 12.7 1.0 C H:ARG173 5.0 11.8 1.0

Sodium binding site 2 out of 2 in the Thrombin Inhibition By Pyridin Derivatives


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Thrombin Inhibition By Pyridin Derivatives within 5.0Å range: probe atom residue distance (Å) B Occ H:Na2 b:13.3 occ:1.00 O H:HOH1350 2.4 14.5 1.0 O H:HOH1215 2.4 14.2 1.0 O H:ARG221A 2.4 14.1 1.0 O H:LYS224 2.4 12.2 1.0 O H:HOH1073 2.5 11.5 1.0 O H:HOH1203 2.6 14.8 1.0 C H:ARG221A 3.4 13.6 1.0 C H:LYS224 3.4 11.5 1.0 N H:LYS224 3.8 12.7 1.0 O H:HOH1077 3.9 13.0 1.0 N H:ARG221A 3.9 12.9 1.0 O H:HOH1255 4.0 17.8 1.0 C H:ASP221 4.0 13.7 1.0 CA H:LYS224 4.1 11.8 1.0 O H:TYR184A 4.1 13.2 1.0 O H:HOH1158 4.2 34.3 1.0 N H:GLY223 4.2 15.3 1.0 N H:ASP222 4.2 15.1 1.0 CA H:ARG221A 4.3 14.2 1.0 O H:HOH1074 4.3 12.1 1.0 CA H:ASP222 4.3 15.8 1.0 CA H:ASP221 4.4 13.8 1.0 N H:TYR225 4.4 10.5 1.0 CB H:LYS224 4.5 13.0 1.0 O H:ASP221 4.5 15.2 1.0 C H:ASP222 4.5 15.7 1.0 OD1 H:ASP221 4.6 14.2 1.0 CA H:TYR225 4.6 10.3 1.0 C H:GLY223 4.8 13.8 1.0 O H:HOH1186 4.9 15.4 1.0

A.Biela, M.Khayat, H.Tan, J.Kong, A.Heine, D.Hangauer, G.Klebe. Impact of Ligand and Protein Desolvation on Ligand Binding to the S1 Pocket of Thrombin J.Mol.Biol. V. 418 350 2012.
ISSN: ISSN 0022-2836
PubMed: 22366545
DOI: 10.1016/J.JMB.2012.01.054