Sodium in PDB 2zgx: Thrombin Inhibition

All present enzymatic activity of Thrombin Inhibition:
3.4.21.5;

The structure of Thrombin Inhibition, PDB code: 2zgx was solved by B.Baum, A.Heine, G.Klebe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	10.00 / 1.80
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	70.420, 71.450, 72.460, 90.00, 100.70, 90.00
R / Rfree (%)	18.4 / 24.9

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

Sodium binding site 1 out of 2 in the Thrombin Inhibition


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Thrombin Inhibition within 5.0Å range: probe atom residue distance (Å) B Occ H:Na1701 b:19.7 occ:1.00 O H:HOH2029 2.3 15.8 1.0 O H:LYS224 2.3 17.7 1.0 O H:ARG221A 2.3 22.7 1.0 O H:HOH2044 2.4 16.4 1.0 O H:HOH2093 2.6 16.0 1.0 O H:HOH2065 2.6 19.4 1.0 C H:ARG221A 3.3 24.4 1.0 C H:LYS224 3.4 16.5 1.0 N H:LYS224 3.8 14.3 1.0 O H:HOH2034 3.9 20.1 1.0 O H:HOH2030 3.9 18.4 1.0 N H:ARG221A 3.9 19.3 1.0 CA H:LYS224 4.1 12.3 1.0 N H:ASP222 4.1 23.0 1.0 C H:ASP221 4.1 21.6 1.0 O H:TYR184A 4.2 16.7 1.0 CA H:ASP222 4.2 23.6 1.0 O H:HOH2018 4.2 13.7 1.0 CA H:ARG221A 4.3 23.7 1.0 N H:GLY223 4.3 20.6 1.0 C H:ASP222 4.4 21.7 1.0 CA H:ASP221 4.4 16.5 1.0 N H:TYR225 4.4 14.8 1.0 CB H:LYS224 4.6 15.8 1.0 O H:ASP221 4.7 22.3 1.0 OD1 H:ASP221 4.7 23.1 1.0 O H:HOH2109 4.7 27.5 1.0 CA H:TYR225 4.7 15.4 1.0 C H:GLY223 4.8 21.8 1.0

Sodium binding site 2 out of 2 in the Thrombin Inhibition


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Thrombin Inhibition within 5.0Å range: probe atom residue distance (Å) B Occ H:Na1702 b:18.1 occ:1.00 O H:HOH2049 2.4 17.6 1.0 O H:THR172 2.4 14.2 1.0 O H:LYS169 2.4 19.3 1.0 O H:HOH2078 2.4 27.3 1.0 O H:HOH2035 2.9 19.6 1.0 C H:LYS169 3.5 18.9 1.0 C H:THR172 3.6 10.9 1.0 CA H:ASP170 4.0 19.3 1.0 N H:ASP170 4.2 17.5 1.0 N H:THR172 4.3 16.4 1.0 C H:ASP170 4.4 16.6 1.0 CA H:ARG173 4.4 16.7 1.0 N H:ARG173 4.5 12.8 1.0 O H:HOH2149 4.5 36.2 1.0 CA H:LYS169 4.5 15.4 1.0 CA H:THR172 4.5 17.4 1.0 OD1 H:ASP170 4.6 16.8 1.0 O H:ASP170 4.7 17.0 1.0 CG2 H:THR172 4.8 14.4 1.0 N H:SER171 4.8 12.1 1.0 CB H:LYS169 4.9 15.6 1.0 C H:ARG173 4.9 18.4 1.0

B.Baum, L.Muley, A.Heine, M.Smolinski, D.Hangauer, G.Klebe. Think Twice: Understanding the High Potency of Bis(Phenyl)Methane Inhibitors of Thrombin J.Mol.Biol. V. 391 552 2009.
ISSN: ISSN 0022-2836
PubMed: 19520086
DOI: 10.1016/J.JMB.2009.06.016