Sodium in PDB 3d49: Thrombin Inhibition

All present enzymatic activity of Thrombin Inhibition:
3.4.21.5;

The structure of Thrombin Inhibition, PDB code: 3d49 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 / 1.50
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	70.350, 71.480, 72.470, 90.00, 100.39, 90.00
R / Rfree (%)	19.8 / 25.3

The binding sites of Sodium atom in the Thrombin Inhibition (pdb code 3d49). 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: 3d49:
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:Na1800 b:18.5 occ:1.00 O H:ARG221A 2.3 19.3 1.0 O H:HOH2080 2.3 21.9 1.0 O H:HOH2125 2.3 19.7 1.0 O H:LYS224 2.4 16.4 1.0 O H:HOH2020 2.5 17.2 1.0 O H:HOH2058 2.8 22.6 1.0 C H:ARG221A 3.3 19.6 1.0 C H:LYS224 3.4 13.9 1.0 N H:ARG221A 3.9 17.1 1.0 N H:LYS224 3.9 16.7 1.0 O H:HOH2025 3.9 17.2 1.0 O H:HOH2076 4.0 23.4 1.0 C H:ASP221 4.0 22.6 1.0 CA H:LYS224 4.1 16.9 0.4 CA H:LYS224 4.1 17.2 0.6 N H:ASP222 4.2 21.2 1.0 O H:TYR184A 4.2 20.1 1.0 N H:GLY223 4.2 23.2 1.0 CA H:ASP222 4.2 20.3 1.0 CA H:ARG221A 4.2 22.3 1.0 O H:HOH2013 4.3 19.4 1.0 CA H:ASP221 4.4 22.8 1.0 CB H:LYS224 4.4 14.5 0.4 N H:TYR225 4.4 14.0 1.0 C H:ASP222 4.4 21.5 1.0 O H:ASP221 4.5 26.1 1.0 CB H:LYS224 4.5 14.7 0.6 OD1 H:ASP221 4.7 20.6 1.0 CA H:TYR225 4.7 14.4 1.0 O H:HOH2126 4.8 30.9 1.0 C H:GLY223 4.8 20.1 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:Na1801 b:13.3 occ:1.00 O H:THR172 2.3 13.9 1.0 O H:LYS169 2.4 15.2 1.0 O H:HOH2048 2.5 20.4 1.0 O H:HOH2034 2.5 21.8 1.0 C H:LYS169 3.5 17.7 1.0 C H:THR172 3.5 15.2 1.0 CA H:ASP170 4.0 15.7 1.0 N H:ASP170 4.2 16.6 1.0 N H:THR172 4.2 13.0 1.0 C H:ASP170 4.4 12.8 1.0 N H:ARG173 4.4 14.8 1.0 CA H:ARG173 4.4 17.5 1.0 CA H:THR172 4.5 15.4 1.0 CA H:LYS169 4.5 13.6 1.0 OD1 H:ASP170 4.7 15.9 1.0 O H:ASP170 4.7 14.8 1.0 CG2 H:THR172 4.8 14.5 1.0 N H:SER171 4.9 11.6 1.0 CB H:LYS169 4.9 11.2 1.0 C H:ARG173 4.9 15.4 1.0 O H:HOH2049 5.0 24.6 1.0 O H:ILE174 5.0 17.0 1.0

B.Baum, D.Hangauer, A.Heine, G.Klebe. Understanding Thrombin Inhibition To Be Published.