Sodium in PDB 3dt0: Understanding Thrombin Inhibition

All present enzymatic activity of Understanding Thrombin Inhibition:
3.4.21.5;

The structure of Understanding Thrombin Inhibition, PDB code: 3dt0 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 / 2.40
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	70.020, 71.380, 72.290, 90.00, 100.14, 90.00
R / Rfree (%)	17.6 / 28.6

The structure of Understanding Thrombin Inhibition also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Sodium atom in the Understanding Thrombin Inhibition (pdb code 3dt0). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Understanding Thrombin Inhibition, PDB code: 3dt0:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Understanding Thrombin Inhibition


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Understanding Thrombin Inhibition within 5.0Å range: probe atom residue distance (Å) B Occ H:Na902 b:31.7 occ:1.00 O H:ARG221A 2.4 40.1 1.0 O H:LYS224 2.5 28.6 1.0 O H:HOH1068 3.1 31.8 1.0 C H:LYS224 3.4 25.6 1.0 C H:ARG221A 3.4 33.0 1.0 N H:ARG221A 3.5 30.6 1.0 C H:ASP221 3.6 26.0 1.0 O H:HOH1020 3.7 24.7 1.0 CA H:ASP221 3.7 20.2 1.0 O H:HOH1097 4.0 33.7 1.0 CA H:LYS224 4.1 21.3 1.0 CB H:LYS224 4.1 24.5 1.0 CA H:ARG221A 4.1 31.7 1.0 N H:TYR225 4.2 29.9 1.0 N H:LYS224 4.2 17.0 1.0 CA H:TYR225 4.3 25.9 1.0 O H:ASP221 4.3 37.3 1.0 N H:ASP221 4.3 22.0 1.0 N H:ASP222 4.4 24.6 1.0 OD2 H:ASP189 4.5 20.4 1.0 CA H:ASP222 4.5 25.8 1.0 OD1 H:ASP221 4.6 37.2 1.0 O H:HOH1086 4.7 35.2 1.0 N H:GLY223 4.8 22.5 1.0 O H:HOH1014 4.9 33.2 1.0 C H:ASP222 4.9 22.1 1.0 CG H:ASP189 4.9 25.3 1.0 CB H:ASP221 4.9 22.6 1.0

Sodium binding site 2 out of 2 in the Understanding Thrombin Inhibition


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Understanding Thrombin Inhibition within 5.0Å range: probe atom residue distance (Å) B Occ H:Na903 b:18.3 occ:1.00 O H:THR172 2.2 14.8 1.0 O H:LYS169 2.3 16.3 1.0 O H:HOH1061 2.6 18.0 1.0 C H:LYS169 3.4 15.7 1.0 C H:THR172 3.4 11.5 1.0 N H:THR172 4.1 13.1 1.0 CA H:ASP170 4.2 8.8 1.0 N H:ASP170 4.2 11.9 1.0 CA H:THR172 4.3 10.1 1.0 CA H:LYS169 4.3 22.6 1.0 CA H:ARG173 4.4 16.2 1.0 C H:ASP170 4.4 10.9 1.0 N H:ARG173 4.4 10.4 1.0 CG2 H:THR172 4.5 4.0 1.0 C H:ARG173 4.7 19.6 1.0 CB H:LYS169 4.7 24.4 1.0 O H:ASP170 4.7 31.6 1.0 N H:SER171 4.8 8.4 1.0 O H:ILE174 4.9 30.4 1.0 O H:ARG173 4.9 30.5 1.0

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