Sodium in PDB 2ziq: Thrombin Inhibition

All present enzymatic activity of Thrombin Inhibition:
3.4.21.5;

The structure of Thrombin Inhibition, PDB code: 2ziq 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 / 1.65
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	70.200, 71.600, 72.300, 90.00, 100.30, 90.00
R / Rfree (%)	18.7 / 22.5

The binding sites of Sodium atom in the Thrombin Inhibition (pdb code 2ziq). 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: 2ziq:
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:Na702 b:21.2 occ:1.00 O H:HOH1041 2.3 19.9 1.0 O H:LYS224 2.3 17.4 1.0 O H:ARG221A 2.3 18.1 1.0 O H:HOH1038 2.4 20.5 1.0 O H:HOH1025 2.5 14.8 1.0 O H:HOH1064 2.7 20.8 1.0 C H:ARG221A 3.4 23.4 1.0 C H:LYS224 3.4 14.3 1.0 O H:HOH1037 3.8 18.6 1.0 N H:LYS224 3.8 15.0 1.0 O H:HOH1066 3.8 24.6 1.0 N H:ARG221A 4.0 19.5 1.0 C H:ASP221 4.1 24.7 1.0 O H:TYR184A 4.1 18.0 1.0 CA H:LYS224 4.2 10.0 1.0 N H:ASP222 4.2 22.4 1.0 N H:GLY223 4.2 21.1 1.0 CA H:ASP222 4.2 20.5 1.0 CA H:ARG221A 4.3 23.1 1.0 O H:HOH1048 4.3 16.1 1.0 CA H:ASP221 4.3 19.2 1.0 C H:ASP222 4.4 22.9 1.0 N H:TYR225 4.4 15.4 1.0 O H:ASP221 4.6 22.7 1.0 O H:HOH1091 4.6 27.2 1.0 CB H:LYS224 4.6 16.6 1.0 OD1 H:ASP221 4.7 21.4 1.0 CA H:TYR225 4.7 15.8 1.0 C H:GLY223 4.8 21.1 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:Na703 b:13.8 occ:1.00 O H:THR172 2.2 15.4 1.0 O H:LYS169 2.4 16.7 1.0 O H:HOH1177 2.4 15.4 1.0 O H:HOH1049 2.5 20.9 1.0 O H:HOH1029 2.5 20.8 1.0 C H:LYS169 3.5 15.2 1.0 C H:THR172 3.5 11.6 1.0 CA H:ASP170 4.0 11.5 1.0 N H:ASP170 4.2 16.0 1.0 N H:THR172 4.2 13.8 1.0 N H:ARG173 4.3 14.6 1.0 CA H:ARG173 4.3 15.7 1.0 C H:ASP170 4.4 14.6 1.0 CA H:THR172 4.5 15.2 1.0 CA H:LYS169 4.5 13.3 1.0 CG2 H:THR172 4.7 15.1 1.0 OD1 H:ASP170 4.7 14.5 1.0 O H:ASP170 4.8 13.6 1.0 CB H:LYS169 4.9 13.0 1.0 N H:SER171 4.9 11.3 1.0 C H:ARG173 4.9 18.5 1.0 O H:ILE174 4.9 18.4 1.0

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