Sodium in PDB 5a2m: Thrombin Inhibitor

All present enzymatic activity of Thrombin Inhibitor:
3.4.21.5;

The structure of Thrombin Inhibitor, PDB code: 5a2m was solved by E.Ruehmann, A.Heine, G.Klebe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.62 / 1.40
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	70.114, 71.242, 72.368, 90.00, 100.13, 90.00
R / Rfree (%)	13.7 / 15.9

The structure of Thrombin Inhibitor also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Sodium atom in the Thrombin Inhibitor (pdb code 5a2m). 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 Inhibitor, PDB code: 5a2m:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Thrombin Inhibitor


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Thrombin Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ H:Na1247 b:16.1 occ:1.00 O H:LYS169 2.3 17.8 1.0 O H:THR172 2.3 17.0 1.0 O H:HOH2148 2.5 26.0 1.0 HA H:ASP170 3.2 21.0 1.0 C H:LYS169 3.4 17.1 1.0 H H:THR172 3.5 19.3 1.0 C H:THR172 3.6 16.5 1.0 HA H:ARG173 3.7 20.3 1.0 CA H:ASP170 4.0 17.5 1.0 N H:ASP170 4.1 17.1 1.0 HG21 H:THR172 4.1 21.8 1.0 HB3 H:LYS169 4.2 23.8 1.0 N H:THR172 4.3 16.1 1.0 C H:ASP170 4.4 17.4 1.0 HA H:LYS169 4.4 20.1 1.0 CA H:ARG173 4.5 16.9 1.0 N H:ARG173 4.5 16.4 1.0 CA H:LYS169 4.5 16.7 1.0 CA H:THR172 4.5 16.8 1.0 HG23 H:THR172 4.6 21.8 1.0 OD1 H:ASP170 4.6 19.6 1.0 O H:ASP170 4.8 17.7 1.0 CG2 H:THR172 4.8 18.2 1.0 CB H:LYS169 4.8 19.8 1.0 N H:SER171 4.8 17.6 1.0 H H:SER171 4.9 21.1 1.0 H H:ASP170 4.9 20.5 1.0 O H:ILE174 4.9 17.8 1.0 C H:ARG173 5.0 18.4 1.0

Sodium binding site 2 out of 2 in the Thrombin Inhibitor


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Thrombin Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ H:Na1248 b:19.7 occ:1.00 O H:HOH2172 2.3 19.9 1.0 O H:HOH2189 2.3 21.1 1.0 O H:ARG221A 2.4 22.5 1.0 O H:LYS224 2.4 18.1 1.0 O H:HOH2162 2.5 17.3 1.0 O H:HOH2164 2.7 25.5 1.0 H H:LYS224 3.2 24.6 1.0 C H:ARG221A 3.4 22.3 1.0 C H:LYS224 3.4 18.0 1.0 HA H:ASP221 3.7 25.3 1.0 HA H:ASP222 3.8 30.3 1.0 HB2 H:LYS224 3.8 24.4 1.0 N H:LYS224 3.8 20.5 1.0 H H:GLY223 3.8 29.5 1.0 O H:HOH2159 3.8 19.2 1.0 N H:ARG221A 3.9 21.1 1.0 H H:ARG221A 3.9 25.4 1.0 O H:HOH2171 4.0 25.4 1.0 HA H:TYR225 4.0 19.4 1.0 C H:ASP221 4.1 21.0 1.0 O H:TYR184A 4.1 20.9 1.0 CA H:LYS224 4.1 19.6 1.0 N H:GLY223 4.2 24.6 1.0 N H:ASP222 4.2 24.6 1.0 O H:HOH2163 4.2 19.3 1.0 CA H:ARG221A 4.3 22.6 1.0 CA H:ASP222 4.3 25.3 1.0 CA H:ASP221 4.4 21.1 1.0 N H:TYR225 4.4 16.3 1.0 CB H:LYS224 4.5 20.3 1.0 C H:ASP222 4.5 24.6 1.0 O H:ASP221 4.6 22.1 1.0 OD1 H:ASP221 4.6 20.9 1.0 CA H:TYR225 4.7 16.1 1.0 HB2 H:ARG221A 4.8 27.9 1.0 C H:GLY223 4.8 21.7 1.0 O H:HOH2173 4.9 20.1 1.0 HB2 H:ASP189 4.9 19.1 1.0 HA H:ARG221A 5.0 27.1 1.0 HA3 H:GLY184 5.0 17.8 1.0 H H:ASP221 5.0 23.4 1.0 H H:ASP222 5.0 29.5 1.0

E.Ruehmann, A.Heine, G.Klebe. Thrombin Inhibition To Be Published.