Sodium in PDB 3eq0: Thrombin Inhibitor

All present enzymatic activity of Thrombin Inhibitor:
3.4.21.5;

The structure of Thrombin Inhibitor, PDB code: 3eq0 was solved by B.Baum, A.Heine, G.Klebe, T.Steinmetzer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	10.00 / 1.53
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	70.100, 71.400, 72.400, 90.00, 100.40, 90.00
R / Rfree (%)	19.6 / 24.9

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 3eq0). 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: 3eq0:
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:Na902 b:19.2 occ:1.00 O H:HOH1126 2.2 23.5 1.0 O H:ARG221A 2.3 20.1 1.0 O H:HOH1052 2.4 19.7 1.0 O H:HOH1011 2.5 15.3 1.0 O H:LYS224 2.5 18.8 1.0 O H:HOH1062 2.6 25.2 1.0 C H:ARG221A 3.3 24.4 1.0 C H:LYS224 3.5 22.3 1.0 N H:LYS224 3.8 18.8 1.0 O H:HOH1028 3.9 20.7 1.0 N H:ARG221A 3.9 19.9 1.0 O H:HOH1047 4.0 25.5 1.0 O H:TYR184A 4.1 23.7 1.0 C H:ASP221 4.1 22.2 1.0 O H:HOH1025 4.1 17.6 1.0 N H:ASP222 4.2 21.7 1.0 CA H:LYS224 4.2 18.3 0.5 CA H:LYS224 4.2 17.9 0.5 CA H:ARG221A 4.3 23.6 1.0 CA H:ASP222 4.3 25.4 1.0 N H:GLY223 4.3 23.1 1.0 CA H:ASP221 4.5 16.5 1.0 N H:TYR225 4.5 16.9 1.0 C H:ASP222 4.5 24.9 1.0 CB H:LYS224 4.6 19.9 0.5 O H:ASP221 4.6 20.8 1.0 OD1 H:ASP221 4.7 23.9 1.0 CB H:LYS224 4.7 20.8 0.5 CA H:TYR225 4.7 14.9 1.0 C H:GLY223 4.8 21.4 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:Na903 b:15.4 occ:1.00 O H:HOH1029 2.4 17.6 1.0 O H:LYS169 2.4 20.1 1.0 O H:THR172 2.4 13.9 1.0 O H:HOH1155 2.5 23.5 1.0 O H:HOH1200 2.8 25.4 1.0 C H:LYS169 3.5 16.6 1.0 C H:THR172 3.6 14.5 1.0 CA H:ASP170 4.0 17.6 1.0 N H:ASP170 4.2 17.1 1.0 N H:THR172 4.3 15.4 1.0 C H:ASP170 4.4 19.7 1.0 CA H:ARG173 4.4 17.9 1.0 N H:ARG173 4.5 17.6 1.0 CA H:LYS169 4.5 15.9 1.0 OD1 H:ASP170 4.5 18.1 1.0 CA H:THR172 4.6 19.2 1.0 O H:ASP170 4.8 17.9 1.0 CG2 H:THR172 4.8 18.9 1.0 N H:SER171 4.9 15.8 1.0 CB H:LYS169 4.9 20.3 1.0 C H:ARG173 5.0 17.6 1.0

B.Baum, T.Steinmetzer, A.Heine, G.Klebe. Thrombin Inhibition To Be Published.