Sodium in PDB 3u98: Human Thrombin in Complex with MI001

All present enzymatic activity of Human Thrombin in Complex with MI001:
3.4.21.5;

The structure of Human Thrombin in Complex with MI001, PDB code: 3u98 was solved by A.Biela, A.Heine, G.Klebe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	22.56 / 1.45
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	70.300, 71.500, 72.200, 90.00, 100.40, 90.00
R / Rfree (%)	16.4 / 18.7

The binding sites of Sodium atom in the Human Thrombin in Complex with MI001 (pdb code 3u98). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Human Thrombin in Complex with MI001, PDB code: 3u98:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Human Thrombin in Complex with MI001


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Human Thrombin in Complex with MI001 within 5.0Å range: probe atom residue distance (Å) B Occ H:Na3 b:12.9 occ:1.00 O H:THR172 2.4 14.0 1.0 O H:HOH1145 2.4 16.1 1.0 O H:LYS169 2.4 14.4 1.0 O H:HOH1170 2.4 21.9 1.0 O H:HOH1159 2.4 20.2 1.0 C H:LYS169 3.5 14.6 1.0 C H:THR172 3.6 13.2 1.0 CA H:ASP170 4.1 13.1 1.0 N H:ASP170 4.2 13.9 1.0 N H:THR172 4.3 14.4 1.0 CA H:ARG173 4.4 14.4 1.0 N H:ARG173 4.5 13.4 1.0 C H:ASP170 4.5 13.8 1.0 O H:HOH1232 4.5 38.0 1.0 CA H:LYS169 4.5 13.2 1.0 CA H:THR172 4.5 13.0 1.0 CG2 H:THR172 4.7 15.2 1.0 OD1 H:ASP170 4.7 18.6 1.0 CB H:LYS169 4.8 14.8 1.0 O H:ASP170 4.8 16.1 1.0 O H:ILE174 4.9 16.4 1.0 N H:SER171 4.9 13.9 1.0 C H:ARG173 4.9 15.5 1.0

Sodium binding site 2 out of 2 in the Human Thrombin in Complex with MI001


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Human Thrombin in Complex with MI001 within 5.0Å range: probe atom residue distance (Å) B Occ H:Na4 b:17.0 occ:1.00 O H:ARG221A 2.3 17.4 1.0 O H:HOH1168 2.4 19.2 1.0 O H:HOH1161 2.4 18.6 1.0 O H:LYS224 2.5 16.8 1.0 O H:HOH1152 2.5 14.8 1.0 O H:HOH1181 2.6 20.0 1.0 C H:ARG221A 3.4 17.7 1.0 C H:LYS224 3.5 14.8 1.0 N H:LYS224 3.8 16.1 1.0 O H:HOH1157 3.9 16.2 1.0 O H:HOH1169 3.9 22.1 1.0 N H:ARG221A 3.9 15.5 1.0 O H:TYR184A 4.1 17.9 1.0 C H:ASP221 4.1 16.3 1.0 N H:GLY223 4.2 20.2 1.0 N H:ASP222 4.2 21.0 1.0 CA H:LYS224 4.2 16.9 1.0 O H:HOH1047 4.2 14.9 1.0 CA H:ASP222 4.2 18.7 1.0 CA H:ARG221A 4.3 16.3 1.0 CA H:ASP221 4.4 16.8 1.0 C H:ASP222 4.4 19.2 1.0 N H:TYR225 4.5 13.3 1.0 CB H:LYS224 4.6 15.0 1.0 O H:ASP221 4.6 20.7 1.0 OD1 H:ASP221 4.6 16.9 1.0 CA H:TYR225 4.8 12.6 1.0 C H:GLY223 4.8 16.4 1.0 O H:HOH1167 4.9 22.6 1.0

A.Biela, F.Sielaff, A.Heine, T.Steinmetzer, G.Klebe. Thrombin Inhibition To Be Published.