Sodium in PDB 3u9a: Human Thrombin in Complex with MI330

All present enzymatic activity of Human Thrombin in Complex with MI330:
3.4.21.5;

The structure of Human Thrombin in Complex with MI330, PDB code: 3u9a 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)	35.74 / 1.58
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	69.900, 71.200, 72.600, 90.00, 100.10, 90.00
R / Rfree (%)	16.4 / 19.6

The structure of Human Thrombin in Complex with MI330 also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Sodium atom in the Human Thrombin in Complex with MI330 (pdb code 3u9a). 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 MI330, PDB code: 3u9a:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Human Thrombin in Complex with MI330


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 MI330 within 5.0Å range: probe atom residue distance (Å) B Occ H:Na5 b:16.1 occ:1.00 O H:THR172 2.3 18.3 1.0 O H:LYS169 2.4 18.4 1.0 O H:HOH1069 2.4 21.4 1.0 O H:HOH1095 2.4 26.4 1.0 O H:HOH1092 2.5 23.5 1.0 C H:LYS169 3.4 20.2 1.0 C H:THR172 3.6 19.2 1.0 CA H:ASP170 4.0 18.9 1.0 N H:ASP170 4.2 18.8 1.0 N H:THR172 4.3 18.3 1.0 CA H:ARG173 4.4 18.8 1.0 C H:ASP170 4.4 21.1 1.0 N H:ARG173 4.4 17.2 1.0 O H:HOH1192 4.5 40.2 1.0 CA H:LYS169 4.5 14.9 1.0 CA H:THR172 4.5 21.3 1.0 OD1 H:ASP170 4.7 23.0 1.0 CG2 H:THR172 4.7 20.6 1.0 O H:ASP170 4.8 19.6 1.0 CB H:LYS169 4.9 18.5 1.0 N H:SER171 4.9 20.2 1.0 O H:ILE174 4.9 18.8 1.0 C H:ARG173 4.9 22.4 1.0 O H:HOH1151 4.9 28.1 1.0

Sodium binding site 2 out of 2 in the Human Thrombin in Complex with MI330


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 MI330 within 5.0Å range: probe atom residue distance (Å) B Occ H:Na6 b:20.8 occ:1.00 O H:ARG221A 2.3 23.0 1.0 O H:HOH1098 2.3 22.7 1.0 O H:HOH1140 2.4 20.6 1.0 O H:LYS224 2.4 20.3 1.0 O H:HOH1065 2.4 19.1 1.0 O H:HOH1061 2.6 24.1 1.0 C H:ARG221A 3.3 22.1 1.0 C H:LYS224 3.4 20.4 1.0 N H:LYS224 3.8 21.8 1.0 O H:HOH1040 3.9 18.5 1.0 N H:ARG221A 3.9 22.3 1.0 O H:HOH1077 3.9 25.1 1.0 C H:ASP221 4.0 21.0 1.0 CA H:LYS224 4.1 20.9 1.0 N H:ASP222 4.2 25.0 1.0 N H:GLY223 4.2 25.1 1.0 O H:TYR184A 4.2 22.8 1.0 O H:HOH1076 4.2 20.4 1.0 CA H:ARG221A 4.2 22.1 1.0 CA H:ASP222 4.3 25.0 1.0 CA H:ASP221 4.4 18.2 1.0 N H:TYR225 4.4 18.0 1.0 CB H:LYS224 4.5 17.4 1.0 C H:ASP222 4.5 21.9 1.0 O H:ASP221 4.5 24.9 1.0 OD1 H:ASP221 4.6 20.9 1.0 CA H:TYR225 4.7 19.4 1.0 C H:GLY223 4.8 26.6 1.0

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