Sodium in PDB 3f68: Thrombin Inhibition

All present enzymatic activity of Thrombin Inhibition:
3.4.21.5;

The structure of Thrombin Inhibition, PDB code: 3f68 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 / 1.75
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	70.280, 71.950, 72.500, 90.00, 100.05, 90.00
R / Rfree (%)	19.6 / 25.6

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

Chlorine

(Cl)

1 atom

The binding sites of Sodium atom in the Thrombin Inhibition (pdb code 3f68). 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: 3f68:
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:Na902 b:28.5 occ:1.00 O H:HOH1043 2.1 28.4 1.0 O H:LYS224 2.3 29.6 1.0 O H:ARG221A 2.3 29.4 1.0 O H:HOH1081 2.6 31.5 1.0 O H:HOH1041 2.7 22.4 1.0 O H:HOH1050 2.9 35.1 1.0 C H:LYS224 3.4 28.3 1.0 C H:ARG221A 3.5 40.2 1.0 N H:LYS224 3.8 18.5 1.0 O H:HOH1035 3.9 29.0 1.0 N H:ARG221A 4.0 29.0 1.0 C H:ASP221 4.1 38.7 1.0 O H:HOH1082 4.1 34.3 1.0 CA H:LYS224 4.1 14.4 1.0 CA H:ASP221 4.3 29.9 1.0 O H:TYR184A 4.3 29.6 1.0 N H:ASP222 4.3 38.9 1.0 CA H:ARG221A 4.3 34.3 1.0 CA H:ASP222 4.4 30.7 1.0 N H:GLY223 4.4 31.2 1.0 N H:TYR225 4.4 29.2 1.0 O H:HOH1022 4.5 25.7 1.0 C H:ASP222 4.5 37.2 1.0 O H:ASP221 4.6 28.2 1.0 CB H:LYS224 4.6 19.4 1.0 OD1 H:ASP221 4.6 35.6 1.0 CA H:TYR225 4.7 28.8 1.0 O H:HOH1062 4.8 44.1 1.0 C H:GLY223 4.8 31.5 1.0 N H:ASP221 4.9 23.5 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:Na903 b:22.4 occ:1.00 O H:THR172 2.3 22.0 1.0 O H:HOH1070 2.3 31.9 1.0 O H:LYS169 2.4 22.6 1.0 O H:HOH1052 2.5 24.3 1.0 O H:HOH1023 2.6 24.4 1.0 C H:LYS169 3.4 26.8 1.0 C H:THR172 3.5 21.3 1.0 CA H:ASP170 4.0 22.2 1.0 N H:ASP170 4.1 24.2 1.0 N H:THR172 4.2 22.5 1.0 C H:ASP170 4.4 20.5 1.0 N H:ARG173 4.4 19.0 1.0 CA H:ARG173 4.5 25.6 1.0 CA H:LYS169 4.5 23.0 1.0 CA H:THR172 4.5 27.2 1.0 CG2 H:THR172 4.7 13.7 1.0 OD1 H:ASP170 4.7 20.8 1.0 O H:ASP170 4.8 20.7 1.0 N H:SER171 4.8 17.1 1.0 CB H:LYS169 4.9 22.6 1.0 C H:ARG173 4.9 31.5 1.0 O H:ILE174 5.0 24.2 1.0 O H:HOH1045 5.0 43.6 1.0

B.Baum, L.Muley, A.Heine, M.Smolinski, D.Hangauer, G.Klebe. Think Twice: Understanding the High Potency of Bis(Phenyl)Methane Inhibitors of Thrombin. J.Mol.Biol. V. 391 552 2009.
ISSN: ISSN 0022-2836
PubMed: 19520086
DOI: 10.1016/J.JMB.2009.06.016