Sodium in PDB 3dux: Understanding Thrombin Inhibition

All present enzymatic activity of Understanding Thrombin Inhibition:
3.4.21.5;

The structure of Understanding Thrombin Inhibition, PDB code: 3dux 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 / 1.60
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	70.020, 71.440, 72.790, 90.00, 100.50, 90.00
R / Rfree (%)	20.1 / 24.7

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

Chlorine

(Cl)

1 atom

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

Sodium binding site 1 out of 2 in the Understanding Thrombin Inhibition


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Understanding Thrombin Inhibition within 5.0Å range: probe atom residue distance (Å) B Occ H:Na902 b:20.6 occ:1.00 O H:ARG221A 2.3 23.5 1.0 O H:HOH1072 2.3 21.8 1.0 O H:HOH1053 2.4 18.8 1.0 O H:LYS224 2.4 20.4 1.0 O H:HOH1071 2.7 20.8 1.0 C H:ARG221A 3.4 24.3 1.0 C H:LYS224 3.5 18.9 1.0 N H:LYS224 3.8 20.6 1.0 N H:ARG221A 4.0 22.9 1.0 O H:HOH1032 4.0 25.0 1.0 O H:HOH1060 4.1 24.4 1.0 O H:TYR184A 4.1 21.0 1.0 CA H:LYS224 4.2 17.7 1.0 N H:GLY223 4.2 20.3 1.0 N H:ASP222 4.2 21.1 1.0 CA H:ASP222 4.2 25.2 1.0 O H:HOH1014 4.2 19.0 1.0 C H:ASP221 4.2 26.8 1.0 CA H:ARG221A 4.3 22.5 1.0 C H:ASP222 4.4 20.6 1.0 CA H:ASP221 4.5 20.9 1.0 N H:TYR225 4.5 19.7 1.0 CB H:LYS224 4.7 22.1 1.0 OD1 H:ASP221 4.7 24.7 1.0 O H:ASP221 4.8 24.3 1.0 CA H:TYR225 4.8 20.8 1.0 C H:GLY223 4.8 20.5 1.0 O H:HOH1064 4.9 25.0 1.0 CD2 H:TYR225 5.0 14.7 1.0

Sodium binding site 2 out of 2 in the Understanding Thrombin Inhibition


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Understanding Thrombin Inhibition within 5.0Å range: probe atom residue distance (Å) B Occ H:Na903 b:15.4 occ:1.00 O H:PHE204A 2.3 12.5 1.0 O H:HOH1106 2.3 24.9 1.0 O H:HOH1044 2.4 16.8 1.0 C H:PHE204A 3.3 13.7 1.0 CA H:PHE204A 3.9 15.7 1.0 O H:PRO204 4.5 10.8 1.0 N H:ASN204B 4.5 11.4 1.0 CA H:ASN204B 4.8 11.6 1.0 CB H:PHE204A 4.8 17.3 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