Sodium in PDB 2gde: Thrombin in Complex with Inhibitor

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

The structure of Thrombin in Complex with Inhibitor, PDB code: 2gde was solved by Y.Xue, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	69.50 / 2.00
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	70.084, 72.169, 70.357, 90.00, 99.06, 90.00
R / Rfree (%)	20.9 / 24.8

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

Chlorine

(Cl)

1 atom

The binding sites of Sodium atom in the Thrombin in Complex with Inhibitor (pdb code 2gde). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Thrombin in Complex with Inhibitor, PDB code: 2gde:

Sodium binding site 1 out of 1 in the Thrombin in Complex with Inhibitor


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Thrombin in Complex with Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ H:Na402 b:61.3 occ:1.00 O H:HOH434 2.8 48.4 1.0 O H:LYS224 3.1 45.7 1.0 O H:HOH441 3.2 43.8 1.0 CA H:ASP221 3.3 53.1 1.0 O H:ARG221A 3.4 55.3 1.0 O H:HOH452 3.4 45.7 1.0 OD1 H:ASP189 3.5 48.2 1.0 N H:ASP221 3.5 52.2 1.0 N H:ARG221A 3.5 54.4 1.0 C H:LYS224 3.6 46.4 1.0 C H:ASP221 3.7 53.9 1.0 CG H:ASP189 3.9 48.5 1.0 CA H:TYR225 4.1 44.0 1.0 N H:TYR225 4.1 44.9 1.0 CB H:ASP189 4.1 47.1 1.0 C H:ARG221A 4.3 54.7 1.0 OD1 H:ASP221 4.3 51.4 1.0 CB H:LYS224 4.4 46.9 1.0 O H:GLY188 4.5 49.3 1.0 CB H:ASP221 4.5 53.0 1.0 CA H:ARG221A 4.5 54.2 1.0 C H:TYR225 4.5 43.0 1.0 CA H:LYS224 4.5 47.1 1.0 O H:ASP221 4.6 54.4 1.0 O H:HOH454 4.6 43.6 1.0 OD2 H:ASP189 4.7 46.1 1.0 N H:GLY226 4.7 40.7 1.0 C H:CYS220 4.7 51.7 1.0 CG H:ASP221 4.9 52.1 1.0 N H:LYS224 4.9 48.8 1.0

S.Hanessian, J.R.Del Valle, Y.Xue, N.Blomberg. Total Synthesis and Structural Confirmation of Chlorodysinosin A. J.Am.Chem.Soc. V. 128 10491 2006.
ISSN: ISSN 0002-7863
PubMed: 16895415
DOI: 10.1021/JA0625834