Sodium in PDB 2v3o: Thrombin with 3-Cycle with F

All present enzymatic activity of Thrombin with 3-Cycle with F:
3.4.21.5;

The structure of Thrombin with 3-Cycle with F, PDB code: 2v3o was solved by D.W.Banner, H.P.Wessel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	71.07 / 1.79
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	70.610, 71.820, 72.280, 90.00, 100.60, 90.00
R / Rfree (%)	17.6 / 21.2

The structure of Thrombin with 3-Cycle with F also contains other interesting chemical elements:

Fluorine	(F)	1 atom
Calcium	(Ca)	1 atom

The binding sites of Sodium atom in the Thrombin with 3-Cycle with F (pdb code 2v3o). 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 with 3-Cycle with F, PDB code: 2v3o:

Sodium binding site 1 out of 1 in the Thrombin with 3-Cycle with F


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Thrombin with 3-Cycle with F within 5.0Å range: probe atom residue distance (Å) B Occ H:Na1248 b:22.6 occ:1.00 O H:LYS224 2.3 22.2 1.0 O H:ARG221A 2.3 21.3 1.0 O H:HOH2273 2.5 18.6 1.0 O H:HOH2308 2.6 13.0 1.0 O H:HOH2300 2.6 16.0 1.0 O H:HOH2259 2.7 16.5 1.0 C H:ARG221A 3.3 22.4 1.0 C H:LYS224 3.4 21.3 1.0 N H:LYS224 3.8 21.5 1.0 O H:HOH2304 3.9 19.8 1.0 O H:HOH2272 4.0 16.4 1.0 N H:ARG221A 4.0 23.1 1.0 CA H:LYS224 4.0 22.0 1.0 O H:TYR184A 4.1 24.0 1.0 C H:ASP221 4.1 23.4 1.0 N H:GLY223 4.1 23.0 1.0 N H:ASP222 4.1 22.6 1.0 CA H:ASP222 4.2 23.2 1.0 CA H:ARG221A 4.3 22.9 1.0 O H:HOH2271 4.4 15.9 1.0 CB H:LYS224 4.4 21.7 1.0 N H:TYR225 4.4 21.6 1.0 C H:ASP222 4.4 22.5 1.0 CA H:ASP221 4.5 23.4 1.0 O H:ASP221 4.6 22.9 1.0 O H:HOH2274 4.7 24.2 1.0 OD1 H:ASP221 4.7 22.0 1.0 C H:GLY223 4.8 22.5 1.0 CA H:TYR225 4.8 21.0 1.0 CA H:GLY223 5.0 22.4 1.0

K.Mueller, C.Faeh, F.Diederich. Fluorine in Pharmaceuticals: Looking Beyond Intuition. Science V. 317 1881 2007.
ISSN: ISSN 0036-8075
PubMed: 17901324
DOI: 10.1126/SCIENCE.1131943