Sodium in PDB 2v3h: Thrombin with 3-Cycle No F

All present enzymatic activity of Thrombin with 3-Cycle No F:
3.4.21.5;

The structure of Thrombin with 3-Cycle No F, PDB code: 2v3h was solved by D.W.Banner, U.Obst, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	71.25 / 1.79
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	70.440, 71.780, 72.410, 90.00, 100.40, 90.00
R / Rfree (%)	17.3 / 20.7

The structure of Thrombin with 3-Cycle No F also contains other interesting chemical elements:

Calcium

(Ca)

1 atom

The binding sites of Sodium atom in the Thrombin with 3-Cycle No F (pdb code 2v3h). 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 No F, PDB code: 2v3h:

Sodium binding site 1 out of 1 in the Thrombin with 3-Cycle No 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 No F within 5.0Å range: probe atom residue distance (Å) B Occ H:Na1247 b:25.1 occ:1.00 O H:HOH2306 2.3 20.4 1.0 O H:ARG221A 2.3 24.5 1.0 O H:LYS224 2.3 24.2 1.0 O H:HOH2260 2.6 19.1 1.0 O H:HOH2298 2.7 19.9 1.0 O H:HOH2261 2.7 19.8 1.0 C H:ARG221A 3.4 24.9 1.0 C H:LYS224 3.4 23.7 1.0 N H:LYS224 3.8 23.8 1.0 N H:ARG221A 3.9 25.5 1.0 O H:HOH2273 3.9 18.1 1.0 CA H:LYS224 4.1 24.2 1.0 C H:ASP221 4.1 25.7 1.0 O H:TYR184A 4.1 25.5 1.0 O H:HOH2302 4.1 21.4 1.0 N H:ASP222 4.2 24.3 1.0 CA H:ARG221A 4.3 25.3 1.0 N H:GLY223 4.3 24.6 1.0 CA H:ASP222 4.3 24.8 1.0 O H:HOH2272 4.4 19.0 1.0 CA H:ASP221 4.4 25.5 1.0 N H:TYR225 4.4 24.2 1.0 CB H:LYS224 4.4 24.0 1.0 C H:ASP222 4.5 24.1 1.0 O H:HOH2274 4.6 24.4 1.0 O H:ASP221 4.6 26.2 1.0 OD1 H:ASP221 4.8 25.1 1.0 CA H:TYR225 4.8 23.9 1.0 C H:GLY223 4.8 24.4 1.0 O H:HOH2293 5.0 22.0 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