Sodium in PDB 2cf9: Complex of Recombinant Human Thrombin with An Inhibitor

All present enzymatic activity of Complex of Recombinant Human Thrombin with An Inhibitor:
3.4.21.5;

The structure of Complex of Recombinant Human Thrombin with An Inhibitor, PDB code: 2cf9 was solved by E.Schweizer, A.Hoffmann-Roeder, J.A.Olsen, U.Obst-Sander, B.Wagner, M.Kansy, D.W.Banner, F.Diederich, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	71.80 / 1.79
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	71.290, 71.840, 73.060, 90.00, 100.56, 90.00
R / Rfree (%)	16 / 19.8

The structure of Complex of Recombinant Human Thrombin with An Inhibitor also contains other interesting chemical elements:

Calcium

(Ca)

1 atom

The binding sites of Sodium atom in the Complex of Recombinant Human Thrombin with An Inhibitor (pdb code 2cf9). 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 Complex of Recombinant Human Thrombin with An Inhibitor, PDB code: 2cf9:

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


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Complex of Recombinant Human Thrombin with An Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ H:Na1248 b:21.6 occ:1.00 O H:HOH2375 2.2 21.5 1.0 O H:ARG221A 2.3 17.6 1.0 O H:HOH2366 2.4 21.4 1.0 O H:LYS224 2.5 15.3 1.0 O H:HOH2316 2.7 13.6 1.0 O H:HOH2315 2.9 23.8 1.0 C H:ARG221A 3.3 17.1 1.0 C H:LYS224 3.6 15.0 1.0 N H:ARG221A 3.8 17.3 1.0 O H:HOH2334 3.9 15.4 1.0 N H:LYS224 4.0 14.6 1.0 C H:ASP221 4.0 17.2 1.0 O H:HOH2370 4.1 20.1 1.0 CA H:ARG221A 4.1 17.5 1.0 N H:ASP222 4.2 17.0 1.0 O H:TYR184A 4.2 18.1 1.0 CA H:LYS224 4.3 15.0 1.0 CA H:ASP221 4.3 17.0 1.0 CA H:ASP222 4.3 16.9 1.0 O H:HOH2335 4.3 16.1 1.0 N H:GLY223 4.4 16.1 1.0 O H:HOH2336 4.4 27.2 1.0 O H:ASP221 4.5 17.5 1.0 OD1 H:ASP221 4.5 15.4 1.0 N H:TYR225 4.6 15.0 1.0 CB H:LYS224 4.6 15.0 1.0 C H:ASP222 4.6 16.4 1.0 CA H:TYR225 4.8 15.1 1.0 O H:HOH2360 4.9 19.3 1.0

E.Schweizer, A.Hoffmann-Roeder, J.A.Olsen, P.Seiler, U.Obst-Sander, B.Wagner, M.Kansy, D.W.Banner, F.Diederich. Multipolar Interactions in the D Pocket of Thrombin: Large Differences Between Tricyclic Imide and Lactam Inhibitors. Org.Biomol.Chem. V. 4 2364 2006.
ISSN: ISSN 1477-0520
PubMed: 16763681
DOI: 10.1039/B602585D