Sodium in PDB 1vzq: Complex of Thrombin with Designed Inhibitor 7165

All present enzymatic activity of Complex of Thrombin with Designed Inhibitor 7165:
3.4.21.5;

The structure of Complex of Thrombin with Designed Inhibitor 7165, PDB code: 1vzq was solved by K.Shaerer, M.Morgenthaler, P.Seiler, F.Diederich, D.W.Banner, T.Tschopp, U.Obst-Sander, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	18.55 / 1.54
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	70.900, 71.400, 72.400, 90.00, 100.40, 90.00
R / Rfree (%)	n/a / n/a

The structure of Complex of Thrombin with Designed Inhibitor 7165 also contains other interesting chemical elements:

Calcium

(Ca)

1 atom

The binding sites of Sodium atom in the Complex of Thrombin with Designed Inhibitor 7165 (pdb code 1vzq). 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 Thrombin with Designed Inhibitor 7165, PDB code: 1vzq:

Sodium binding site 1 out of 1 in the Complex of Thrombin with Designed Inhibitor 7165


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Complex of Thrombin with Designed Inhibitor 7165 within 5.0Å range: probe atom residue distance (Å) B Occ H:Na1257 b:16.6 occ:1.00 O H:HOH2312 2.2 16.6 1.0 O H:ARG221A 2.3 17.0 1.0 O H:LYS224 2.4 14.0 1.0 O H:HOH2305 2.4 15.9 1.0 O H:HOH2260 2.5 12.1 1.0 O H:HOH2261 2.9 15.6 1.0 C H:ARG221A 3.3 16.8 1.0 C H:LYS224 3.5 13.4 1.0 N H:LYS224 3.8 13.2 1.0 N H:ARG221A 3.8 14.9 1.0 O H:HOH2276 4.0 13.4 1.0 O H:HOH2307 4.0 19.0 1.0 C H:ASP221 4.0 14.4 1.0 CA H:LYS224 4.1 13.8 1.0 O H:TYR184A 4.2 15.2 1.0 N H:ASP222 4.2 17.7 1.0 CA H:ARG221A 4.2 16.0 1.0 CA H:ASP222 4.2 18.2 1.0 N H:GLY223 4.3 17.9 1.0 O H:HOH2275 4.3 14.6 1.0 CA H:ASP221 4.3 13.9 1.0 CB H:LYS224 4.5 13.2 1.0 N H:TYR225 4.5 11.2 1.0 C H:ASP222 4.5 17.9 1.0 O H:ASP221 4.5 17.0 1.0 OD1 H:ASP221 4.6 14.6 1.0 O H:HOH2277 4.7 23.7 1.0 CA H:TYR225 4.7 11.8 1.0 C H:GLY223 4.8 14.8 1.0 O H:HOH2298 4.8 17.2 1.0

K.Schaerer, M.Morgenthaler, P.Seiler, F.Diederich, D.W.Banner, T.Tschopp, U.Obst-Sander. Enantiomerically Pure Thrombin Inhibitors For Exploring the Molecular-Recognition Features of the Oxyanion Hole Helv.Chim.Acta V. 87 2517 2004.
ISSN: ISSN 0018-019X