Sodium in PDB 3u69: Unliganded Wild-Type Human Thrombin

All present enzymatic activity of Unliganded Wild-Type Human Thrombin:
3.4.21.5;

The structure of Unliganded Wild-Type Human Thrombin, PDB code: 3u69 was solved by A.C.Figueiredo, C.C.Clement, M.Philipp, P.J.Barbosa Pereira, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.30 / 1.55
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	57.555, 72.995, 83.042, 90.00, 90.00, 90.00
R / Rfree (%)	13.3 / 16.7

The structure of Unliganded Wild-Type Human Thrombin also contains other interesting chemical elements:

Iodine	(I)	1 atom
Chlorine	(Cl)	1 atom

The binding sites of Sodium atom in the Unliganded Wild-Type Human Thrombin (pdb code 3u69). 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 Unliganded Wild-Type Human Thrombin, PDB code: 3u69:

Sodium binding site 1 out of 1 in the Unliganded Wild-Type Human Thrombin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Unliganded Wild-Type Human Thrombin within 5.0Å range: probe atom residue distance (Å) B Occ H:Na1 b:13.3 occ:1.00 O H:ARG553 2.3 12.6 1.0 O H:LYS556 2.3 11.5 1.0 O H:HOH6 2.4 13.4 1.0 O H:HOH11 2.4 10.5 1.0 O H:HOH19 2.4 13.8 1.0 O H:HOH29 2.6 14.9 1.0 H H:LYS556 3.3 15.0 1.0 C H:ARG553 3.4 12.8 1.0 C H:LYS556 3.4 12.0 1.0 HA H:ASP552 3.7 14.8 1.0 HA H:ASP554 3.8 19.3 1.0 HB2 H:LYS556 3.9 16.2 1.0 N H:ARG553 3.9 13.5 1.0 H H:GLY555 3.9 15.4 1.0 O H:HOH18 3.9 10.8 1.0 N H:LYS556 3.9 12.5 1.0 H H:ARG553 3.9 16.2 1.0 O H:HOH66 4.0 17.1 1.0 HA H:TYR557 4.0 13.1 1.0 C H:ASP552 4.1 11.5 1.0 O H:TYR510 4.1 10.7 1.0 CA H:LYS556 4.2 11.9 1.0 O H:HOH27 4.2 11.4 1.0 CA H:ARG553 4.2 14.2 1.0 N H:ASP554 4.3 14.0 1.0 N H:GLY555 4.3 12.8 1.0 CA H:ASP552 4.4 12.3 1.0 CA H:ASP554 4.4 16.1 1.0 N H:TYR557 4.5 12.0 1.0 CB H:LYS556 4.5 13.5 1.0 O H:ASP552 4.6 15.3 1.0 OD1 H:ASP552 4.6 13.8 1.0 C H:ASP554 4.6 13.5 1.0 CA H:TYR557 4.7 10.9 1.0 HB2 H:ARG553 4.8 19.4 1.0 C H:GLY555 4.9 14.3 1.0 O H:HOH65 4.9 20.0 1.0 HA H:ARG553 4.9 17.0 1.0 HB3 H:LYS556 5.0 16.2 1.0 O H:HOH52 5.0 16.6 1.0 H H:ASP552 5.0 15.1 1.0

A.C.Figueiredo, C.C.Clement, S.Zakia, J.Gingold, M.Philipp, P.J.Pereira. Rational Design and Characterization of D-Phe-Pro-D-Arg-Derived Direct Thrombin Inhibitors. Plos One V. 7 34354 2012.
ISSN: ESSN 1932-6203
PubMed: 22457833
DOI: 10.1371/JOURNAL.PONE.0034354