Sodium in PDB 3u8r: Human Thrombin Complexed with D-Phe-Pro-D-Arg-Ile

All present enzymatic activity of Human Thrombin Complexed with D-Phe-Pro-D-Arg-Ile:
3.4.21.5;

The structure of Human Thrombin Complexed with D-Phe-Pro-D-Arg-Ile, PDB code: 3u8r was solved by A.C.Figueiredo, C.C.Clement, M.Philipp, P.J.B.Pereira, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.84 / 1.47
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	51.563, 76.527, 83.260, 90.00, 90.00, 90.00
R / Rfree (%)	12.9 / 16.1

The structure of Human Thrombin Complexed with D-Phe-Pro-D-Arg-Ile also contains other interesting chemical elements:

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

The binding sites of Sodium atom in the Human Thrombin Complexed with D-Phe-Pro-D-Arg-Ile (pdb code 3u8r). 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 Human Thrombin Complexed with D-Phe-Pro-D-Arg-Ile, PDB code: 3u8r:

Sodium binding site 1 out of 1 in the Human Thrombin Complexed with D-Phe-Pro-D-Arg-Ile


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Human Thrombin Complexed with D-Phe-Pro-D-Arg-Ile within 5.0Å range: probe atom residue distance (Å) B Occ H:Na602 b:13.4 occ:1.00 O H:ARG553 2.3 13.3 1.0 O H:LYS556 2.4 10.8 1.0 O H:HOH750 2.4 17.4 1.0 O H:HOH721 2.5 10.0 1.0 O H:HOH726 2.5 14.2 1.0 O H:HOH741 2.7 17.5 1.0 H H:LYS556 3.2 12.0 1.0 C H:ARG553 3.4 11.5 1.0 C H:LYS556 3.5 8.6 1.0 HA H:ASP552 3.6 14.4 1.0 HA H:ASP554 3.8 17.7 1.0 N H:LYS556 3.8 10.2 1.0 H H:GLY555 3.9 17.8 1.0 HB2 H:LYS556 3.9 13.6 1.0 N H:ARG553 4.0 12.3 1.0 O H:HOH764 4.0 13.2 1.0 O H:HOH744 4.0 19.4 1.0 H H:ARG553 4.1 14.6 1.0 C H:ASP552 4.1 10.3 1.0 HA H:TYR557 4.1 9.7 1.0 O H:TYR510 4.1 11.8 1.0 CA H:LYS556 4.1 9.2 1.0 O H:HOH710 4.2 11.2 1.0 N H:GLY555 4.2 14.9 1.0 N H:ASP554 4.3 14.3 1.0 CA H:ARG553 4.3 12.2 1.0 CA H:ASP554 4.3 14.9 1.0 CA H:ASP552 4.3 12.2 1.0 C H:ASP554 4.5 15.5 1.0 N H:TYR557 4.5 8.9 1.0 O H:ASP552 4.5 13.9 1.0 CB H:LYS556 4.5 11.4 1.0 OD1 H:ASP552 4.6 14.9 1.0 O H:HOH704 4.6 18.4 1.0 CA H:TYR557 4.8 8.2 1.0 C H:GLY555 4.8 10.7 1.0 HB2 H:ARG553 4.9 19.8 1.0 H H:ASP552 4.9 13.2 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