Iodine in PDB 3u8o: Human Thrombin Complexed with D-Phe-Pro-D-Arg-D-Thr

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

The structure of Human Thrombin Complexed with D-Phe-Pro-D-Arg-D-Thr, PDB code: 3u8o 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)	36.34 / 1.28
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	57.446, 72.680, 83.090, 90.00, 90.00, 90.00
R / Rfree (%)	12.8 / 14.9

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

Chlorine	(Cl)	1 atom
Sodium	(Na)	1 atom

The binding sites of Iodine atom in the Human Thrombin Complexed with D-Phe-Pro-D-Arg-D-Thr (pdb code 3u8o). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total only one binding site of Iodine was determined in the Human Thrombin Complexed with D-Phe-Pro-D-Arg-D-Thr, PDB code: 3u8o:

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


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Human Thrombin Complexed with D-Phe-Pro-D-Arg-D-Thr within 5.0Å range: probe atom residue distance (Å) B Occ H:I603 b:17.8 occ:0.50 H H:MET400 2.6 15.9 1.0 HG2 H:LYS427 2.7 38.6 1.0 HA H:SER399 3.2 16.5 1.0 HB2 H:LYS426 3.2 22.2 1.0 HE3 H:MET400 3.3 29.7 0.8 HB2 H:MET400 3.5 17.9 0.8 N H:MET400 3.5 13.3 1.0 O H:HOH733 3.5 21.7 1.0 HB2 H:MET400 3.5 19.6 0.2 CG H:LYS427 3.6 32.2 1.0 HZ1 H:LYS397 3.6 28.5 0.5 HE2 H:MET400 3.7 29.7 0.8 HG2 H:MET400 3.7 22.5 0.2 H H:LYS427 3.8 20.0 1.0 HB3 H:SER399 3.9 17.4 1.0 HD3 H:LYS427 3.9 43.5 1.0 CE H:MET400 3.9 24.8 0.8 HG3 H:LYS427 3.9 38.6 1.0 HD2 H:LYS427 4.0 43.5 1.0 CA H:SER399 4.0 13.8 1.0 HG3 H:MET400 4.0 22.8 0.8 CD H:LYS427 4.1 36.3 1.0 CB H:LYS426 4.1 18.5 1.0 CB H:MET400 4.2 16.4 0.2 CB H:MET400 4.2 14.9 0.8 N H:LYS427 4.2 16.7 1.0 H H:LYS426 4.3 17.0 1.0 HZ2 H:LYS397 4.3 28.5 0.5 C H:SER399 4.3 12.3 1.0 CG H:MET400 4.3 18.8 0.2 HB3 H:LYS426 4.3 22.2 1.0 NZ H:LYS397 4.4 23.8 0.5 CA H:MET400 4.4 13.2 0.8 CA H:MET400 4.4 14.1 0.2 CB H:SER399 4.4 14.5 1.0 O H:MET400 4.5 13.9 1.0 HE1 H:MET400 4.6 29.7 0.8 CG H:MET400 4.6 19.0 0.8 HG3 H:MET400 4.6 22.5 0.2 CB H:LYS427 4.6 27.4 1.0 HB3 H:LYS427 4.7 32.8 1.0 C H:LYS426 4.7 16.0 1.0 OG H:SER399 4.7 17.2 1.0 HD2 H:LYS426 4.7 28.9 1.0 O H:ILE398 4.7 14.4 1.0 CA H:LYS426 4.8 15.6 1.0 N H:LYS426 4.8 14.2 1.0 C H:MET400 4.9 13.0 1.0 HZ3 H:LYS397 4.9 28.5 0.5 HE3 H:LYS397 4.9 27.4 0.5 CA H:LYS427 5.0 19.1 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