Sodium in PDB 1riw: Thrombin in Complex with Natural Product Inhibitor Oscillarin

All present enzymatic activity of Thrombin in Complex with Natural Product Inhibitor Oscillarin:
3.4.21.5;

The structure of Thrombin in Complex with Natural Product Inhibitor Oscillarin, PDB code: 1riw was solved by S.Hanessian, M.Tremblay, J.F.W.Petersen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.68 / 2.04
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	71.055, 72.366, 70.830, 90.00, 100.19, 90.00
R / Rfree (%)	n/a / n/a

The binding sites of Sodium atom in the Thrombin in Complex with Natural Product Inhibitor Oscillarin (pdb code 1riw). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Thrombin in Complex with Natural Product Inhibitor Oscillarin, PDB code: 1riw:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Thrombin in Complex with Natural Product Inhibitor Oscillarin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Thrombin in Complex with Natural Product Inhibitor Oscillarin within 5.0Å range: probe atom residue distance (Å) B Occ C:Na701 b:25.3 occ:1.00 O C:THR207 2.3 26.0 1.0 O C:LYS204 2.4 25.8 1.0 O C:HOH1027 2.5 31.5 1.0 O C:HOH1035 3.1 35.9 1.0 C C:LYS204 3.5 25.6 1.0 C C:THR207 3.5 26.2 1.0 CA C:ASP205 4.0 25.4 1.0 N C:ASP205 4.1 25.4 1.0 N C:THR207 4.2 25.4 1.0 C C:ASP205 4.3 25.2 1.0 CG C:LYS204 4.3 27.6 1.0 N C:ARG208 4.4 27.0 1.0 CA C:THR207 4.5 25.6 1.0 CA C:ARG208 4.5 28.0 1.0 CA C:LYS204 4.6 25.6 1.0 OD2 C:ASP205 4.7 26.1 1.0 O C:ASP205 4.7 25.0 1.0 N C:SER206 4.8 25.1 1.0 NZ C:LYS204 4.9 30.5 1.0 CG2 C:THR207 5.0 24.5 1.0

Sodium binding site 2 out of 2 in the Thrombin in Complex with Natural Product Inhibitor Oscillarin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Thrombin in Complex with Natural Product Inhibitor Oscillarin within 5.0Å range: probe atom residue distance (Å) B Occ C:Na702 b:29.9 occ:1.00 O C:HOH1009 2.3 26.0 1.0 O C:HOH1022 2.4 28.7 1.0 O C:ARG263 2.4 29.3 1.0 O C:LYS266 2.5 24.7 1.0 O C:HOH1012 2.6 22.6 1.0 O C:HOH1016 2.6 25.4 1.0 C C:ARG263 3.4 28.9 1.0 C C:LYS266 3.5 25.0 1.0 N C:ARG263 3.8 27.8 1.0 N C:LYS266 3.8 26.3 1.0 O C:TYR220 4.0 27.0 1.0 C C:ASP262 4.0 27.1 1.0 O C:HOH1013 4.0 26.1 1.0 O C:HOH1028 4.2 34.3 1.0 N C:ASP264 4.2 29.1 1.0 CA C:LYS266 4.2 25.4 1.0 CA C:ASP264 4.2 29.1 1.0 N C:GLY265 4.3 28.4 1.0 CA C:ARG263 4.3 28.8 1.0 CA C:ASP262 4.3 26.4 1.0 O C:HOH1004 4.3 18.4 1.0 OD1 C:ASP262 4.4 25.4 1.0 O C:ASP262 4.5 26.8 1.0 C C:ASP264 4.5 28.7 1.0 N C:TYR267 4.6 24.4 1.0 CB C:LYS266 4.6 25.3 1.0 CA C:TYR267 4.8 24.0 1.0 C C:GLY265 4.8 27.1 1.0 O C:HOH1067 5.0 45.1 1.0

S.Hanessian, M.Tremblay, J.F.W.Petersen. The N-Acyloxyiminium Ion Aza-Prins Route to Octahydroindoles: Total Synthesis and Structural Confirmation of the Antithrombotic Marine Natural Product Oscillarin J.Am.Chem.Soc. V. 126 6064 2004.
ISSN: ISSN 0002-7863
PubMed: 15137772
DOI: 10.1021/JA030669G