Sodium in PDB 2vwo: Aminopyrrolidine Factor Xa Inhibitor

All present enzymatic activity of Aminopyrrolidine Factor Xa Inhibitor:
3.4.21.6;

The structure of Aminopyrrolidine Factor Xa Inhibitor, PDB code: 2vwo was solved by K.Groebke-Zbinden, D.W.Banner, J.M.Benz, F.Blasco, G.Decoret, J.Himber, B.Kuhn, N.Panday, F.Ricklin, P.Risch, D.Schlatter, M.Stahl, R.Unger, W.Haap, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.09 / 1.6
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	105.281, 105.281, 49.405, 90.00, 90.00, 90.00
R / Rfree (%)	19.4 / 22.8

The structure of Aminopyrrolidine Factor Xa Inhibitor also contains other interesting chemical elements:

Fluorine	(F)	2 atoms
Calcium	(Ca)	1 atom
Chlorine	(Cl)	3 atoms

The binding sites of Sodium atom in the Aminopyrrolidine Factor Xa Inhibitor (pdb code 2vwo). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Aminopyrrolidine Factor Xa Inhibitor, PDB code: 2vwo:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Aminopyrrolidine Factor Xa Inhibitor


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Aminopyrrolidine Factor Xa Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1247 b:18.1 occ:1.00 O A:LYS224 2.3 16.2 0.5 O A:LYS224 2.3 16.2 0.5 O A:ARG222 2.3 17.2 1.0 O A:TYR185 2.3 18.0 1.0 O A:HOH2163 2.4 22.1 1.0 O A:ASP185A 2.5 19.0 1.0 O A:HOH2188 2.7 18.4 1.0 C A:ASP185A 3.3 19.8 1.0 C A:ARG222 3.4 17.0 1.0 C A:LYS224 3.4 15.2 0.5 C A:LYS224 3.4 15.2 0.5 C A:TYR185 3.4 18.0 1.0 N A:LYS224 3.7 15.6 0.5 N A:LYS224 3.7 15.6 0.5 CA A:ASP185A 3.8 19.9 1.0 C A:ALA221 4.1 17.6 1.0 N A:ASP185A 4.1 18.2 1.0 CA A:LYS224 4.1 15.4 0.5 N A:ARG222 4.1 17.0 1.0 N A:GLY223A 4.1 17.5 1.0 CA A:LYS224 4.1 15.5 0.5 N A:THR185B 4.2 21.2 1.0 N A:LYS223 4.2 17.6 1.0 CA A:LYS223 4.3 18.5 1.0 O A:ALA221 4.3 18.6 1.0 CA A:ARG222 4.4 16.5 1.0 O A:HOH2165 4.4 18.2 1.0 CA A:ALA221 4.5 17.6 1.0 C A:LYS223 4.5 17.8 1.0 N A:TYR225 4.5 14.7 1.0 CA A:THR185B 4.6 22.2 1.0 CB A:LYS224 4.6 15.3 0.5 CA A:TYR185 4.7 17.6 1.0 CB A:LYS224 4.7 15.3 0.5 O A:LYS186 4.7 22.0 1.0 C A:GLY223A 4.7 16.6 1.0 CA A:TYR225 4.8 14.2 1.0 N A:TYR185 4.9 16.4 1.0 CA A:GLY223A 4.9 17.1 1.0

Sodium binding site 2 out of 3 in the Aminopyrrolidine Factor Xa Inhibitor


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Aminopyrrolidine Factor Xa Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1248 b:29.5 occ:1.00 O A:HOH2105 2.0 30.7 1.0 O A:HOH2038 2.1 33.8 1.0 O A:HOH2106 2.1 21.8 1.0 O A:HOH2039 2.1 35.0 1.0 O A:HOH2131 2.2 30.7 1.0 O A:HOH2103 2.3 26.8 0.5 O A:HOH2046 4.1 42.9 1.0 O A:THR132 4.1 25.2 1.0 O A:GLN133 4.3 23.2 1.0 O A:HOH2108 4.3 22.8 1.0 O A:HOH2135 4.3 47.8 1.0 O A:HOH2133 4.4 27.3 1.0 C A:THR132 4.5 24.1 1.0 O A:MET131B 4.6 23.9 1.0 CA A:THR132 4.6 24.3 1.0 CB A:TYR162 4.7 15.3 1.0

Sodium binding site 3 out of 3 in the Aminopyrrolidine Factor Xa Inhibitor


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Aminopyrrolidine Factor Xa Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1249 b:44.4 occ:0.50 O A:HOH2011 2.0 19.3 0.5 O A:HOH2010 2.3 51.5 1.0 OE1 A:GLN20 2.3 24.3 0.5 CD A:GLN20 3.4 24.1 0.5 OE1 A:GLU26 4.0 24.2 0.5 NE2 A:GLN20 4.1 23.7 0.5 OE2 A:GLU26 4.2 25.9 1.0 O A:GLU21 4.3 23.3 1.0 CB A:GLN20 4.5 21.9 1.0 CG A:GLN20 4.5 22.9 0.5 CD A:GLU26 4.5 26.8 1.0

K.G.Zbinden, L.Anselm, D.W.Banner, J.M.Benz, F.Blasco, G.Decoret, J.Himber, B.Kuhn, N.Panday, F.Ricklin, P.Risch, D.Schlatter, M.Stahl, S.Thomi, R.Unger, W.Haap. Design of Novel Aminopyrrolidine Factor Xa Inhibitors From A Screening Hit. Eur.J.Med.Chem. V. 44 2787 2009.
ISSN: ISSN 0223-5234
PubMed: 19200624
DOI: 10.1016/J.EJMECH.2008.12.025