Sodium in PDB 4ax9: Human Thrombin Complexed with Napsagatran, RO0466240

All present enzymatic activity of Human Thrombin Complexed with Napsagatran, RO0466240:
3.4.21.5;

The structure of Human Thrombin Complexed with Napsagatran, RO0466240, PDB code: 4ax9 was solved by D.W.Banner, A.D'arcy, F.K.Winkler, K.Hilpert, S.Spinelli, C.Cambillau, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.87 / 1.90
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	71.400, 72.040, 72.700, 90.00, 100.80, 90.00
R / Rfree (%)	16.09 / 19.609

The binding sites of Sodium atom in the Human Thrombin Complexed with Napsagatran, RO0466240 (pdb code 4ax9). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Human Thrombin Complexed with Napsagatran, RO0466240, PDB code: 4ax9:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Human Thrombin Complexed with Napsagatran, RO0466240


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 Napsagatran, RO0466240 within 5.0Å range: probe atom residue distance (Å) B Occ H:Na1244 b:19.2 occ:1.00 O H:HOH2145 2.2 25.9 1.0 O H:THR172 2.4 16.5 1.0 O H:HOH2142 2.5 29.1 1.0 O H:LYS169 2.5 19.1 1.0 O H:HOH2141 2.7 33.3 1.0 C H:THR172 3.6 17.5 1.0 C H:LYS169 3.6 19.4 1.0 CA H:ASP170 4.2 19.6 1.0 N H:ASP170 4.3 18.7 1.0 N H:THR172 4.4 16.1 1.0 CA H:ARG173 4.4 21.0 1.0 N H:ARG173 4.5 18.6 1.0 C H:ASP170 4.6 19.2 1.0 CA H:THR172 4.6 17.4 1.0 O H:HOH2147 4.6 39.8 1.0 CG H:LYS169 4.7 32.6 1.0 OD1 H:ASP170 4.7 21.1 1.0 CA H:LYS169 4.7 19.4 1.0 O H:ASP170 4.9 18.5 1.0 C H:ARG173 4.9 21.3 1.0 CG2 H:THR172 4.9 16.3 1.0

Sodium binding site 2 out of 2 in the Human Thrombin Complexed with Napsagatran, RO0466240


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Human Thrombin Complexed with Napsagatran, RO0466240 within 5.0Å range: probe atom residue distance (Å) B Occ H:Na1245 b:22.5 occ:1.00 O H:LYS224 2.3 18.9 1.0 O H:HOH2166 2.4 22.4 1.0 O H:ARG221A 2.4 23.0 1.0 O H:HOH2180 2.4 19.1 1.0 O H:HOH2159 2.5 17.2 1.0 O H:HOH2160 2.7 21.6 1.0 C H:ARG221A 3.4 25.1 1.0 C H:LYS224 3.4 19.1 1.0 N H:LYS224 3.9 20.8 1.0 O H:HOH2165 3.9 26.6 1.0 O H:HOH2155 3.9 20.8 1.0 N H:ARG221A 3.9 23.3 1.0 C H:ASP221 4.1 22.7 1.0 O H:TYR184A 4.1 20.4 1.0 CA H:LYS224 4.2 18.8 1.0 O H:HOH2158 4.3 14.9 1.0 N H:ASP222 4.3 24.4 1.0 CA H:ARG221A 4.3 24.8 1.0 CA H:ASP221 4.3 21.3 1.0 N H:GLY223 4.4 22.9 1.0 CA H:ASP222 4.4 25.1 1.0 N H:TYR225 4.4 17.0 1.0 C H:ASP222 4.6 23.5 1.0 OD1 H:ASP221 4.6 22.0 1.0 O H:ASP221 4.6 23.0 1.0 CB H:LYS224 4.6 20.4 1.0 CA H:TYR225 4.7 17.0 1.0 O H:HOH2167 4.8 28.2 1.0 C H:GLY223 4.9 22.3 1.0

K.Hilpert, J.Ackermann, D.W.Banner, A.Gast, K.Gubernator, P.Hadvary, L.Labler, K.Muller, G.Schmid, T.B.Tschopp. Design and Synthesis of Potent and Highly Selective Thrombin Inhibitors. J.Med.Chem. V. 37 3889 1994.
ISSN: ISSN 0022-2623
PubMed: 7966150
DOI: 10.1021/JM00049A008