Sodium in PDB 6ymp: Thrombin in Complex with 3-((5-(Tert-Butyl)Isoxazol-3-Yl)Methyl) Oxetan-3-Amine (J54)

All present enzymatic activity of Thrombin in Complex with 3-((5-(Tert-Butyl)Isoxazol-3-Yl)Methyl) Oxetan-3-Amine (J54):
3.4.21.5;

The structure of Thrombin in Complex with 3-((5-(Tert-Butyl)Isoxazol-3-Yl)Methyl) Oxetan-3-Amine (J54), PDB code: 6ymp was solved by W.Scanlan, A.Heine, G.Klebe, N.Abazi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.68 / 1.42
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	70.52, 71.369, 72.515, 90, 100.36, 90
R / Rfree (%)	13.1 / 15.4

The binding sites of Sodium atom in the Thrombin in Complex with 3-((5-(Tert-Butyl)Isoxazol-3-Yl)Methyl) Oxetan-3-Amine (J54) (pdb code 6ymp). 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 3-((5-(Tert-Butyl)Isoxazol-3-Yl)Methyl) Oxetan-3-Amine (J54), PDB code: 6ymp:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Thrombin in Complex with 3-((5-(Tert-Butyl)Isoxazol-3-Yl)Methyl) Oxetan-3-Amine (J54)


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 3-((5-(Tert-Butyl)Isoxazol-3-Yl)Methyl) Oxetan-3-Amine (J54) within 5.0Å range: probe atom residue distance (Å) B Occ H:Na301 b:14.6 occ:1.00 O H:THR172 2.3 15.2 1.0 O H:LYS169 2.4 16.1 1.0 O H:HOH573 2.4 25.5 1.0 O H:HOH586 2.4 17.6 1.0 O H:HOH493 2.6 22.4 1.0 HA H:ASP170 3.3 18.2 1.0 C H:LYS169 3.5 15.4 1.0 H H:THR172 3.5 16.8 1.0 C H:THR172 3.5 14.8 1.0 HA H:ARG173 3.6 17.9 1.0 CA H:ASP170 4.0 15.1 1.0 N H:ASP170 4.2 15.0 1.0 HB3 H:LYS169 4.2 20.1 1.0 N H:THR172 4.3 14.0 1.0 HG23 H:THR172 4.3 20.4 1.0 CA H:ARG173 4.4 14.9 1.0 O H:HOH454 4.4 36.8 1.0 N H:ARG173 4.4 14.3 1.0 C H:ASP170 4.4 14.8 1.0 HA H:LYS169 4.4 17.1 1.0 HG22 H:THR172 4.5 20.4 1.0 CA H:LYS169 4.5 14.2 1.0 CA H:THR172 4.5 15.0 1.0 OD1 H:ASP170 4.7 18.6 1.0 O H:ASP170 4.8 15.2 1.0 CG2 H:THR172 4.8 17.0 1.0 N H:SER171 4.9 15.5 1.0 CB H:LYS169 4.9 16.7 1.0 C H:ARG173 4.9 15.4 1.0 H H:SER171 4.9 18.6 1.0 O H:ILE174 5.0 14.7 1.0

Sodium binding site 2 out of 2 in the Thrombin in Complex with 3-((5-(Tert-Butyl)Isoxazol-3-Yl)Methyl) Oxetan-3-Amine (J54)


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 3-((5-(Tert-Butyl)Isoxazol-3-Yl)Methyl) Oxetan-3-Amine (J54) within 5.0Å range: probe atom residue distance (Å) B Occ H:Na302 b:18.9 occ:1.00 O H:HOH578 2.3 19.0 1.0 O H:ARG221A 2.3 19.9 1.0 O H:HOH496 2.4 19.1 1.0 O H:LYS224 2.4 16.1 1.0 O H:HOH491 2.5 16.4 1.0 O H:HOH509 2.7 20.9 1.0 H H:LYS224 3.3 20.6 1.0 C H:ARG221A 3.4 20.1 1.0 C H:LYS224 3.4 15.8 1.0 HA H:ASP221 3.7 24.2 1.0 HA H:ASP222 3.7 26.1 1.0 HB2 H:LYS224 3.8 20.6 1.0 O H:HOH519 3.9 16.4 1.0 N H:LYS224 3.9 17.2 1.0 N H:ARG221A 3.9 20.3 1.0 H H:GLY223 3.9 24.8 1.0 H H:ARG221A 3.9 24.4 1.0 O H:HOH502 4.0 22.9 1.0 C H:ASP221 4.1 19.9 1.0 HA H:TYR225 4.1 17.1 1.0 CA H:LYS224 4.1 16.5 1.0 O H:TYR184A 4.2 17.6 1.0 N H:ASP222 4.2 21.4 1.0 CA H:ARG221A 4.2 20.8 1.0 O H:HOH505 4.2 16.8 1.0 N H:GLY223 4.3 20.7 1.0 CA H:ASP222 4.3 21.7 1.0 CA H:ASP221 4.3 20.1 1.0 N H:TYR225 4.4 14.7 1.0 CB H:LYS224 4.5 17.1 1.0 C H:ASP222 4.5 21.4 1.0 O H:ASP221 4.5 22.1 1.0 OD1 H:ASP221 4.6 19.9 1.0 CA H:TYR225 4.8 14.2 1.0 HB2 H:ARG221A 4.8 26.6 1.0 C H:GLY223 4.8 18.6 1.0 H H:ASP221 4.9 22.7 1.0 HA H:ARG221A 4.9 24.9 1.0 O H:HOH525 5.0 20.9 1.0 HB3 H:LYS224 5.0 20.6 1.0 HB2 H:ASP189 5.0 18.7 1.0 H H:ASP222 5.0 25.7 1.0

W.Scanlan, A.Heine, G.Klebe. Thrombin in Complex with 3-((5-(Tert-Butyl)Isoxazol-3-Yl)Methyl)Oxetan-3-Amine (J54) To Be Published.