Sodium in PDB 6ysx: Thrombin in Complex with 4-Amino-N-(5-Methylisoxazol-3-Yl) Benzenesulfonamide (J80)

All present enzymatic activity of Thrombin in Complex with 4-Amino-N-(5-Methylisoxazol-3-Yl) Benzenesulfonamide (J80):
3.4.21.5;

The structure of Thrombin in Complex with 4-Amino-N-(5-Methylisoxazol-3-Yl) Benzenesulfonamide (J80), PDB code: 6ysx 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)	43.56 / 1.48
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	70.676, 71.42, 72.525, 90, 100.35, 90
R / Rfree (%)	13.3 / 16.2

The binding sites of Sodium atom in the Thrombin in Complex with 4-Amino-N-(5-Methylisoxazol-3-Yl) Benzenesulfonamide (J80) (pdb code 6ysx). 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 4-Amino-N-(5-Methylisoxazol-3-Yl) Benzenesulfonamide (J80), PDB code: 6ysx:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Thrombin in Complex with 4-Amino-N-(5-Methylisoxazol-3-Yl) Benzenesulfonamide (J80)


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 4-Amino-N-(5-Methylisoxazol-3-Yl) Benzenesulfonamide (J80) within 5.0Å range: probe atom residue distance (Å) B Occ H:Na301 b:20.6 occ:1.00 O H:ARG221A 2.3 22.4 1.0 O H:HOH570 2.3 20.1 1.0 O H:LYS224 2.4 17.6 1.0 O H:HOH464 2.4 20.2 1.0 O H:HOH485 2.5 17.4 1.0 O H:HOH512 2.7 22.0 1.0 H H:LYS224 3.3 22.3 1.0 C H:ARG221A 3.4 22.5 1.0 C H:LYS224 3.4 16.3 1.0 HA H:ASP221 3.7 26.8 1.0 HB2 H:LYS224 3.8 22.6 1.0 HA H:ASP222 3.8 29.4 1.0 N H:LYS224 3.9 18.6 1.0 N H:ARG221A 3.9 21.7 1.0 O H:HOH515 3.9 18.1 1.0 H H:ARG221A 3.9 26.0 1.0 H H:GLY223 3.9 26.2 1.0 HA H:TYR225 4.0 19.2 1.0 O H:HOH495 4.0 24.5 1.0 C H:ASP221 4.1 22.0 1.0 CA H:LYS224 4.1 17.7 1.0 O H:TYR184A 4.2 20.9 1.0 CA H:ARG221A 4.2 22.7 1.0 N H:ASP222 4.2 23.6 1.0 O H:HOH491 4.3 17.5 1.0 N H:GLY223 4.3 21.8 1.0 CA H:ASP222 4.3 24.5 1.0 CA H:ASP221 4.4 22.3 1.0 N H:TYR225 4.4 17.2 1.0 CB H:LYS224 4.4 18.8 1.0 C H:ASP222 4.5 23.0 1.0 O H:ASP221 4.6 24.0 1.0 OD1 H:ASP221 4.6 21.4 1.0 CA H:TYR225 4.7 16.0 1.0 HB2 H:ARG221A 4.8 28.7 1.0 O H:HOH486 4.8 21.1 1.0 C H:GLY223 4.8 19.2 1.0 HB3 H:LYS224 4.9 22.6 1.0 H H:ASP221 4.9 25.2 1.0 HA H:ARG221A 4.9 27.2 1.0 HB2 H:ASP189 5.0 21.6 1.0 HA3 H:GLY184 5.0 18.6 1.0

Sodium binding site 2 out of 2 in the Thrombin in Complex with 4-Amino-N-(5-Methylisoxazol-3-Yl) Benzenesulfonamide (J80)


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 4-Amino-N-(5-Methylisoxazol-3-Yl) Benzenesulfonamide (J80) within 5.0Å range: probe atom residue distance (Å) B Occ H:Na302 b:15.8 occ:1.00 O H:THR172 2.3 16.8 1.0 O H:HOH580 2.4 18.5 1.0 O H:LYS169 2.4 17.0 1.0 O H:HOH561 2.4 26.2 1.0 O H:HOH434 2.6 23.9 1.0 HA H:ASP170 3.3 18.9 1.0 C H:LYS169 3.5 15.9 1.0 H H:THR172 3.5 19.1 1.0 C H:THR172 3.6 16.6 1.0 HA H:ARG173 3.7 19.5 1.0 CA H:ASP170 4.0 15.7 1.0 HB3 H:LYS169 4.2 22.9 1.0 HG23 H:THR172 4.2 21.1 1.0 N H:ASP170 4.2 16.2 1.0 N H:THR172 4.3 15.9 1.0 HA H:LYS169 4.4 18.7 1.0 C H:ASP170 4.4 15.9 1.0 CA H:ARG173 4.4 16.2 1.0 N H:ARG173 4.4 15.9 1.0 O H:HOH472 4.5 37.5 1.0 CA H:LYS169 4.5 15.6 1.0 CA H:THR172 4.5 16.7 1.0 HG22 H:THR172 4.6 21.1 1.0 OD1 H:ASP170 4.7 20.0 1.0 CG2 H:THR172 4.8 17.5 1.0 O H:ASP170 4.8 16.9 1.0 CB H:LYS169 4.8 19.1 1.0 N H:SER171 4.9 16.7 1.0 C H:ARG173 4.9 18.2 1.0 O H:ILE174 4.9 17.5 1.0 H H:SER171 4.9 20.0 1.0 O H:HOH600 5.0 51.0 1.0 H H:ASP170 5.0 19.5 1.0

W.Scanlan, A.Heine, G.Klebe. Thrombin in Complex with 4-Amino-N-(5-Methylisoxazol-3-Yl)Benzenesulfonamide (J80) To Be Published.