Sodium in PDB 6yn3: Thrombin in Complex with 4-Hydroxybenzamide (J89)

All present enzymatic activity of Thrombin in Complex with 4-Hydroxybenzamide (J89):
3.4.21.5;

The structure of Thrombin in Complex with 4-Hydroxybenzamide (J89), PDB code: 6yn3 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)	38.53 / 1.49
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	70.773, 71.377, 72.729, 90, 100.7, 90
R / Rfree (%)	13.8 / 16.7

The binding sites of Sodium atom in the Thrombin in Complex with 4-Hydroxybenzamide (J89) (pdb code 6yn3). 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-Hydroxybenzamide (J89), PDB code: 6yn3:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Thrombin in Complex with 4-Hydroxybenzamide (J89)


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-Hydroxybenzamide (J89) within 5.0Å range: probe atom residue distance (Å) B Occ H:Na302 b:15.2 occ:1.00 O H:THR172 2.3 15.8 1.0 O H:HOH572 2.4 18.8 1.0 O H:LYS169 2.4 15.8 1.0 O H:HOH553 2.5 23.5 1.0 O H:HOH478 2.6 22.1 1.0 HA H:ASP170 3.3 18.1 1.0 C H:LYS169 3.5 14.8 1.0 H H:THR172 3.5 17.6 1.0 C H:THR172 3.5 14.9 1.0 HA H:ARG173 3.7 17.9 1.0 CA H:ASP170 4.0 15.1 1.0 N H:ASP170 4.2 15.4 1.0 HB3 H:LYS169 4.2 19.8 1.0 N H:THR172 4.3 14.7 1.0 HG23 H:THR172 4.3 19.8 1.0 O H:HOH451 4.3 39.1 1.0 C H:ASP170 4.4 14.3 1.0 CA H:ARG173 4.4 14.9 1.0 N H:ARG173 4.4 14.4 1.0 HA H:LYS169 4.4 17.0 1.0 HG22 H:THR172 4.5 19.8 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 18.7 1.0 O H:ASP170 4.8 15.7 1.0 CG2 H:THR172 4.8 16.5 1.0 CB H:LYS169 4.8 16.5 1.0 N H:SER171 4.9 15.6 1.0 H H:SER171 4.9 18.7 1.0 C H:ARG173 4.9 15.7 1.0 O H:ILE174 5.0 16.6 1.0 H H:ASP170 5.0 18.5 1.0

Sodium binding site 2 out of 2 in the Thrombin in Complex with 4-Hydroxybenzamide (J89)


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-Hydroxybenzamide (J89) within 5.0Å range: probe atom residue distance (Å) B Occ H:Na303 b:17.5 occ:1.00 O H:ARG221A 2.3 21.4 1.0 O H:HOH467 2.3 19.2 1.0 O H:HOH567 2.4 17.8 1.0 O H:LYS224 2.4 16.4 1.0 O H:HOH486 2.5 16.4 1.0 O H:HOH523 2.7 19.2 1.0 H H:LYS224 3.3 21.2 1.0 C H:ARG221A 3.4 19.8 1.0 C H:LYS224 3.4 16.8 1.0 HA H:ASP221 3.7 23.1 1.0 HA H:ASP222 3.8 25.5 1.0 HB2 H:LYS224 3.8 20.7 1.0 O H:HOH498 3.9 15.7 1.0 N H:LYS224 3.9 17.7 1.0 H H:GLY223 3.9 23.4 1.0 N H:ARG221A 3.9 19.9 1.0 H H:ARG221A 3.9 23.9 1.0 O H:HOH497 4.0 23.1 1.0 HA H:TYR225 4.1 19.1 1.0 C H:ASP221 4.1 19.7 1.0 O H:TYR184A 4.1 18.7 1.0 CA H:LYS224 4.2 16.6 1.0 N H:ASP222 4.2 21.0 1.0 N H:GLY223 4.2 19.5 1.0 O H:HOH482 4.2 16.9 1.0 CA H:ARG221A 4.3 20.4 1.0 CA H:ASP222 4.3 21.3 1.0 CA H:ASP221 4.4 19.2 1.0 N H:TYR225 4.4 15.7 1.0 CB H:LYS224 4.5 17.3 1.0 C H:ASP222 4.5 20.1 1.0 O H:ASP221 4.6 21.8 1.0 OD1 H:ASP221 4.6 19.6 1.0 CA H:TYR225 4.7 15.9 1.0 HB2 H:ARG221A 4.8 25.5 1.0 C H:GLY223 4.8 17.7 1.0 HA H:ARG221A 5.0 24.5 1.0 HB3 H:LYS224 5.0 20.7 1.0 O H:HOH459 5.0 19.4 1.0 H H:ASP221 5.0 21.7 1.0 HB2 H:ASP189 5.0 19.5 1.0 H H:ASP222 5.0 25.2 1.0

W.Scanlan, A.Heine, G.Klebe. Thrombin in Complex with 4-Hydroxybenzamide (J89) To Be Published.