Sodium in PDB 6ysj: Thrombin in Complex with 2-Amino-1-(4-Bromophenyl)Ethan-1-One (J10)

All present enzymatic activity of Thrombin in Complex with 2-Amino-1-(4-Bromophenyl)Ethan-1-One (J10):
3.4.21.5;

The structure of Thrombin in Complex with 2-Amino-1-(4-Bromophenyl)Ethan-1-One (J10), PDB code: 6ysj was solved by W.Scanlan, A.Heine, G.Klebe, N.Abazi, A.Paulus, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.49 / 1.45
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	70.451, 71.379, 72.448, 90, 100.34, 90
R / Rfree (%)	13.4 / 16.8

The structure of Thrombin in Complex with 2-Amino-1-(4-Bromophenyl)Ethan-1-One (J10) also contains other interesting chemical elements:

Bromine

(Br)

2 atoms

The binding sites of Sodium atom in the Thrombin in Complex with 2-Amino-1-(4-Bromophenyl)Ethan-1-One (J10) (pdb code 6ysj). 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 2-Amino-1-(4-Bromophenyl)Ethan-1-One (J10), PDB code: 6ysj:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Thrombin in Complex with 2-Amino-1-(4-Bromophenyl)Ethan-1-One (J10)


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 2-Amino-1-(4-Bromophenyl)Ethan-1-One (J10) within 5.0Å range: probe atom residue distance (Å) B Occ H:Na301 b:18.5 occ:1.00 O H:HOH484 2.3 19.8 1.0 O H:HOH561 2.3 20.1 1.0 O H:ARG221A 2.3 20.6 1.0 O H:LYS224 2.4 16.2 1.0 O H:HOH466 2.5 16.2 1.0 O H:HOH490 2.7 21.2 1.0 H H:LYS224 3.3 21.8 1.0 C H:ARG221A 3.4 21.1 1.0 C H:LYS224 3.5 15.5 1.0 HA H:ASP221 3.6 23.9 1.0 HA H:ASP222 3.7 28.0 1.0 HB2 H:LYS224 3.9 22.9 1.0 H H:GLY223 3.9 25.1 1.0 N H:LYS224 3.9 18.2 1.0 O H:HOH500 3.9 17.3 1.0 N H:ARG221A 3.9 21.0 1.0 O H:HOH481 4.0 23.6 1.0 H H:ARG221A 4.0 25.2 1.0 C H:ASP221 4.1 20.6 1.0 HA H:TYR225 4.1 17.4 1.0 O H:TYR184A 4.1 18.2 1.0 CA H:LYS224 4.2 17.3 1.0 O H:HOH476 4.2 16.5 1.0 N H:ASP222 4.2 21.8 1.0 N H:GLY223 4.2 20.9 1.0 CA H:ARG221A 4.3 21.4 1.0 CA H:ASP222 4.3 23.3 1.0 CA H:ASP221 4.3 19.9 1.0 N H:TYR225 4.5 15.3 1.0 CB H:LYS224 4.5 19.1 1.0 C H:ASP222 4.5 22.5 1.0 O H:ASP221 4.6 22.2 1.0 OD1 H:ASP221 4.6 21.2 1.0 CA H:TYR225 4.8 14.4 1.0 HB2 H:ARG221A 4.8 27.6 1.0 C H:GLY223 4.9 18.3 1.0 H H:ASP221 4.9 23.8 1.0 O H:HOH505 4.9 21.1 1.0 HA3 H:GLY184 5.0 16.4 1.0 HA H:ARG221A 5.0 25.7 1.0 HB3 H:LYS224 5.0 22.9 1.0

Sodium binding site 2 out of 2 in the Thrombin in Complex with 2-Amino-1-(4-Bromophenyl)Ethan-1-One (J10)


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 2-Amino-1-(4-Bromophenyl)Ethan-1-One (J10) within 5.0Å range: probe atom residue distance (Å) B Occ H:Na302 b:15.2 occ:1.00 O H:THR172 2.3 15.5 1.0 O H:HOH576 2.4 17.9 1.0 O H:HOH553 2.4 23.5 1.0 O H:LYS169 2.4 15.4 1.0 O H:HOH463 2.6 22.3 1.0 HA H:ASP170 3.3 17.6 1.0 C H:LYS169 3.5 14.1 1.0 H H:THR172 3.5 17.6 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 14.6 1.0 N H:ASP170 4.2 14.3 1.0 N H:THR172 4.2 14.7 1.0 HB3 H:LYS169 4.3 19.9 1.0 HG23 H:THR172 4.3 19.4 1.0 CA H:ARG173 4.4 14.9 1.0 C H:ASP170 4.4 14.9 1.0 N H:ARG173 4.4 14.2 1.0 O H:HOH455 4.4 42.3 1.0 HA H:LYS169 4.4 17.4 1.0 CA H:THR172 4.5 15.6 1.0 CA H:LYS169 4.5 14.4 1.0 OD1 H:ASP170 4.7 18.7 1.0 HG22 H:THR172 4.7 19.4 1.0 O H:ASP170 4.8 15.3 1.0 N H:SER171 4.9 15.3 1.0 CG2 H:THR172 4.9 16.2 1.0 CB H:LYS169 4.9 16.6 1.0 C H:ARG173 4.9 16.7 1.0 H H:SER171 4.9 18.3 1.0 O H:ILE174 5.0 15.9 1.0 O H:HOH543 5.0 25.4 1.0

W.Scanlan, A.Heine, G.Klebe. Thrombin in Complex with 2-Amino-1-(4-Bromophenyl)Ethan-1-One (J10) To Be Published.