Sodium in PDB 7ac9: Thrombin in Complex with D-Arginine (J77)

All present enzymatic activity of Thrombin in Complex with D-Arginine (J77):
3.4.21.5;

The structure of Thrombin in Complex with D-Arginine (J77), PDB code: 7ac9 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)	43.54 / 1.39
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	70.469, 71.37, 72.598, 90, 100.47, 90
R / Rfree (%)	14 / 16.3

The binding sites of Sodium atom in the Thrombin in Complex with D-Arginine (J77) (pdb code 7ac9). 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 D-Arginine (J77), PDB code: 7ac9:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Thrombin in Complex with D-Arginine (J77)


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 D-Arginine (J77) within 5.0Å range: probe atom residue distance (Å) B Occ H:Na301 b:20.7 occ:1.00 O H:HOH569 2.3 20.5 1.0 O H:ARG221A 2.3 23.3 1.0 O H:HOH470 2.4 21.8 1.0 O H:LYS224 2.4 18.7 1.0 O H:HOH464 2.5 18.0 1.0 O H:HOH494 2.7 21.6 1.0 H H:LYS224 3.2 23.4 1.0 C H:ARG221A 3.4 23.7 1.0 C H:LYS224 3.5 18.0 1.0 HA H:ASP221 3.7 26.8 1.0 HA H:ASP222 3.7 30.5 1.0 HB2 H:LYS224 3.8 23.3 1.0 N H:LYS224 3.8 19.5 1.0 O H:HOH496 3.9 18.2 1.0 N H:ARG221A 3.9 23.0 1.0 H H:GLY223 3.9 27.9 1.0 H H:ARG221A 3.9 27.6 1.0 O H:HOH505 4.0 26.1 1.0 C H:ASP221 4.1 23.0 1.0 HA H:TYR225 4.1 19.5 1.0 O H:TYR184A 4.1 20.4 1.0 CA H:LYS224 4.1 18.6 1.0 N H:ASP222 4.2 25.0 1.0 N H:GLY223 4.3 23.3 1.0 O H:HOH488 4.3 19.4 1.0 CA H:ARG221A 4.3 24.0 1.0 CA H:ASP222 4.3 25.4 1.0 CA H:ASP221 4.4 22.3 1.0 CB H:LYS224 4.5 19.4 1.0 N H:TYR225 4.5 16.6 1.0 C H:ASP222 4.5 24.2 1.0 O H:ASP221 4.5 24.9 1.0 OD1 H:ASP221 4.6 22.4 1.0 CA H:TYR225 4.8 16.2 1.0 C H:GLY223 4.8 20.2 1.0 HB2 H:ARG221A 4.8 30.2 1.0 O H:HOH436 4.8 28.8 1.0 H H:ASP221 4.9 26.0 1.0 HB3 H:LYS224 4.9 23.3 1.0 HA H:ARG221A 5.0 28.8 1.0 H H:ASP222 5.0 30.1 1.0 HA3 H:GLY184 5.0 18.3 1.0

Sodium binding site 2 out of 2 in the Thrombin in Complex with D-Arginine (J77)


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 D-Arginine (J77) within 5.0Å range: probe atom residue distance (Å) B Occ H:Na302 b:17.3 occ:0.79 O H:LYS169 2.3 18.8 1.0 O H:THR172 2.4 17.3 1.0 O H:HOH552 2.4 31.4 1.0 O H:HOH463 2.6 25.9 1.0 HA H:ASP170 3.2 20.8 1.0 C H:LYS169 3.4 17.7 1.0 H H:THR172 3.5 20.3 1.0 C H:THR172 3.6 16.7 1.0 HA H:ARG173 3.7 20.4 1.0 CA H:ASP170 4.0 17.4 1.0 N H:ASP170 4.1 16.9 1.0 N H:THR172 4.3 16.9 1.0 HB3 H:LYS169 4.3 22.9 1.0 C H:ASP170 4.4 16.9 1.0 HG23 H:THR172 4.4 20.5 1.0 HA H:LYS169 4.4 20.7 1.0 N H:ARG173 4.5 16.9 1.0 CA H:ARG173 4.5 17.0 1.0 CA H:LYS169 4.5 17.3 1.0 HG22 H:THR172 4.5 20.5 1.0 O H:HOH430 4.5 44.1 1.0 CA H:THR172 4.5 17.2 1.0 OD1 H:ASP170 4.6 20.5 1.0 O H:ASP170 4.8 17.8 1.0 N H:SER171 4.8 17.5 1.0 H H:SER171 4.9 21.0 1.0 O H:HOH551 4.9 25.1 1.0 CG2 H:THR172 4.9 17.1 1.0 CB H:LYS169 4.9 19.1 1.0 H H:ASP170 5.0 20.3 1.0 C H:ARG173 5.0 18.1 1.0

W.Scanlan, A.Heine, G.Klebe. Thrombin in Complex with D-Arginine (J77) To Be Published.