Sodium in PDB 6i51: Thrombin in Complex with Fragment J02

All present enzymatic activity of Thrombin in Complex with Fragment J02:
3.4.21.5;

The structure of Thrombin in Complex with Fragment J02, PDB code: 6i51 was solved by N.Abazi, A.Heine, G.Klebe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	23.76 / 1.40
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	70.389, 71.120, 72.459, 90.00, 100.30, 90.00
R / Rfree (%)	14.5 / 16.9

The binding sites of Sodium atom in the Thrombin in Complex with Fragment J02 (pdb code 6i51). 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 Fragment J02, PDB code: 6i51:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Thrombin in Complex with Fragment J02


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 Fragment J02 within 5.0Å range: probe atom residue distance (Å) B Occ H:Na305 b:17.3 occ:1.00 O H:THR172 2.3 16.8 1.0 O H:HOH554 2.4 20.7 1.0 O H:LYS169 2.4 18.3 1.0 O H:HOH534 2.4 24.6 1.0 O H:HOH440 2.6 25.1 1.0 HA H:ASP170 3.3 21.0 1.0 C H:LYS169 3.4 17.2 1.0 H H:THR172 3.5 20.7 1.0 C H:THR172 3.6 16.5 1.0 HA H:ARG173 3.7 20.5 1.0 CA H:ASP170 4.0 17.5 1.0 N H:ASP170 4.1 18.0 1.0 HB3 H:LYS169 4.2 23.8 1.0 HG23 H:THR172 4.2 22.4 1.0 N H:THR172 4.3 17.3 1.0 O H:HOH468 4.4 50.9 1.0 HA H:LYS169 4.4 20.8 1.0 C H:ASP170 4.4 17.9 1.0 CA H:ARG173 4.4 17.0 1.0 N H:ARG173 4.4 16.7 1.0 CA H:LYS169 4.5 17.3 1.0 HG22 H:THR172 4.5 22.4 1.0 CA H:THR172 4.5 16.9 1.0 OD1 H:ASP170 4.6 20.9 1.0 O H:ASP170 4.8 18.3 1.0 CG2 H:THR172 4.8 18.6 1.0 CB H:LYS169 4.8 19.8 1.0 N H:SER171 4.9 17.9 1.0 H H:SER171 4.9 21.6 1.0 O H:ILE174 4.9 17.6 1.0 C H:ARG173 4.9 17.8 1.0 O H:HOH570 4.9 54.8 1.0 H H:ASP170 5.0 21.6 1.0

Sodium binding site 2 out of 2 in the Thrombin in Complex with Fragment J02


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 Fragment J02 within 5.0Å range: probe atom residue distance (Å) B Occ H:Na306 b:22.9 occ:1.00 O H:ARG221A 2.3 24.6 1.0 O H:HOH548 2.3 23.6 1.0 O H:HOH449 2.4 24.5 1.0 O H:LYS224 2.4 19.9 1.0 O H:HOH465 2.5 20.0 1.0 O H:HOH477 2.7 25.0 1.0 H H:LYS224 3.3 26.1 1.0 C H:ARG221A 3.4 25.1 1.0 C H:LYS224 3.5 19.4 1.0 HA H:ASP222 3.7 33.3 1.0 HA H:ASP221 3.7 31.7 1.0 O H:HOH504 3.8 19.7 1.0 HB2 H:LYS224 3.8 25.9 1.0 N H:LYS224 3.9 21.7 1.0 H H:GLY223 3.9 31.1 1.0 N H:ARG221A 3.9 25.8 1.0 H H:ARG221A 3.9 31.0 1.0 O H:HOH447 4.0 28.4 1.0 HA H:TYR225 4.0 22.3 1.0 C H:ASP221 4.1 26.7 1.0 O H:TYR184A 4.1 22.0 1.0 CA H:LYS224 4.2 20.1 1.0 N H:ASP222 4.2 26.3 1.0 N H:GLY223 4.2 25.9 1.0 O H:HOH460 4.2 21.5 1.0 CA H:ARG221A 4.2 26.4 1.0 CA H:ASP222 4.3 27.7 1.0 CA H:ASP221 4.4 26.4 1.0 N H:TYR225 4.5 18.7 1.0 C H:ASP222 4.5 26.4 1.0 CB H:LYS224 4.5 21.5 1.0 O H:ASP221 4.6 28.9 1.0 OD1 H:ASP221 4.6 26.6 1.0 O H:HOH492 4.7 26.4 1.0 CA H:TYR225 4.7 18.5 1.0 C H:GLY223 4.8 22.5 1.0 HB2 H:ARG221A 4.8 35.3 1.0 HB2 H:ASP189 4.9 23.9 1.0 HA H:ARG221A 5.0 31.8 1.0 H H:ASP222 5.0 31.6 1.0 H H:ASP221 5.0 30.7 1.0

N.Abazi, A.Heine, G.Klebe. Fragment Screening of Thrombin Using A 96 Member Fragment Library To Be Published.