Sodium in PDB 6yqv: Thrombin in Complex with 5-Chlorothiophene-2-Sulfonamide (J94)

All present enzymatic activity of Thrombin in Complex with 5-Chlorothiophene-2-Sulfonamide (J94):
3.4.21.5;

The structure of Thrombin in Complex with 5-Chlorothiophene-2-Sulfonamide (J94), PDB code: 6yqv 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)	50.00 / 1.45
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	70.556, 71.427, 72.541, 90, 100.37, 90
R / Rfree (%)	13.2 / 16.3

The structure of Thrombin in Complex with 5-Chlorothiophene-2-Sulfonamide (J94) also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Sodium atom in the Thrombin in Complex with 5-Chlorothiophene-2-Sulfonamide (J94) (pdb code 6yqv). 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 5-Chlorothiophene-2-Sulfonamide (J94), PDB code: 6yqv:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Thrombin in Complex with 5-Chlorothiophene-2-Sulfonamide (J94)


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 5-Chlorothiophene-2-Sulfonamide (J94) within 5.0Å range: probe atom residue distance (Å) B Occ H:Na301 b:20.3 occ:1.00 O H:HOH566 2.3 21.4 1.0 O H:ARG221A 2.3 22.1 1.0 O H:HOH506 2.3 20.6 1.0 O H:LYS224 2.4 17.8 1.0 O H:HOH476 2.5 18.0 1.0 O H:HOH490 2.8 23.2 1.0 H H:LYS224 3.3 23.1 1.0 C H:ARG221A 3.4 21.7 1.0 C H:LYS224 3.4 17.2 1.0 HA H:ASP221 3.6 25.9 1.0 HA H:ASP222 3.8 28.2 1.0 HB2 H:LYS224 3.8 24.1 1.0 O H:HOH515 3.8 19.3 1.0 N H:LYS224 3.9 19.2 1.0 N H:ARG221A 3.9 22.2 1.0 H H:ARG221A 3.9 26.7 1.0 H H:GLY223 4.0 24.6 1.0 HA H:TYR225 4.0 18.8 1.0 O H:HOH493 4.0 24.1 1.0 C H:ASP221 4.0 22.1 1.0 CA H:LYS224 4.1 18.6 1.0 O H:TYR184A 4.2 20.1 1.0 CA H:ARG221A 4.2 22.5 1.0 O H:HOH486 4.2 18.2 1.0 N H:ASP222 4.2 23.0 1.0 N H:GLY223 4.3 20.5 1.0 CA H:ASP221 4.3 21.5 1.0 CA H:ASP222 4.3 23.4 1.0 N H:TYR225 4.4 16.4 1.0 CB H:LYS224 4.5 20.1 1.0 O H:ASP221 4.5 24.3 1.0 C H:ASP222 4.5 21.9 1.0 OD1 H:ASP221 4.7 22.4 1.0 CA H:TYR225 4.7 15.7 1.0 HB2 H:ARG221A 4.8 27.9 1.0 C H:GLY223 4.9 19.2 1.0 H H:ASP221 4.9 24.7 1.0 HA H:ARG221A 4.9 27.0 1.0 HB3 H:LYS224 5.0 24.1 1.0 O H:HOH461 5.0 20.5 1.0 HA3 H:GLY184 5.0 18.3 1.0 HB2 H:ASP189 5.0 22.1 1.0

Sodium binding site 2 out of 2 in the Thrombin in Complex with 5-Chlorothiophene-2-Sulfonamide (J94)


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 5-Chlorothiophene-2-Sulfonamide (J94) within 5.0Å range: probe atom residue distance (Å) B Occ H:Na302 b:15.8 occ:1.00 O H:THR172 2.3 15.5 1.0 O H:LYS169 2.4 16.5 1.0 O H:HOH564 2.4 24.3 1.0 O H:HOH448 2.6 23.4 1.0 HA H:ASP170 3.3 19.4 1.0 C H:LYS169 3.5 15.5 1.0 H H:THR172 3.5 19.1 1.0 C H:THR172 3.5 15.3 1.0 HA H:ARG173 3.7 19.2 1.0 CA H:ASP170 4.0 16.1 1.0 O H:HOH603 4.1 55.1 1.0 N H:ASP170 4.2 15.8 1.0 HB3 H:LYS169 4.2 22.4 1.0 N H:THR172 4.3 15.9 1.0 HG23 H:THR172 4.3 22.1 1.0 HA H:LYS169 4.4 18.1 1.0 CA H:ARG173 4.4 16.0 1.0 C H:ASP170 4.4 15.3 1.0 N H:ARG173 4.4 15.6 1.0 HG22 H:THR172 4.4 22.1 1.0 CA H:LYS169 4.5 15.1 1.0 O H:HOH433 4.5 41.9 1.0 CA H:THR172 4.5 16.4 1.0 OD1 H:ASP170 4.7 20.0 1.0 O H:ASP170 4.8 16.0 1.0 CG2 H:THR172 4.8 18.4 1.0 CB H:LYS169 4.9 18.6 1.0 N H:SER171 4.9 15.9 1.0 C H:ARG173 4.9 16.6 1.0 H H:SER171 5.0 19.1 1.0 O H:ILE174 5.0 17.1 1.0 O H:HOH602 5.0 48.6 1.0 H H:ASP170 5.0 19.0 1.0 O H:HOH552 5.0 25.8 1.0

W.Scanlan, A.Heine, G.Klebe. Thrombin in Complex with 5-Chlorothiophene-2-Sulfonamide (J94) To Be Published.