Sodium in PDB 6t54: Thrombin in Complex with A D-Phe-Pro-2-Bromothiophene Derivative

All present enzymatic activity of Thrombin in Complex with A D-Phe-Pro-2-Bromothiophene Derivative:
3.4.21.5;

The structure of Thrombin in Complex with A D-Phe-Pro-2-Bromothiophene Derivative, PDB code: 6t54 was solved by K.Ngo, 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)	43.56 / 1.57
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	70.291, 71.383, 72.751, 90.00, 100.57, 90.00
R / Rfree (%)	13.8 / 17

The structure of Thrombin in Complex with A D-Phe-Pro-2-Bromothiophene Derivative also contains other interesting chemical elements:

Bromine

(Br)

1 atom

The binding sites of Sodium atom in the Thrombin in Complex with A D-Phe-Pro-2-Bromothiophene Derivative (pdb code 6t54). 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 A D-Phe-Pro-2-Bromothiophene Derivative, PDB code: 6t54:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Thrombin in Complex with A D-Phe-Pro-2-Bromothiophene Derivative


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 A D-Phe-Pro-2-Bromothiophene Derivative within 5.0Å range: probe atom residue distance (Å) B Occ H:Na301 b:17.9 occ:1.00 O H:ARG221A 2.3 20.5 1.0 O H:HOH544 2.3 20.3 1.0 O H:HOH466 2.4 19.0 1.0 O H:LYS224 2.4 16.5 1.0 O H:HOH461 2.4 16.3 1.0 O H:HOH492 2.7 20.6 1.0 H H:LYS224 3.3 21.8 1.0 C H:ARG221A 3.4 20.7 1.0 C H:LYS224 3.4 16.5 1.0 HA H:ASP221 3.6 23.1 1.0 HA H:ASP222 3.8 26.4 1.0 O H:HOH518 3.8 19.1 1.0 HB2 H:LYS224 3.9 22.2 1.0 N H:LYS224 3.9 18.2 1.0 N H:ARG221A 3.9 21.5 1.0 H H:GLY223 3.9 26.0 1.0 O H:HOH447 4.0 21.1 1.0 H H:ARG221A 4.0 25.8 1.0 HA H:TYR225 4.0 16.8 1.0 C H:ASP221 4.1 20.5 1.0 O H:TYR184A 4.1 18.9 1.0 CA H:LYS224 4.1 17.9 1.0 O H:HOH448 4.2 16.8 1.0 N H:ASP222 4.2 21.3 1.0 CA H:ARG221A 4.3 21.8 1.0 N H:GLY223 4.3 21.7 1.0 CA H:ASP221 4.3 19.3 1.0 CA H:ASP222 4.3 22.0 1.0 N H:TYR225 4.4 14.9 1.0 CB H:LYS224 4.5 18.5 1.0 C H:ASP222 4.5 21.0 1.0 O H:ASP221 4.6 21.5 1.0 OD1 H:ASP221 4.6 19.1 1.0 CA H:TYR225 4.7 14.0 1.0 HB2 H:ARG221A 4.8 26.8 1.0 C H:GLY223 4.9 19.1 1.0 H H:ASP221 4.9 21.2 1.0 HB2 H:ASP189 4.9 18.9 1.0 HA3 H:GLY184 4.9 15.1 1.0 HB3 H:LYS224 5.0 22.2 1.0 HA H:ARG221A 5.0 26.2 1.0 CD1 H:TYR225 5.0 15.6 1.0 H H:ASP222 5.0 25.6 1.0

Sodium binding site 2 out of 2 in the Thrombin in Complex with A D-Phe-Pro-2-Bromothiophene Derivative


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 A D-Phe-Pro-2-Bromothiophene Derivative within 5.0Å range: probe atom residue distance (Å) B Occ H:Na302 b:16.7 occ:1.00 O H:THR172 2.3 16.9 1.0 O H:LYS169 2.4 15.7 1.0 O H:HOH533 2.5 26.2 1.0 O H:HOH458 3.0 26.1 1.0 HA H:ASP170 3.2 18.7 1.0 HG2 H:LYS169 3.5 26.5 1.0 HZ2 H:LYS169 3.5 43.3 1.0 C H:LYS169 3.5 14.9 1.0 H H:THR172 3.5 17.8 1.0 C H:THR172 3.6 16.2 1.0 HA H:ARG173 3.7 20.0 1.0 CA H:ASP170 4.0 15.6 1.0 N H:ASP170 4.2 15.9 1.0 HG3 H:LYS169 4.2 26.5 1.0 CG H:LYS169 4.2 22.1 1.0 N H:THR172 4.2 14.9 1.0 NZ H:LYS169 4.3 36.1 1.0 C H:ASP170 4.4 14.5 1.0 O H:HOH488 4.4 43.0 1.0 HZ3 H:LYS169 4.4 43.3 1.0 N H:ARG173 4.4 15.5 1.0 CA H:ARG173 4.4 16.7 1.0 HA H:LYS169 4.5 15.6 1.0 HG22 H:THR172 4.5 19.7 1.0 CA H:THR172 4.5 16.5 1.0 HG23 H:THR172 4.6 19.7 1.0 CA H:LYS169 4.6 13.0 1.0 HZ1 H:LYS169 4.7 43.3 1.0 OD1 H:ASP170 4.7 19.4 1.0 O H:ASP170 4.7 14.4 1.0 N H:SER171 4.9 14.0 1.0 H H:SER171 5.0 16.8 1.0 CG2 H:THR172 5.0 16.4 1.0 CB H:LYS169 5.0 16.1 1.0 H H:ASP170 5.0 19.1 1.0

K.Ngo, N.Abazi, A.Heine, G.Klebe. Thrombin in Complex with A D-Phe-Pro-2-Bromothiophene Derivative To Be Published.