Sodium in PDB 6zgo: Thrombin in Complex with D-Phe-Pro-2-Chlorofuran Derivative (13L)

All present enzymatic activity of Thrombin in Complex with D-Phe-Pro-2-Chlorofuran Derivative (13L):
3.4.21.5;

The structure of Thrombin in Complex with D-Phe-Pro-2-Chlorofuran Derivative (13L), PDB code: 6zgo was solved by A.Sandner, A.Heine, G.Klebe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	33.54 / 1.79
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	70.114, 70.867, 72.606, 90, 100.57, 90
R / Rfree (%)	18.5 / 22.5

The structure of Thrombin in Complex with D-Phe-Pro-2-Chlorofuran Derivative (13L) also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Sodium atom in the Thrombin in Complex with D-Phe-Pro-2-Chlorofuran Derivative (13L) (pdb code 6zgo). 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-Phe-Pro-2-Chlorofuran Derivative (13L), PDB code: 6zgo:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Thrombin in Complex with D-Phe-Pro-2-Chlorofuran Derivative (13L)


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-Phe-Pro-2-Chlorofuran Derivative (13L) within 5.0Å range: probe atom residue distance (Å) B Occ H:Na301 b:26.2 occ:1.00 O H:THR172 2.4 22.4 1.0 O H:LYS169 2.4 21.7 1.0 O H:HOH496 2.5 28.4 1.0 O H:HOH413 3.0 30.4 1.0 C H:LYS169 3.5 22.1 1.0 C H:THR172 3.6 21.9 1.0 CA H:ASP170 4.0 21.8 1.0 N H:ASP170 4.2 22.6 1.0 N H:THR172 4.3 20.6 1.0 CG H:LYS169 4.3 31.7 1.0 C H:ASP170 4.3 21.9 1.0 CA H:ARG173 4.4 24.0 1.0 N H:ARG173 4.5 21.8 1.0 CA H:LYS169 4.6 21.7 1.0 CA H:THR172 4.6 21.4 1.0 NZ H:LYS169 4.6 41.6 1.0 O H:ASP170 4.6 22.1 1.0 OD1 H:ASP170 4.7 23.6 1.0 N H:SER171 4.8 21.7 1.0 CG2 H:THR172 5.0 20.6 1.0 CB H:LYS169 5.0 24.9 1.0

Sodium binding site 2 out of 2 in the Thrombin in Complex with D-Phe-Pro-2-Chlorofuran Derivative (13L)


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-Phe-Pro-2-Chlorofuran Derivative (13L) within 5.0Å range: probe atom residue distance (Å) B Occ H:Na302 b:37.8 occ:1.00 O H:LYS224 2.3 27.6 1.0 O H:HOH463 2.4 27.4 1.0 O H:HOH447 2.4 26.6 1.0 O H:ARG221A 2.4 34.1 1.0 O H:HOH472 2.4 32.6 1.0 O H:HOH461 2.9 26.1 1.0 C H:LYS224 3.3 26.6 1.0 C H:ARG221A 3.5 34.0 1.0 O H:HOH479 3.7 23.5 1.0 N H:LYS224 3.9 27.3 1.0 N H:ARG221A 3.9 35.5 1.0 O H:TYR184A 4.1 27.6 1.0 C H:ASP221 4.1 36.8 1.0 CA H:LYS224 4.1 25.6 1.0 O H:HOH471 4.1 22.8 1.0 O H:HOH456 4.2 29.2 1.0 N H:ASP222 4.3 34.1 1.0 N H:TYR225 4.3 25.5 1.0 CA H:ASP221 4.3 36.2 1.0 CA H:ARG221A 4.3 35.1 1.0 N H:GLY223 4.4 29.2 1.0 CA H:ASP222 4.4 34.6 1.0 CB H:LYS224 4.5 24.7 1.0 CA H:TYR225 4.6 24.6 1.0 C H:ASP222 4.6 31.7 1.0 O H:ASP221 4.7 37.1 1.0 OD1 H:ASP221 4.7 37.2 1.0 O H:HOH457 4.8 35.8 1.0 C H:GLY223 4.9 28.2 1.0 CD1 H:TYR225 4.9 25.8 1.0 N H:ASP221 5.0 36.6 1.0

A.Sandner, A.Heine, G.Klebe. Thrombin in Complex with D-Phe-Pro-2-Chlorofuran Derivative (13L) To Be Published.