Sodium in PDB 6y02: Thrombin in Complex with 13K

All present enzymatic activity of Thrombin in Complex with 13K:
3.4.21.5;

The structure of Thrombin in Complex with 13K, PDB code: 6y02 was solved by A.Sandner, 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)	43.55 / 1.48
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	70.131, 71.404, 72.892, 90, 100.51, 90
R / Rfree (%)	13.9 / 16.4

The structure of Thrombin in Complex with 13K also contains other interesting chemical elements:

Bromine

(Br)

1 atom

The binding sites of Sodium atom in the Thrombin in Complex with 13K (pdb code 6y02). 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 13K, PDB code: 6y02:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Thrombin in Complex with 13K


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 13K within 5.0Å range: probe atom residue distance (Å) B Occ H:Na301 b:16.9 occ:1.00 O H:THR172 2.3 16.0 1.0 O H:LYS169 2.4 16.7 0.4 O H:LYS169 2.4 17.6 0.6 O H:HOH469 2.9 25.8 1.0 HA H:ASP170 3.3 19.6 1.0 HG2 H:LYS169 3.5 27.9 0.6 C H:LYS169 3.5 16.3 0.4 C H:LYS169 3.5 16.9 0.6 HG2 H:LYS169 3.5 25.0 0.4 H H:THR172 3.5 18.5 1.0 C H:THR172 3.6 15.8 1.0 HA H:ARG173 3.6 19.7 1.0 HZ3 H:LYS169 3.8 31.2 0.4 CA H:ASP170 4.0 16.4 1.0 N H:ASP170 4.2 15.6 1.0 HG3 H:LYS169 4.2 27.9 0.6 N H:THR172 4.3 15.4 1.0 CG H:LYS169 4.3 23.2 0.6 CG H:LYS169 4.3 20.8 0.4 C H:ASP170 4.4 16.7 1.0 HG23 H:THR172 4.4 21.2 1.0 HG3 H:LYS169 4.4 25.0 0.4 CA H:ARG173 4.4 16.4 1.0 N H:ARG173 4.4 16.5 1.0 HA H:LYS169 4.5 20.5 0.6 HA H:LYS169 4.5 19.7 0.4 CA H:THR172 4.5 15.9 1.0 CA H:LYS169 4.6 17.1 0.6 CA H:LYS169 4.6 16.4 0.4 NZ H:LYS169 4.6 26.0 0.4 HZ2 H:LYS169 4.7 31.2 0.4 HG22 H:THR172 4.7 21.2 1.0 O H:ASP170 4.7 17.9 1.0 OD1 H:ASP170 4.8 24.6 1.0 N H:SER171 4.8 16.8 1.0 HE2 H:LYS169 4.9 34.1 0.6 H H:SER171 4.9 20.2 1.0 CG2 H:THR172 5.0 17.7 1.0 CB H:LYS169 5.0 19.4 0.6 CB H:LYS169 5.0 18.0 0.4

Sodium binding site 2 out of 2 in the Thrombin in Complex with 13K


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 13K within 5.0Å range: probe atom residue distance (Å) B Occ H:Na302 b:22.4 occ:1.00 O H:ARG221A 2.3 23.7 1.0 O H:HOH474 2.3 23.3 1.0 O H:HOH547 2.3 26.6 1.0 O H:LYS224 2.4 19.4 1.0 O H:HOH484 2.4 20.6 1.0 O H:HOH490 2.8 26.4 1.0 H H:LYS224 3.3 23.1 1.0 C H:ARG221A 3.4 23.7 1.0 C H:LYS224 3.5 18.7 1.0 HA H:ASP221 3.6 29.7 1.0 HA H:ASP222 3.8 30.4 1.0 O H:HOH495 3.8 24.1 1.0 H H:ARG221A 3.8 28.7 1.0 N H:ARG221A 3.8 23.9 1.0 HB2 H:LYS224 3.9 24.1 1.0 N H:LYS224 3.9 19.3 1.0 H H:GLY223 4.0 28.0 1.0 HA H:TYR225 4.0 18.6 1.0 O H:HOH437 4.1 26.1 1.0 C H:ASP221 4.1 25.0 1.0 CA H:LYS224 4.2 18.4 1.0 O H:TYR184A 4.2 19.8 1.0 O H:HOH476 4.2 19.7 1.0 CA H:ARG221A 4.2 24.6 1.0 N H:ASP222 4.3 24.9 1.0 N H:GLY223 4.3 23.3 1.0 CA H:ASP221 4.3 24.7 1.0 CA H:ASP222 4.3 25.4 1.0 N H:TYR225 4.5 16.8 1.0 CB H:LYS224 4.5 20.1 1.0 C H:ASP222 4.6 23.9 1.0 OD1 H:ASP221 4.6 24.1 1.0 O H:ASP221 4.7 27.4 1.0 CA H:TYR225 4.8 15.5 1.0 HB2 H:ARG221A 4.8 31.8 1.0 H H:ASP221 4.8 28.2 1.0 C H:GLY223 4.9 19.9 1.0 O H:HOH499 4.9 26.1 1.0 HA3 H:GLY184 5.0 18.4 1.0 HA H:ARG221A 5.0 29.5 1.0 HB3 H:LYS224 5.0 24.1 1.0 HB2 H:ASP189 5.0 23.9 1.0

A.Sandner, A.Heine, G.Klebe. Thrombin in Complex with 13K To Be Published.