Sodium in PDB 6yhg: Thrombin in Complex with D-Phe-Pro-M-Methoxybenzylamide Derivative (16A)

All present enzymatic activity of Thrombin in Complex with D-Phe-Pro-M-Methoxybenzylamide Derivative (16A):
3.4.21.5;

The structure of Thrombin in Complex with D-Phe-Pro-M-Methoxybenzylamide Derivative (16A), PDB code: 6yhg was solved by A.Sandner, A.Heine, G.Klebe, C.Collins, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.63 / 1.33
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	70.25, 71.251, 72.742, 90, 100.61, 90
R / Rfree (%)	12.3 / 14.5

The binding sites of Sodium atom in the Thrombin in Complex with D-Phe-Pro-M-Methoxybenzylamide Derivative (16A) (pdb code 6yhg). 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-M-Methoxybenzylamide Derivative (16A), PDB code: 6yhg:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Thrombin in Complex with D-Phe-Pro-M-Methoxybenzylamide Derivative (16A)


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-M-Methoxybenzylamide Derivative (16A) within 5.0Å range: probe atom residue distance (Å) B Occ H:Na302 b:13.2 occ:1.00 O H:HOH591 2.3 14.6 1.0 O H:ARG221A 2.3 14.2 1.0 O H:LYS224 2.3 11.5 0.4 O H:HOH470 2.4 14.0 1.0 O H:LYS224 2.4 11.4 0.6 O H:HOH504 2.5 11.9 1.0 O H:HOH525 2.7 16.8 1.0 H H:LYS224 3.2 15.5 0.4 H H:LYS224 3.3 15.6 0.6 C H:ARG221A 3.4 14.3 1.0 C H:LYS224 3.4 11.1 0.4 C H:LYS224 3.4 11.2 0.6 HA H:ASP221 3.7 15.9 1.0 HB2 H:LYS224 3.8 15.5 0.6 HA H:ASP222 3.8 20.9 1.0 HB2 H:LYS224 3.8 14.1 0.4 O H:HOH548 3.8 12.7 1.0 N H:ARG221A 3.9 13.6 1.0 N H:LYS224 3.9 12.9 0.4 N H:LYS224 3.9 13.0 0.6 H H:ARG221A 3.9 16.3 1.0 H H:GLY223 4.0 20.6 1.0 O H:HOH487 4.0 17.9 1.0 HA H:TYR225 4.0 10.8 1.0 C H:ASP221 4.1 14.3 1.0 CA H:LYS224 4.1 12.0 0.4 CA H:LYS224 4.1 12.4 0.6 O H:TYR184A 4.1 13.5 1.0 N H:ASP222 4.2 16.7 1.0 CA H:ARG221A 4.2 14.4 1.0 O H:HOH511 4.3 12.3 1.0 N H:GLY223 4.3 17.2 1.0 CA H:ASP222 4.3 17.4 1.0 CA H:ASP221 4.4 13.2 1.0 N H:TYR225 4.4 9.8 1.0 CB H:LYS224 4.4 12.9 0.6 CB H:LYS224 4.5 11.8 0.4 O H:ASP221 4.5 15.8 1.0 C H:ASP222 4.6 17.5 1.0 OD1 H:ASP221 4.6 14.3 1.0 CA H:TYR225 4.7 9.0 1.0 HB2 H:ARG221A 4.8 19.8 1.0 O H:HOH539 4.9 15.4 1.0 HB3 H:LYS224 4.9 15.5 0.6 C H:GLY223 4.9 14.0 1.0 H H:ASP221 4.9 15.8 1.0 HA H:ARG221A 4.9 17.3 1.0 HA3 H:GLY184 5.0 11.5 1.0 H H:ASP222 5.0 20.0 1.0

Sodium binding site 2 out of 2 in the Thrombin in Complex with D-Phe-Pro-M-Methoxybenzylamide Derivative (16A)


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-M-Methoxybenzylamide Derivative (16A) within 5.0Å range: probe atom residue distance (Å) B Occ H:Na303 b:10.9 occ:1.00 O H:HOH466 2.4 15.2 1.0 O H:PHE204A 2.4 8.8 1.0 C H:PHE204A 3.5 8.8 1.0 HA H:PHE204A 3.5 11.0 1.0 CA H:PHE204A 4.0 9.2 1.0 HA H:ASN204B 4.2 12.4 1.0 O H:PRO204 4.5 9.7 1.0 N H:ASN204B 4.6 9.4 1.0 HB3 H:PHE204A 4.6 12.3 1.0 HD21 H:ASN205 4.6 36.4 1.0 CA H:ASN204B 4.9 10.4 1.0 CB H:PHE204A 5.0 10.3 1.0

A.Sandner, A.Heine, G.Klebe. Thrombin in Complex with D-Phe-Pro-M-Methoxybenzylamide Derivative (16A) To Be Published.