Sodium in PDB 3biu: Human Thrombin-in Complex with Ub-THR10

All present enzymatic activity of Human Thrombin-in Complex with Ub-THR10:
3.4.21.5;

The structure of Human Thrombin-in Complex with Ub-THR10, PDB code: 3biu was solved by C.Gerlach, M.Smolinski, H.Steuber, C.A.Sotriffer, A.Heine, D.G.Hangauer, G.Klebe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	10.00 / 2.30
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	70.700, 71.500, 72.800, 90.00, 100.90, 90.00
R / Rfree (%)	16.4 / 26.3

The binding sites of Sodium atom in the Human Thrombin-in Complex with Ub-THR10 (pdb code 3biu). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Human Thrombin-in Complex with Ub-THR10, PDB code: 3biu:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Human Thrombin-in Complex with Ub-THR10


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Human Thrombin-in Complex with Ub-THR10 within 5.0Å range: probe atom residue distance (Å) B Occ H:Na601 b:20.6 occ:1.00 O H:HOH1117 2.3 23.3 1.0 O H:LYS224 2.4 21.1 1.0 O H:HOH1044 2.4 19.9 1.0 O H:ARG221A 2.4 33.0 1.0 O H:HOH1082 2.5 26.3 1.0 O H:HOH1023 2.9 16.0 1.0 C H:ARG221A 3.4 28.5 1.0 C H:LYS224 3.5 24.3 1.0 N H:LYS224 3.7 16.7 1.0 O H:HOH1071 3.8 21.5 1.0 N H:ARG221A 4.0 17.9 1.0 O H:HOH1001 4.0 13.4 1.0 N H:GLY223 4.1 31.2 1.0 O H:TYR184A 4.1 19.6 1.0 CA H:LYS224 4.1 23.2 1.0 N H:ASP222 4.1 27.9 1.0 C H:ASP221 4.2 19.8 1.0 CA H:ASP222 4.2 24.1 1.0 CA H:ARG221A 4.3 23.2 1.0 O H:HOH1034 4.3 17.0 1.0 C H:ASP222 4.3 23.0 1.0 CB H:LYS224 4.6 33.0 1.0 CA H:ASP221 4.6 20.2 1.0 OD1 H:ASP221 4.6 17.4 1.0 O H:ASP221 4.6 34.9 1.0 N H:TYR225 4.6 14.7 1.0 O H:HOH1016 4.7 22.5 1.0 C H:GLY223 4.7 23.5 1.0 CA H:GLY223 4.9 20.8 1.0 CA H:TYR225 4.9 13.2 1.0 CD1 H:TYR225 4.9 11.0 1.0

Sodium binding site 2 out of 2 in the Human Thrombin-in Complex with Ub-THR10


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Human Thrombin-in Complex with Ub-THR10 within 5.0Å range: probe atom residue distance (Å) B Occ H:Na602 b:30.1 occ:1.00 O H:HOH1009 2.3 14.2 1.0 O H:THR172 2.5 16.0 1.0 O H:LYS169 2.5 29.3 1.0 O H:HOH1002 2.7 19.4 1.0 C H:LYS169 3.5 19.6 1.0 C H:THR172 3.7 14.5 1.0 CA H:ASP170 4.0 22.8 1.0 N H:ASP170 4.1 17.7 1.0 N H:THR172 4.4 9.8 1.0 OD1 H:ASP170 4.4 24.1 1.0 CA H:LYS169 4.5 23.0 1.0 C H:ASP170 4.5 21.2 1.0 N H:ARG173 4.5 16.5 1.0 CA H:ARG173 4.6 20.7 1.0 O H:HOH1153 4.6 44.3 1.0 CA H:THR172 4.6 14.7 1.0 CB H:LYS169 4.7 22.0 1.0 N H:SER171 4.9 13.7 1.0 O H:ASP170 5.0 28.3 1.0

C.Gerlach, M.Smolinski, H.Steuber, C.A.Sotriffer, A.Heine, D.G.Hangauer, G.Klebe. Thermodynamic Inhibition Profile of A Cyclopentyl and A Cyclohexyl Derivative Towards Thrombin: the Same But For Different Reasons Angew.Chem.Int.Ed.Engl. V. 46 8511 2007.
ISSN: ISSN 1433-7851
PubMed: 17902081
DOI: 10.1002/ANIE.200701169