Sodium in PDB 1d6w: Structure of Thrombin Complexed with Selective Non-Electrophilic Inhibitors Having Cyclohexyl Moieties at P1

All present enzymatic activity of Structure of Thrombin Complexed with Selective Non-Electrophilic Inhibitors Having Cyclohexyl Moieties at P1:
3.4.21.5;

The structure of Structure of Thrombin Complexed with Selective Non-Electrophilic Inhibitors Having Cyclohexyl Moieties at P1, PDB code: 1d6w was solved by I.Mochalkin, A.Tulinsky, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	9.00 / 2.00
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	71.430, 71.670, 72.450, 90.00, 101.00, 90.00
R / Rfree (%)	n/a / n/a

The binding sites of Sodium atom in the Structure of Thrombin Complexed with Selective Non-Electrophilic Inhibitors Having Cyclohexyl Moieties at P1 (pdb code 1d6w). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Structure of Thrombin Complexed with Selective Non-Electrophilic Inhibitors Having Cyclohexyl Moieties at P1, PDB code: 1d6w:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Structure of Thrombin Complexed with Selective Non-Electrophilic Inhibitors Having Cyclohexyl Moieties at P1


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of Thrombin Complexed with Selective Non-Electrophilic Inhibitors Having Cyclohexyl Moieties at P1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na950 b:27.9 occ:0.98 O A:HOH494 2.2 18.0 0.8 O A:THR172 2.4 23.5 1.0 O A:LYS169 2.5 23.4 1.0 O A:HOH497 2.9 33.6 1.0 C A:THR172 3.6 22.9 1.0 C A:LYS169 3.6 21.7 1.0 CA A:ASP170 4.1 22.2 1.0 N A:ASP170 4.2 21.6 1.0 N A:THR172 4.4 23.0 1.0 N A:ARG173 4.4 23.7 1.0 C A:ASP170 4.5 22.5 1.0 CA A:ARG173 4.5 25.9 1.0 OD2 A:ASP170 4.5 25.2 1.0 CA A:THR172 4.6 21.6 1.0 CA A:LYS169 4.7 22.9 1.0 O A:HOH493 4.7 33.3 0.6 CG2 A:THR172 4.9 15.4 1.0 N A:SER171 5.0 22.9 1.0 O A:ASP170 5.0 22.6 1.0

Sodium binding site 2 out of 2 in the Structure of Thrombin Complexed with Selective Non-Electrophilic Inhibitors Having Cyclohexyl Moieties at P1


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of Thrombin Complexed with Selective Non-Electrophilic Inhibitors Having Cyclohexyl Moieties at P1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na951 b:31.0 occ:0.95 O A:HOH459 2.2 28.2 1.0 O A:LYS224 2.4 28.4 1.0 O A:ARG221A 2.4 31.6 1.0 O A:HOH460 2.7 23.9 0.9 O A:HOH530 2.7 28.7 0.6 O A:HOH430 3.3 29.7 1.0 C A:ARG221A 3.4 31.8 1.0 C A:LYS224 3.4 27.5 1.0 O A:HOH405 3.5 23.7 0.8 N A:ARG221A 3.7 30.3 1.0 C A:ASP221 3.9 29.6 1.0 N A:LYS224 4.0 28.4 1.0 O A:HOH496 4.0 28.2 0.9 O A:HOH407 4.0 19.4 1.0 CA A:ASP221 4.0 29.1 1.0 OD1 A:ASP221 4.1 29.8 1.0 CA A:ARG221A 4.1 31.4 1.0 CA A:LYS224 4.2 27.7 1.0 O A:TYR184A 4.3 28.2 1.0 O A:HOH415 4.3 32.8 1.0 N A:ASP222 4.3 32.1 1.0 N A:TYR225 4.4 25.8 1.0 O A:ASP221 4.5 29.7 1.0 OD1 A:ASP189 4.5 24.0 1.0 CA A:ASP222 4.5 32.3 1.0 CA A:TYR225 4.7 24.0 1.0 N A:GLY223 4.7 30.7 1.0 N A:ASP221 4.7 29.0 1.0 CB A:LYS224 4.7 30.3 1.0 C A:ASP222 4.8 31.7 1.0

R.Krishnan, I.Mochalkin, R.Arni, A.Tulinsky. Structure of Thrombin Complexed with Selective Non-Electrophilic Inhibitors Having Cyclohexyl Moieties at P1. Acta Crystallogr.,Sect.D V. 56 294 2000.
ISSN: ISSN 0907-4449
PubMed: 10713516
DOI: 10.1107/S0907444900000068