Sodium in PDB 1doj: Crystal Structure of Human Alpha-Thrombin*Rwj-51438 Complex at 1.7 A

All present enzymatic activity of Crystal Structure of Human Alpha-Thrombin*Rwj-51438 Complex at 1.7 A:
3.4.21.5;

The structure of Crystal Structure of Human Alpha-Thrombin*Rwj-51438 Complex at 1.7 A, PDB code: 1doj was solved by R.Recacha, M.J.Costanzo, B.E.Maryanoff, M.Carson, L.Delucas, D.Chattopadhyay, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	8.00 / 1.70
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	62.982, 117.521, 47.989, 90.00, 90.00, 90.00
R / Rfree (%)	17.4 / 21.7

The binding sites of Sodium atom in the Crystal Structure of Human Alpha-Thrombin*Rwj-51438 Complex at 1.7 A (pdb code 1doj). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of Human Alpha-Thrombin*Rwj-51438 Complex at 1.7 A, PDB code: 1doj:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Human Alpha-Thrombin*Rwj-51438 Complex at 1.7 A


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Human Alpha-Thrombin*Rwj-51438 Complex at 1.7 A within 5.0Å range: probe atom residue distance (Å) B Occ A:Na300 b:14.8 occ:1.00 O A:ARG221A 2.4 14.9 1.0 O A:LYS224 2.5 12.1 1.0 O A:HOH713 2.5 16.8 1.0 O A:HOH714 2.5 14.3 1.0 O A:HOH595 2.6 14.6 1.0 O A:HOH531 2.6 12.2 1.0 C A:ARG221A 3.4 15.0 1.0 C A:LYS224 3.5 13.0 1.0 N A:LYS224 3.8 14.1 1.0 N A:ARG221A 3.8 12.6 1.0 O A:HOH715 3.9 15.3 1.0 O A:HOH596 3.9 12.0 1.0 O A:TYR184A 4.0 13.5 1.0 C A:ASP221 4.0 12.7 1.0 N A:ASP222 4.1 14.7 1.0 CA A:ASP222 4.2 15.4 1.0 CA A:LYS224 4.2 14.1 1.0 N A:GLY223 4.2 15.0 1.0 O A:HOH597 4.3 11.6 1.0 CA A:ARG221A 4.3 13.5 1.0 CA A:ASP221 4.3 12.7 1.0 C A:ASP222 4.4 15.9 1.0 O A:HOH749 4.5 20.6 1.0 CB A:LYS224 4.5 14.9 1.0 O A:ASP221 4.5 14.5 1.0 N A:TYR225 4.6 11.8 1.0 OD1 A:ASP221 4.6 13.7 1.0 C A:GLY223 4.8 15.1 1.0 CA A:TYR225 4.8 12.0 1.0 CD1 A:TYR225 5.0 15.2 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Human Alpha-Thrombin*Rwj-51438 Complex at 1.7 A


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Human Alpha-Thrombin*Rwj-51438 Complex at 1.7 A within 5.0Å range: probe atom residue distance (Å) B Occ A:Na301 b:35.3 occ:1.00 O A:ILE174 2.7 22.9 1.0 O A:THR172 2.7 20.2 1.0 O A:LYS169 2.8 21.9 1.0 O A:HOH684 2.9 33.8 1.0 CA A:LYS169 3.5 19.8 1.0 C A:LYS169 3.5 20.1 1.0 CG A:LYS169 3.6 22.9 0.5 CG1 A:ILE176 3.7 22.0 1.0 C A:THR172 3.7 21.1 1.0 C A:ILE174 3.8 22.6 1.0 CB A:LYS169 3.9 20.9 0.5 CD A:LYS169 3.9 23.2 0.5 CB A:LYS169 4.0 20.1 0.5 CD1 A:ILE176 4.2 25.6 1.0 N A:ILE176 4.2 22.3 1.0 C A:ARG173 4.3 24.5 1.0 N A:ILE174 4.4 23.6 1.0 CA A:ARG175 4.4 23.6 1.0 N A:ARG175 4.5 21.8 1.0 O A:ARG173 4.5 26.7 1.0 CA A:THR172 4.5 21.7 1.0 CB A:THR172 4.5 19.6 1.0 N A:ARG173 4.6 23.1 1.0 CA A:ARG173 4.7 25.5 1.0 N A:THR172 4.7 21.2 1.0 CB A:ILE176 4.7 22.5 1.0 CA A:ILE174 4.7 22.1 1.0 C A:ARG175 4.7 23.4 1.0 O A:CYS168 4.8 14.8 1.0 N A:LYS169 4.8 16.0 1.0 N A:ASP170 4.8 20.7 1.0 CG A:LYS169 4.9 23.1 0.5

R.Recacha, M.J.Costanzo, B.E.Maryanoff, M.Carson, L.Delucas, D.Chattopadhyay. Structure of Human Alpha-Thrombin Complexed with Rwj-51438 at 1.7 A: Unusual Perturbation of the 60A-60I Insertion Loop. Acta Crystallogr.,Sect.D V. 56 1395 2000.
ISSN: ISSN 0907-4449
PubMed: 11053836
DOI: 10.1107/S0907444900010763