Sodium in PDB 5e8e: Crystal Structure of Thrombin Bound to An Exosite 1-Specific Iga Fab

All present enzymatic activity of Crystal Structure of Thrombin Bound to An Exosite 1-Specific Iga Fab:
3.4.21.5;

The structure of Crystal Structure of Thrombin Bound to An Exosite 1-Specific Iga Fab, PDB code: 5e8e was solved by T.P.Baglin, J.Langdown, R.Frasson, J.A.Huntington, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	60.83 / 1.90
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	66.769, 92.229, 147.487, 90.00, 90.00, 90.00
R / Rfree (%)	20.1 / 24.4

The binding sites of Sodium atom in the Crystal Structure of Thrombin Bound to An Exosite 1-Specific Iga Fab (pdb code 5e8e). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Crystal Structure of Thrombin Bound to An Exosite 1-Specific Iga Fab, PDB code: 5e8e:

Sodium binding site 1 out of 1 in the Crystal Structure of Thrombin Bound to An Exosite 1-Specific Iga Fab


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 Thrombin Bound to An Exosite 1-Specific Iga Fab within 5.0Å range: probe atom residue distance (Å) B Occ H:Na610 b:34.1 occ:1.00 O H:HOH822 2.2 35.2 1.0 O H:ARG553 2.4 28.9 1.0 O H:HOH750 2.4 27.0 1.0 O H:HOH770 2.4 29.3 1.0 O H:LYS556 2.5 27.2 1.0 O H:HOH764 2.7 32.4 1.0 C H:ARG553 3.4 29.9 1.0 C H:LYS556 3.6 26.5 1.0 O H:HOH855 3.8 27.5 1.0 O H:HOH803 3.9 30.9 1.0 N H:LYS556 3.9 29.4 1.0 N H:ARG553 4.0 27.8 1.0 C H:ASP552 4.0 27.4 1.0 O H:TYR510 4.0 31.4 1.0 O H:HOH765 4.1 25.9 1.0 N H:ASP554 4.2 30.5 1.0 N H:GLY555 4.2 29.3 1.0 CA H:ASP554 4.3 31.1 1.0 CA H:ASP552 4.3 26.7 1.0 CA H:LYS556 4.3 27.8 1.0 CA H:ARG553 4.3 27.9 1.0 O H:ASP552 4.3 27.6 1.0 OD1 H:ASP552 4.4 30.7 1.0 O H:HOH727 4.5 31.2 1.0 C H:ASP554 4.5 29.4 1.0 CB H:LYS556 4.6 26.7 1.0 N H:TYR557 4.7 26.5 1.0 CA H:TYR557 4.9 26.7 1.0 C H:GLY555 5.0 29.8 1.0

T.P.Baglin, J.Langdown, R.Frasson, J.A.Huntington. Discovery and Characterization of An Antibody Directed Against Exosite I of Thrombin. J.Thromb.Haemost. V. 14 137 2016.
ISSN: ESSN 1538-7836
PubMed: 26469093
DOI: 10.1111/JTH.13171