Sodium in PDB 5l6n: Disulfated Madanin-Thrombin Complex

All present enzymatic activity of Disulfated Madanin-Thrombin Complex:
3.4.21.5;

The structure of Disulfated Madanin-Thrombin Complex, PDB code: 5l6n was solved by J.Ripoll-Rozada, P.J.B.Pereira, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.70 / 1.63
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	44.546, 80.238, 91.369, 90.00, 90.00, 90.00
R / Rfree (%)	16.7 / 19.9

The binding sites of Sodium atom in the Disulfated Madanin-Thrombin Complex (pdb code 5l6n). 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 Disulfated Madanin-Thrombin Complex, PDB code: 5l6n:

Sodium binding site 1 out of 1 in the Disulfated Madanin-Thrombin Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Disulfated Madanin-Thrombin Complex within 5.0Å range: probe atom residue distance (Å) B Occ H:Na602 b:26.9 occ:1.00 O H:ARG553 2.3 21.0 1.0 O H:HOH844 2.3 26.4 1.0 O H:LYS556 2.4 21.1 1.0 O H:HOH796 2.4 25.6 1.0 O H:HOH767 2.5 22.4 1.0 O H:HOH819 2.7 26.8 1.0 C H:ARG553 3.4 23.2 1.0 C H:LYS556 3.5 19.3 1.0 O H:HOH795 3.8 22.2 1.0 N H:ARG553 3.8 20.4 1.0 N H:LYS556 3.9 23.6 1.0 O H:HOH763 3.9 26.9 1.0 C H:ASP552 4.0 22.4 1.0 O H:TYR510 4.2 23.2 1.0 CA H:LYS556 4.2 23.4 1.0 CA H:ARG553 4.2 22.2 1.0 N H:GLY555 4.2 27.3 1.0 N H:ASP554 4.2 23.6 1.0 CA H:ASP552 4.3 22.3 1.0 O H:HOH810 4.3 21.2 1.0 CA H:ASP554 4.3 28.8 1.0 O H:ASP552 4.5 24.6 1.0 C H:ASP554 4.5 28.8 1.0 N H:TYR557 4.5 18.1 1.0 O H:HOH732 4.6 28.3 1.0 CB H:LYS556 4.6 21.9 1.0 OD1 H:ASP552 4.6 24.0 1.0 CA H:TYR557 4.8 16.8 1.0 C H:GLY555 4.9 26.6 1.0 N H:ASP552 5.0 19.7 1.0 CD1 H:TYR557 5.0 22.1 1.0 O H:HOH843 5.0 26.8 1.0

R.E.Thompson, X.Liu, J.Ripoll-Rozada, N.Alonso-Garcia, B.L.Parker, P.J.B.Pereira, R.J.Payne. Tyrosine Sulfation Modulates Activity of Tick-Derived Thrombin Inhibitors. Nat Chem V. 9 909 2017.
ISSN: ESSN 1755-4349
PubMed: 28837178
DOI: 10.1038/NCHEM.2744