Sodium in PDB 6gwe: Crystal Structure of Thrombin Bound to P2 Macrocycle

All present enzymatic activity of Crystal Structure of Thrombin Bound to P2 Macrocycle:
3.4.21.5;

The structure of Crystal Structure of Thrombin Bound to P2 Macrocycle, PDB code: 6gwe was solved by L.Cendron, A.Angelini, S.S.Kale, M.Bergeron-Brlek, Y.Wu, C.Heinis, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	79.72 / 2.30
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	55.943, 80.914, 159.430, 90.00, 90.00, 90.00
R / Rfree (%)	18.6 / 24.4

The binding sites of Sodium atom in the Crystal Structure of Thrombin Bound to P2 Macrocycle (pdb code 6gwe). 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 Thrombin Bound to P2 Macrocycle, PDB code: 6gwe:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Thrombin Bound to P2 Macrocycle


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 P2 Macrocycle within 5.0Å range: probe atom residue distance (Å) B Occ A:Na306 b:52.0 occ:1.00 O A:HOH433 2.3 41.3 1.0 O A:HOH417 2.4 41.5 1.0 O A:LYS224 2.5 42.4 1.0 O A:ARG221 2.5 47.3 1.0 O A:HOH415 2.7 38.2 1.0 O A:HOH438 2.7 43.6 1.0 C A:ARG221 3.4 49.3 1.0 C A:LYS224 3.6 38.0 1.0 O A:HOH418 3.7 34.3 1.0 N A:ARG221 3.8 39.0 1.0 O A:HOH439 3.9 50.7 1.0 C A:ASP221A 4.0 43.7 1.0 N A:LYS224 4.0 46.8 1.0 O A:TYR184 4.1 44.6 1.0 O A:HOH410 4.1 40.4 1.0 N A:ASP222 4.2 48.2 1.0 CA A:ASP221A 4.2 46.2 1.0 CA A:ARG221 4.2 47.5 1.0 CA A:LYS224 4.3 41.2 1.0 CA A:ASP222 4.4 46.4 1.0 OD1 A:ASP221A 4.5 44.0 1.0 N A:GLY223 4.5 47.6 1.0 O A:ASP221A 4.6 39.5 1.0 N A:TYR225 4.6 43.8 1.0 CB A:LYS224 4.6 45.3 1.0 C A:ASP222 4.6 46.8 1.0 CA A:TYR225 4.9 41.5 1.0 O A:HOH437 4.9 41.3 1.0 N A:ASP221A 4.9 49.1 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Thrombin Bound to P2 Macrocycle


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 Thrombin Bound to P2 Macrocycle within 5.0Å range: probe atom residue distance (Å) B Occ H:Na304 b:41.5 occ:1.00 O H:HOH437 2.2 37.9 1.0 O H:ARG221 2.4 42.2 1.0 O H:LYS224 2.6 41.5 1.0 O H:HOH469 2.7 36.2 1.0 O H:HOH462 2.9 32.1 1.0 O H:HOH461 2.9 45.5 1.0 C H:ARG221 3.2 47.3 1.0 C H:LYS224 3.6 42.1 1.0 N H:ARG221 3.7 34.0 1.0 N H:ASP222 3.9 52.8 1.0 C H:ASP221A 3.9 36.5 1.0 N H:LYS224 4.0 43.8 1.0 O H:HOH451 4.0 32.4 1.0 O H:HOH420 4.0 38.4 1.0 CA H:ARG221 4.1 41.6 1.0 CA H:ASP222 4.1 48.3 1.0 O H:TYR184 4.2 37.5 1.0 N H:GLY223 4.3 42.4 1.0 CA H:ASP221A 4.3 31.6 1.0 CA H:LYS224 4.3 48.7 1.0 O H:ASP221A 4.4 39.4 1.0 C H:ASP222 4.4 44.9 1.0 OD1 H:ASP221A 4.4 39.4 1.0 N H:TYR225 4.6 40.0 1.0 CB H:LYS224 4.7 45.0 1.0 CA H:TYR225 4.9 29.8 1.0 C H:GLY223 5.0 42.1 1.0

S.S.Kale, M.Bergeron-Brlek, Y.Wu, M.G.Kumar, M.V.Pham, J.Bortoli, J.Vesin, X.D.Kong, J.F.Machado, K.Deyle, P.Gonschorek, G.Turcatti, L.Cendron, A.Angelini, C.Heinis. Thiol-to-Amine Cyclization Reaction Enables Screening of Large Libraries of Macrocyclic Compounds and the Generation of Sub-Kilodalton Ligands. Sci Adv V. 5 W2851 2019.
ISSN: ESSN 2375-2548
PubMed: 31457083
DOI: 10.1126/SCIADV.AAW2851