Sodium in PDB 6rot: Thrombin in Complex with MI2105

All present enzymatic activity of Thrombin in Complex with MI2105:
3.4.21.5;

The structure of Thrombin in Complex with MI2105, PDB code: 6rot was solved by A.Sandner, A.Heine, G.Klebe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.52 / 1.34
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	69.926, 71.177, 73.006, 90.00, 100.72, 90.00
R / Rfree (%)	13.7 / 15.7

The structure of Thrombin in Complex with MI2105 also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Sodium atom in the Thrombin in Complex with MI2105 (pdb code 6rot). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Thrombin in Complex with MI2105, PDB code: 6rot:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Thrombin in Complex with MI2105


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Thrombin in Complex with MI2105 within 5.0Å range: probe atom residue distance (Å) B Occ H:Na305 b:14.9 occ:1.00 O H:PHE204A 2.4 14.6 1.0 O H:HOH485 2.4 19.7 1.0 C H:PHE204A 3.5 14.2 1.0 HA H:PHE204A 3.5 17.1 1.0 CA H:PHE204A 4.0 14.2 1.0 HA H:ASN204B 4.2 18.7 1.0 O H:PRO204 4.5 14.9 1.0 N H:ASN204B 4.6 15.7 1.0 HB3 H:PHE204A 4.6 17.3 1.0 HD21 H:ASN205 4.7 41.2 1.0 CA H:ASN204B 4.9 15.6 1.0 CB H:PHE204A 5.0 14.4 1.0 HD22 H:ASN205 5.0 41.2 1.0

Sodium binding site 2 out of 2 in the Thrombin in Complex with MI2105


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Thrombin in Complex with MI2105 within 5.0Å range: probe atom residue distance (Å) B Occ H:Na306 b:19.7 occ:1.00 O H:ARG221A 2.3 21.3 1.0 O H:HOH564 2.3 21.9 1.0 O H:LYS224 2.4 17.7 1.0 O H:HOH473 2.4 21.8 1.0 O H:HOH481 2.4 18.4 1.0 O H:HOH502 2.7 22.1 1.0 H H:LYS224 3.3 22.4 1.0 C H:ARG221A 3.4 22.2 1.0 C H:LYS224 3.4 17.4 1.0 HA H:ASP221 3.7 26.8 1.0 HA H:ASP222 3.8 28.1 1.0 N H:LYS224 3.9 18.6 1.0 O H:HOH505 3.9 20.4 1.0 HB2 H:LYS224 3.9 22.4 1.0 N H:ARG221A 3.9 22.2 1.0 H H:GLY223 3.9 26.0 1.0 H H:ARG221A 3.9 26.6 1.0 O H:HOH489 4.0 25.2 1.0 HA H:TYR225 4.0 19.7 1.0 C H:ASP221 4.1 22.9 1.0 O H:TYR184A 4.1 19.3 1.0 CA H:LYS224 4.1 17.9 1.0 O H:HOH482 4.2 19.0 1.0 N H:ASP222 4.2 23.7 1.0 N H:GLY223 4.3 21.7 1.0 CA H:ARG221A 4.3 22.6 1.0 CA H:ASP222 4.3 23.4 1.0 CA H:ASP221 4.4 22.4 1.0 N H:TYR225 4.4 16.8 1.0 CB H:LYS224 4.5 18.7 1.0 C H:ASP222 4.5 22.6 1.0 O H:ASP221 4.6 24.5 1.0 OD1 H:ASP221 4.6 22.6 1.0 CA H:TYR225 4.7 16.4 1.0 C H:GLY223 4.8 19.3 1.0 HB2 H:ARG221A 4.8 27.9 1.0 H H:ASP221 4.9 25.8 1.0 O H:HOH504 4.9 22.6 1.0 HB2 H:ASP189 5.0 21.6 1.0 HA H:ARG221A 5.0 27.1 1.0 HA3 H:GLY184 5.0 19.1 1.0

A.Sandner, T.Hufner-Wulsdorf, A.Heine, T.Steinmetzer, G.Klebe. Strategies For Late-Stage Optimization: Profiling Thermodynamics By Preorganization and Salt Bridge Shielding. J.Med.Chem. V. 62 9753 2019.
ISSN: ISSN 0022-2623
PubMed: 31633354
DOI: 10.1021/ACS.JMEDCHEM.9B01196