Sodium in PDB 3beu: Na+-Dependent Allostery Mediates Coagulation Factor Protease Active Site Selectivity

All present enzymatic activity of Na+-Dependent Allostery Mediates Coagulation Factor Protease Active Site Selectivity:
3.4.21.4;

The structure of Na+-Dependent Allostery Mediates Coagulation Factor Protease Active Site Selectivity, PDB code: 3beu was solved by M.J.Page, C.J.Carrell, E.Di Cera, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	10.00 / 1.05
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	41.786, 72.433, 122.492, 90.00, 90.00, 90.00
R / Rfree (%)	12.1 / 14.6

The structure of Na+-Dependent Allostery Mediates Coagulation Factor Protease Active Site Selectivity also contains other interesting chemical elements:

Calcium

(Ca)

2 atoms

The binding sites of Sodium atom in the Na+-Dependent Allostery Mediates Coagulation Factor Protease Active Site Selectivity (pdb code 3beu). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Na+-Dependent Allostery Mediates Coagulation Factor Protease Active Site Selectivity, PDB code: 3beu:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Na+-Dependent Allostery Mediates Coagulation Factor Protease Active Site Selectivity


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Na+-Dependent Allostery Mediates Coagulation Factor Protease Active Site Selectivity within 5.0Å range: probe atom residue distance (Å) B Occ A:Na248 b:17.5 occ:1.00 O A:HOH451 2.2 30.6 1.0 O A:TYR185 2.4 11.6 1.0 O A:ARG222 2.4 14.2 1.0 O A:LYS224 2.4 12.8 1.0 O A:ASP185A 2.6 14.4 1.0 O A:HOH315 3.3 16.5 1.0 C A:ASP185A 3.4 12.8 1.0 C A:ARG222 3.5 13.9 1.0 C A:TYR185 3.5 10.5 1.0 C A:LYS224 3.5 11.2 1.0 N A:LYS224 3.6 13.5 1.0 N A:GLY223A 3.8 15.3 1.0 CA A:ASP185A 3.9 12.0 1.0 O A:HOH576 3.9 48.0 1.0 CA A:LYS223 4.1 15.1 1.0 CA A:LYS224 4.1 12.8 1.0 O A:HOH289 4.2 13.5 1.0 N A:ASP185A 4.2 11.2 1.0 C A:LYS223 4.2 14.4 1.0 N A:LYS223 4.2 14.4 1.0 N A:ARG222 4.2 12.7 1.0 C A:ALA221 4.2 12.8 1.0 N A:THR185B 4.4 14.0 1.0 C A:GLY223A 4.4 15.1 1.0 O A:ALA221 4.5 15.0 1.0 CA A:ARG222 4.5 13.0 1.0 CA A:GLY223A 4.6 17.5 1.0 CA A:TYR185 4.6 9.8 1.0 N A:TYR225 4.7 11.2 1.0 CA A:THR185B 4.7 15.0 1.0 O A:LYS186 4.7 12.2 1.0 N A:TYR185 4.7 9.5 1.0 CA A:ALA221 4.7 12.4 1.0 CB A:LYS224 4.8 13.0 1.0 CD1 A:TYR225 4.8 13.3 1.0 CE1 A:TYR225 4.9 17.1 1.0 CA A:TYR225 5.0 10.5 1.0

Sodium binding site 2 out of 2 in the Na+-Dependent Allostery Mediates Coagulation Factor Protease Active Site Selectivity


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Na+-Dependent Allostery Mediates Coagulation Factor Protease Active Site Selectivity within 5.0Å range: probe atom residue distance (Å) B Occ B:Na248 b:20.5 occ:1.00 O B:HOH410 2.2 32.9 1.0 O B:LYS224 2.4 16.2 1.0 O B:TYR185 2.4 14.2 1.0 O B:ARG222 2.4 18.2 1.0 O B:ASP185A 2.6 17.9 1.0 C B:ASP185A 3.2 16.1 1.0 O B:HOH334 3.3 19.3 1.0 C B:ARG222 3.4 17.6 1.0 C B:TYR185 3.5 13.6 1.0 C B:LYS224 3.5 15.1 1.0 N B:LYS224 3.7 15.2 1.0 CA B:ASP185A 3.9 15.2 1.0 N B:GLY223A 3.9 17.9 1.0 N B:THR185B 4.1 16.9 1.0 N B:ARG222 4.1 16.4 1.0 C B:ALA221 4.1 16.2 1.0 N B:ASP185A 4.2 15.9 1.0 CA B:LYS224 4.2 15.5 1.0 O B:HOH447 4.2 38.1 1.0 CA B:LYS223 4.2 19.5 1.0 N B:LYS223 4.2 19.2 1.0 O B:HOH294 4.4 15.0 1.0 O B:ALA221 4.4 18.6 1.0 CA B:ARG222 4.4 18.3 1.0 CA B:THR185B 4.4 19.7 1.0 C B:LYS223 4.4 19.7 1.0 CA B:ALA221 4.5 15.1 1.0 C B:GLY223A 4.5 16.8 1.0 N B:TYR225 4.6 14.0 1.0 CA B:TYR185 4.7 12.8 1.0 CA B:GLY223A 4.7 19.1 1.0 N B:TYR185 4.8 12.2 1.0 CB B:LYS224 4.8 16.6 1.0 C B:THR185B 4.8 17.7 1.0 O B:LYS186 4.9 18.2 1.0 CA B:TYR225 5.0 13.3 1.0

M.J.Page, C.J.Carrell, E.Di Cera. Engineering Protein Allostery: 1.05 A Resolution Structure and Enzymatic Properties of A Na+-Activated Trypsin. J.Mol.Biol. V. 378 666 2008.
ISSN: ISSN 0022-2836
PubMed: 18377928
DOI: 10.1016/J.JMB.2008.03.003