Sodium in PDB 4ldz: Crystal Structure of the Full-Length Response Regulator Desr in the Active State

The structure of Crystal Structure of the Full-Length Response Regulator Desr in the Active State, PDB code: 4ldz was solved by F.Trajtenberg, N.Larrieux, A.Buschiazzo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.92 / 2.31
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	45.612, 77.646, 139.751, 90.00, 90.00, 90.00
R / Rfree (%)	18.9 / 22.1

The structure of Crystal Structure of the Full-Length Response Regulator Desr in the Active State also contains other interesting chemical elements:

Fluorine	(F)	6 atoms
Magnesium	(Mg)	2 atoms

The binding sites of Sodium atom in the Crystal Structure of the Full-Length Response Regulator Desr in the Active State (pdb code 4ldz). 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 the Full-Length Response Regulator Desr in the Active State, PDB code: 4ldz:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of the Full-Length Response Regulator Desr in the Active State


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 the Full-Length Response Regulator Desr in the Active State within 5.0Å range: probe atom residue distance (Å) B Occ A:Na205 b:46.5 occ:1.00 O A:MET27 2.4 35.1 1.0 O A:GLU24 2.4 45.1 1.0 O A:ASN22 2.5 51.2 1.0 O A:HOH313 2.5 34.1 1.0 C A:ASN22 3.6 48.4 1.0 C A:MET27 3.6 36.8 1.0 C A:GLU24 3.6 46.4 1.0 CA A:ASN22 4.2 40.9 1.0 N A:GLU24 4.3 42.3 1.0 N A:MET27 4.3 37.4 1.0 CA A:ASP25 4.4 45.9 1.0 N A:ASP25 4.4 44.8 1.0 O A:ASP25 4.5 45.4 1.0 SD A:MET1 4.5 63.5 1.0 C A:LEU23 4.5 49.8 1.0 C A:ASP25 4.5 46.4 1.0 CA A:MET27 4.5 34.3 1.0 N A:GLU28 4.5 34.3 1.0 OD1 A:ASN22 4.6 38.0 1.0 CA A:GLU24 4.6 41.2 1.0 CA A:GLU28 4.6 34.8 1.0 N A:LEU23 4.6 45.0 1.0 O A:LEU23 4.8 53.8 1.0 O A:LEU21 4.8 41.0 1.0 CA A:LEU23 4.9 46.7 1.0 CE A:MET1 4.9 61.2 1.0 CB A:ASN22 5.0 41.1 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of the Full-Length Response Regulator Desr in the Active State


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 the Full-Length Response Regulator Desr in the Active State within 5.0Å range: probe atom residue distance (Å) B Occ B:Na203 b:46.2 occ:1.00 O B:MET27 2.3 35.3 1.0 O B:GLU24 2.3 38.2 1.0 O B:ASN22 2.6 43.8 1.0 C B:MET27 3.5 36.9 1.0 C B:GLU24 3.5 41.0 1.0 C B:ASN22 3.6 41.9 1.0 CA B:ASN22 4.2 35.9 1.0 N B:MET27 4.2 35.2 1.0 CE B:MET1 4.2 60.0 1.0 CA B:MET27 4.3 34.2 1.0 CA B:ASP25 4.3 43.0 1.0 O B:ASP25 4.3 43.3 1.0 C B:ASP25 4.4 43.2 1.0 N B:ASP25 4.4 41.4 1.0 N B:GLU24 4.4 35.5 1.0 N B:GLU28 4.5 34.1 1.0 OE1 B:GLU28 4.5 85.6 1.0 CA B:GLU24 4.5 34.2 1.0 C B:LEU23 4.6 42.1 1.0 CA B:GLU28 4.6 33.6 1.0 OD1 B:ASN22 4.7 42.1 1.0 N B:LEU23 4.7 39.1 1.0 O B:LEU21 4.8 37.3 1.0 O B:LEU23 4.9 45.1 1.0 CB B:MET27 4.9 36.7 1.0 CB B:ASN22 5.0 37.2 1.0 N B:ASP26 5.0 38.2 1.0 CA B:LEU23 5.0 40.2 1.0

F.Trajtenberg, A.Albanesi, N.Ruetalo, H.Botti, A.Mechaly, L.Cybulski, N.Larrieux, D.De Mendoza, A.Buschiazzo. A Non-Canonical Protein Surface Is Key in Allosteric Control of Response Regulators To Be Published.