Sodium in PDB 4dn0: Peld 156-455 From Pseudomonas Aeruginosa PA14 in Complex with C-Di-Gmp

The structure of Peld 156-455 From Pseudomonas Aeruginosa PA14 in Complex with C-Di-Gmp, PDB code: 4dn0 was solved by J.C.Whitney, K.M.Colvin, L.S.Marmont, H.Robinson, M.R.Parsek, P.L.Howell, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.90 / 2.30
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	41.776, 82.043, 91.808, 90.00, 90.00, 90.00
R / Rfree (%)	20.1 / 25.2

The binding sites of Sodium atom in the Peld 156-455 From Pseudomonas Aeruginosa PA14 in Complex with C-Di-Gmp (pdb code 4dn0). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Peld 156-455 From Pseudomonas Aeruginosa PA14 in Complex with C-Di-Gmp, PDB code: 4dn0:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Peld 156-455 From Pseudomonas Aeruginosa PA14 in Complex with C-Di-Gmp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Peld 156-455 From Pseudomonas Aeruginosa PA14 in Complex with C-Di-Gmp within 5.0Å range: probe atom residue distance (Å) B Occ A:Na504 b:59.4 occ:1.00 NE A:ARG425 2.8 43.3 1.0 OE1 A:GLU348 2.8 63.0 1.0 CD A:GLU348 3.3 60.1 1.0 NH1 A:ARG425 3.4 44.5 1.0 CB A:GLU348 3.4 34.4 1.0 CZ A:ARG425 3.5 41.7 1.0 CD A:ARG425 3.8 40.5 1.0 OE2 A:GLU348 3.9 67.6 1.0 CG A:GLU348 3.9 46.5 1.0 CG A:ARG425 4.0 36.2 1.0 CB A:ARG423 4.2 34.3 1.0 O A:ARG423 4.8 33.7 1.0 CA A:GLU348 4.8 34.0 1.0 NH2 A:ARG425 4.8 34.7 1.0

Sodium binding site 2 out of 2 in the Peld 156-455 From Pseudomonas Aeruginosa PA14 in Complex with C-Di-Gmp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Peld 156-455 From Pseudomonas Aeruginosa PA14 in Complex with C-Di-Gmp within 5.0Å range: probe atom residue distance (Å) B Occ A:Na505 b:86.5 occ:1.00 N A:ASP450 3.4 53.5 1.0 CG A:ASP450 3.7 70.9 1.0 OD1 A:ASP450 3.8 72.4 1.0 OD2 A:ASP450 3.9 76.2 1.0 CA A:ASN449 3.9 49.0 1.0 CB A:ASN449 4.0 51.4 1.0 CB A:ASP450 4.0 63.5 1.0 C A:ASN449 4.2 50.1 1.0 CA A:ASP450 4.3 57.2 1.0 CG A:PHE443 4.6 40.9 1.0 CD2 A:PHE443 4.7 40.4 1.0 CD1 A:PHE443 4.8 42.8 1.0 CE2 A:PHE443 5.0 41.6 1.0 CE1 A:PHE443 5.0 48.2 1.0 O A:LEU448 5.0 38.8 1.0

J.C.Whitney, K.M.Colvin, L.S.Marmont, H.Robinson, M.R.Parsek, P.L.Howell. Structure of the Cytoplasmic Region of Peld, A Degenerate Diguanylate Cyclase Receptor That Regulates Exopolysaccharide Production in Pseudomonas Aeruginosa. J.Biol.Chem. V. 287 23582 2012.
ISSN: ISSN 0021-9258
PubMed: 22605337
DOI: 10.1074/JBC.M112.375378