Sodium in PDB 8cb5: The Transcriptional Regulator Prfa From Listeria Monocytogenes in Complex with Tripeptide Glu-Val-Phe

The structure of The Transcriptional Regulator Prfa From Listeria Monocytogenes in Complex with Tripeptide Glu-Val-Phe, PDB code: 8cb5 was solved by M.Oelker, A.E.Sauer-Eriksson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.33 / 2.25
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	48.197, 87.306, 112.642, 90, 90, 90
R / Rfree (%)	21.4 / 26.5

The binding sites of Sodium atom in the The Transcriptional Regulator Prfa From Listeria Monocytogenes in Complex with Tripeptide Glu-Val-Phe (pdb code 8cb5). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the The Transcriptional Regulator Prfa From Listeria Monocytogenes in Complex with Tripeptide Glu-Val-Phe, PDB code: 8cb5:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the The Transcriptional Regulator Prfa From Listeria Monocytogenes in Complex with Tripeptide Glu-Val-Phe


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of The Transcriptional Regulator Prfa From Listeria Monocytogenes in Complex with Tripeptide Glu-Val-Phe within 5.0Å range: probe atom residue distance (Å) B Occ A:Na302 b:57.0 occ:1.00 O A:HOH413 2.3 56.7 1.0 O A:ASN30 2.6 46.9 1.0 O A:HOH407 2.8 41.6 1.0 O A:HOH417 3.1 58.6 1.0 OE1 A:GLU36 3.2 71.2 1.0 O A:ASP33 3.4 63.9 1.0 C A:ASN30 3.7 41.3 1.0 CD A:GLU36 4.0 72.9 1.0 OE2 A:GLU36 4.1 70.6 1.0 CD1 A:PHE29 4.2 42.7 1.0 O A:GLN35 4.2 56.7 1.0 CB A:SER71 4.2 43.8 1.0 CA A:GLN31 4.3 43.0 1.0 CB A:ASP33 4.4 57.3 1.0 N A:ASN30 4.4 37.6 1.0 C A:ASP33 4.4 53.0 1.0 N A:GLN31 4.4 38.6 1.0 O A:TYR83 4.5 34.3 1.0 N A:ASP33 4.5 55.1 1.0 O A:HOH401 4.6 49.8 1.0 OG A:SER71 4.6 49.6 1.0 C A:GLN31 4.6 52.3 1.0 CA A:ASN30 4.7 48.6 1.0 CA A:ASP33 4.7 62.2 1.0 CB A:PHE29 4.7 41.4 1.0 CG A:PHE29 4.7 46.2 1.0 CE1 A:PHE29 4.8 45.1 1.0

Sodium binding site 2 out of 2 in the The Transcriptional Regulator Prfa From Listeria Monocytogenes in Complex with Tripeptide Glu-Val-Phe


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of The Transcriptional Regulator Prfa From Listeria Monocytogenes in Complex with Tripeptide Glu-Val-Phe within 5.0Å range: probe atom residue distance (Å) B Occ B:Na303 b:54.8 occ:1.00 O B:ASN30 2.3 44.3 1.0 O B:HOH407 2.4 55.5 1.0 O B:HOH401 2.5 56.7 1.0 O B:HOH410 2.6 41.4 1.0 OE1 B:GLU36 3.1 50.7 1.0 C B:ASN30 3.5 41.2 1.0 O B:HOH416 3.7 54.4 1.0 OE2 B:GLU36 3.7 60.5 1.0 CD B:GLU36 3.8 62.5 1.0 O B:ASP33 4.1 59.3 1.0 CB B:ASP33 4.1 58.9 1.0 CD1 B:PHE29 4.1 43.1 1.0 N B:ASN30 4.1 37.5 1.0 CA B:GLN31 4.2 47.9 1.0 OG B:SER71 4.2 43.3 1.0 O B:GLN35 4.2 53.2 1.0 N B:GLN31 4.3 45.0 1.0 O B:HOH409 4.4 49.7 1.0 CB B:SER71 4.4 47.8 1.0 O B:TYR83 4.4 43.5 1.0 CA B:ASN30 4.4 39.9 1.0 N B:ASP33 4.5 50.0 1.0 C B:GLN31 4.6 53.7 1.0 CB B:PHE29 4.6 44.2 1.0 CG B:PHE29 4.7 44.9 1.0 CA B:ASP33 4.7 60.1 1.0 O B:HOH408 4.8 42.9 1.0 C B:ASP33 4.8 60.4 1.0 CE1 B:PHE29 4.9 48.8 1.0 O B:GLN31 5.0 50.3 1.0

M.Oelker, C.Lindgren, C.Grundstrom, E.Krypotou, M.Scortti, T.Hainzl, J.Vazquez-Boland, A.E.Sauer-Eriksson. Structural Basis of Promiscuous Inhibition of Virulence Activator Prfa By Nutritional Peptides To Be Published.