Sodium in PDB 8cb8: The Transcriptional Regulator Prfa From Listeria Monocytogenes in Complex with Tetrapeptide Ser-Thr-Leu-Leu

The structure of The Transcriptional Regulator Prfa From Listeria Monocytogenes in Complex with Tetrapeptide Ser-Thr-Leu-Leu, PDB code: 8cb8 was solved by M.Oelker, C.Lindgren, A.E.Sauer-Eriksson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.89 / 2.25
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	47.952, 86.133, 115.217, 90, 90, 90
R / Rfree (%)	22.4 / 28.7

The binding sites of Sodium atom in the The Transcriptional Regulator Prfa From Listeria Monocytogenes in Complex with Tetrapeptide Ser-Thr-Leu-Leu (pdb code 8cb8). 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 Tetrapeptide Ser-Thr-Leu-Leu, PDB code: 8cb8:
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 Tetrapeptide Ser-Thr-Leu-Leu


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 Tetrapeptide Ser-Thr-Leu-Leu within 5.0Å range: probe atom residue distance (Å) B Occ A:Na702 b:37.1 occ:1.00 O A:HOH806 2.3 54.6 1.0 O A:HOH814 2.3 35.2 1.0 O A:HOH818 2.4 30.5 1.0 O A:ASN30 2.5 41.1 1.0 OE1 A:GLU36 2.9 41.5 1.0 C A:ASN30 3.6 26.4 1.0 CD A:GLU36 3.8 47.7 1.0 O A:ASP33 3.8 45.9 1.0 OE2 A:GLU36 3.9 42.5 1.0 OG A:SER71 4.0 31.5 1.0 CD1 A:PHE29 4.2 30.3 1.0 CB A:SER71 4.2 41.0 1.0 O A:GLN35 4.2 41.3 1.0 CA A:GLN31 4.3 40.0 1.0 N A:ASN30 4.4 28.0 1.0 CB A:ASP33 4.4 44.9 1.0 N A:GLN31 4.4 35.3 1.0 O A:TYR83 4.4 27.4 1.0 C A:GLN31 4.5 51.9 1.0 N A:ASP33 4.6 41.0 1.0 CB A:PHE29 4.6 32.3 1.0 CA A:ASN30 4.7 36.9 1.0 C A:ASP33 4.7 44.1 1.0 CG A:PHE29 4.7 28.8 1.0 O A:HOH808 4.8 36.0 1.0 O A:GLN31 4.8 41.4 1.0 CA A:ASP33 4.8 48.0 1.0 CE1 A:PHE29 5.0 40.0 1.0

Sodium binding site 2 out of 2 in the The Transcriptional Regulator Prfa From Listeria Monocytogenes in Complex with Tetrapeptide Ser-Thr-Leu-Leu


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 Tetrapeptide Ser-Thr-Leu-Leu within 5.0Å range: probe atom residue distance (Å) B Occ B:Na702 b:47.0 occ:1.00 O B:HOH820 2.5 34.9 1.0 O B:ASN30 2.6 31.7 1.0 O B:HOH804 2.8 42.8 1.0 OE1 B:GLU36 3.0 40.3 1.0 O B:ASP33 3.0 53.9 1.0 OE2 B:GLU36 3.6 39.9 1.0 CD B:GLU36 3.7 38.3 1.0 C B:ASN30 3.7 26.1 1.0 C B:ASP33 4.1 48.9 1.0 CB B:ASP33 4.1 46.7 1.0 N B:ASP33 4.1 38.0 1.0 CA B:GLN31 4.2 41.8 1.0 O B:GLN35 4.2 40.1 1.0 C B:GLN31 4.3 45.8 1.0 CA B:ASP33 4.3 41.2 1.0 OG B:SER71 4.4 32.5 1.0 N B:GLN31 4.4 30.1 1.0 O B:GLN31 4.4 42.8 1.0 CB B:SER71 4.5 37.1 1.0 O B:TYR83 4.6 27.6 1.0 CD1 B:PHE29 4.6 29.3 1.0 N B:ASN30 4.7 32.9 1.0 O B:HOH809 4.8 42.0 1.0 CA B:ASN30 4.9 36.1 1.0 N B:TRP32 4.9 39.2 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.