Sodium in PDB 8cb4: The Transcriptional Regulator Prfa From Listeria Monocytogenes in Complex with Tripeptide Leu-Leu-Leu

The structure of The Transcriptional Regulator Prfa From Listeria Monocytogenes in Complex with Tripeptide Leu-Leu-Leu, PDB code: 8cb4 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)	44.42 / 2.57
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	48.099, 86.785, 115.864, 90, 90, 90
R / Rfree (%)	20.8 / 27.7

The binding sites of Sodium atom in the The Transcriptional Regulator Prfa From Listeria Monocytogenes in Complex with Tripeptide Leu-Leu-Leu (pdb code 8cb4). 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 Leu-Leu-Leu, PDB code: 8cb4:
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 Leu-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 Tripeptide Leu-Leu-Leu within 5.0Å range: probe atom residue distance (Å) B Occ A:Na301 b:48.9 occ:1.00 O A:ASN30 2.5 45.8 1.0 O A:HOH411 2.5 60.4 1.0 O A:HOH413 2.6 34.8 1.0 O A:HOH402 2.6 42.0 1.0 OE1 A:GLU36 2.9 37.3 1.0 HB3 A:ASP33 3.3 65.4 1.0 HB2 A:SER71 3.4 50.0 1.0 O A:ASP33 3.4 50.9 1.0 HD1 A:PHE29 3.6 46.8 1.0 HB2 A:PHE29 3.6 65.4 1.0 C A:ASN30 3.7 35.8 1.0 CD A:GLU36 3.8 53.0 1.0 HA A:GLN31 3.8 40.7 1.0 H A:ASN30 3.8 28.6 1.0 OE2 A:GLU36 3.9 37.8 1.0 H A:ASP33 4.0 52.8 1.0 OG A:SER71 4.0 37.5 1.0 HG A:SER71 4.0 45.1 1.0 CB A:SER71 4.1 41.6 1.0 HA A:GLU36 4.1 57.7 1.0 O A:GLN35 4.1 42.4 1.0 CD1 A:PHE29 4.2 38.9 1.0 CB A:ASP33 4.2 54.4 1.0 HB3 A:SER71 4.2 50.0 1.0 N A:ASN30 4.3 23.8 1.0 O A:HOH412 4.4 44.1 1.0 C A:ASP33 4.4 62.1 1.0 CA A:GLN31 4.5 33.8 1.0 CB A:PHE29 4.5 54.4 1.0 N A:ASP33 4.5 44.0 1.0 N A:GLN31 4.5 38.5 1.0 HB2 A:ASP33 4.6 65.4 1.0 CA A:ASP33 4.6 46.7 1.0 CA A:ASN30 4.6 39.9 1.0 CG A:PHE29 4.7 28.2 1.0 C A:GLN31 4.8 44.2 1.0 O A:TYR83 4.8 41.6 1.0 HD1 A:TYR37 4.9 62.9 1.0 C A:GLN35 5.0 46.9 1.0 CE1 A:PHE29 5.0 54.0 1.0 CA A:GLU36 5.0 48.0 1.0

Sodium binding site 2 out of 2 in the The Transcriptional Regulator Prfa From Listeria Monocytogenes in Complex with Tripeptide Leu-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 Tripeptide Leu-Leu-Leu within 5.0Å range: probe atom residue distance (Å) B Occ B:Na301 b:55.1 occ:1.00 O B:HOH407 2.4 43.2 1.0 O B:HOH404 2.5 48.5 1.0 O B:ASN30 2.5 38.3 1.0 O B:HOH416 2.6 46.4 1.0 OE1 B:GLU36 3.0 38.6 1.0 HB3 B:ASP33 3.2 72.2 1.0 O B:ASP33 3.3 56.3 1.0 HA B:GLN31 3.5 53.8 1.0 HG B:SER71 3.5 44.5 1.0 C B:ASN30 3.6 37.9 1.0 OE2 B:GLU36 3.6 38.2 1.0 CD B:GLU36 3.7 56.8 1.0 HD1 B:PHE29 3.7 35.0 1.0 HB2 B:SER71 3.7 50.9 1.0 H B:ASP33 3.7 44.2 1.0 H B:ASN30 3.8 41.9 1.0 HB2 B:PHE29 4.0 56.4 1.0 CB B:ASP33 4.1 60.1 1.0 OG B:SER71 4.1 37.0 1.0 O B:GLN35 4.2 48.7 1.0 CA B:GLN31 4.2 44.7 1.0 HA B:GLU36 4.2 55.2 1.0 C B:ASP33 4.3 47.4 1.0 N B:ASP33 4.3 36.7 1.0 N B:GLN31 4.3 37.9 1.0 CD1 B:PHE29 4.3 29.1 1.0 N B:ASN30 4.3 34.9 1.0 CB B:SER71 4.4 42.4 1.0 C B:GLN31 4.4 47.9 1.0 HB2 B:ASP33 4.4 72.2 1.0 CA B:ASP33 4.4 48.4 1.0 O B:GLN31 4.6 52.6 1.0 CA B:ASN30 4.6 43.0 1.0 O B:TYR83 4.6 44.0 1.0 HB3 B:SER71 4.7 50.9 1.0 CB B:PHE29 4.8 46.9 1.0 N B:TRP32 4.8 46.4 1.0 HD1 B:TYR37 5.0 57.3 1.0 CG B:PHE29 5.0 36.8 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.