Sodium in PDB 8cbi: The Transcriptional Regulator Prfa From Listeria Monocytogenes in Complex with Tetrapeptide Thr-Lys-Pro-Arg

The structure of The Transcriptional Regulator Prfa From Listeria Monocytogenes in Complex with Tetrapeptide Thr-Lys-Pro-Arg, PDB code: 8cbi 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)	48.42 / 2.40
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	56.403, 80.953, 61.793, 90, 110.74, 90
R / Rfree (%)	21.8 / 27

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


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 Thr-Lys-Pro-Arg within 5.0Å range: probe atom residue distance (Å) B Occ A:Na301 b:39.9 occ:1.00 O A:HOH406 2.6 33.7 1.0 O A:HOH409 2.7 39.4 1.0 O A:ASN30 2.7 33.7 1.0 HB3 A:ASP33 2.9 44.3 1.0 O A:ASP33 3.0 49.4 1.0 H A:ASP33 3.1 55.3 1.0 HA A:GLN31 3.2 42.7 1.0 HD1 A:PHE29 3.6 61.0 1.0 N A:ASP33 3.6 46.0 1.0 CB A:ASP33 3.7 36.9 1.0 HD1 A:TYR82 3.8 46.0 1.0 C A:GLN31 3.8 35.0 1.0 O A:GLN31 3.8 42.9 1.0 C A:ASN30 3.8 46.3 1.0 CA A:GLN31 3.9 35.5 1.0 C A:ASP33 3.9 32.2 1.0 CA A:ASP33 3.9 45.9 1.0 HB2 A:ASP33 4.0 44.3 1.0 HB2 A:SER71 4.1 36.0 1.0 HA A:TYR82 4.1 55.4 1.0 H A:TYR83 4.2 44.9 1.0 N A:GLN31 4.3 35.3 1.0 CD1 A:PHE29 4.3 50.8 1.0 N A:TRP32 4.4 42.5 1.0 OE1 A:GLU36 4.4 66.9 1.0 O A:TYR83 4.4 30.7 1.0 HE1 A:PHE29 4.5 61.9 1.0 C A:TRP32 4.6 41.5 1.0 CD1 A:TYR82 4.7 38.3 1.0 HB2 A:PHE29 4.7 48.6 1.0 H A:TRP32 4.7 51.0 1.0 HG A:SER71 4.7 47.6 1.0 CE1 A:PHE29 4.8 51.5 1.0 O A:GLN35 4.8 37.8 1.0 CB A:SER71 4.9 30.0 1.0 HA A:ASP33 4.9 55.1 1.0 CG A:ASP33 4.9 48.4 1.0 H A:ASN30 4.9 48.1 1.0 N A:TYR83 4.9 37.4 1.0 CA A:TRP32 5.0 47.8 1.0 HB3 A:SER71 5.0 36.0 1.0

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


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 Thr-Lys-Pro-Arg within 5.0Å range: probe atom residue distance (Å) B Occ B:Na301 b:33.8 occ:1.00 HB2 B:SER71 2.3 51.2 1.0 OG B:SER79 2.5 27.0 1.0 O B:SER71 2.7 35.5 1.0 O B:HOH409 3.2 40.8 1.0 HB2 B:SER79 3.2 37.2 1.0 CB B:SER71 3.3 42.6 1.0 CB B:SER79 3.4 31.0 1.0 HA B:SER79 3.4 41.0 1.0 O B:GLY81 3.5 40.3 1.0 HG3 B:GLU36 3.5 64.8 1.0 C B:SER71 3.5 40.5 1.0 O B:HOH406 3.6 33.8 1.0 O B:HOH407 3.6 35.2 1.0 HG2 B:GLU36 3.7 64.8 1.0 HB3 B:SER71 3.8 51.2 1.0 H B:VAL80 3.8 32.4 1.0 H B:GLY81 3.8 45.9 1.0 CA B:SER71 3.9 34.4 1.0 CA B:SER79 3.9 34.1 1.0 HA B:SER71 3.9 41.3 1.0 OG B:SER71 4.0 37.4 1.0 CG B:GLU36 4.1 54.0 1.0 HG B:SER71 4.1 44.9 1.0 HA B:GLU36 4.1 46.3 1.0 HB3 B:SER79 4.2 37.2 1.0 HG22 B:VAL80 4.3 35.7 1.0 N B:VAL80 4.4 27.0 1.0 C B:GLY81 4.6 45.5 1.0 C B:SER79 4.6 29.4 1.0 N B:GLY81 4.6 38.2 1.0 N B:GLY72 4.7 30.8 1.0 HA2 B:GLY72 4.7 29.4 1.0 O B:ASP33 4.9 41.8 1.0 CA B:GLU36 5.0 38.6 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.