Sodium in PDB 6qw1: The Transcriptional Regulator Prfa-L140F Mutant From Listeria Monocytogenes

The structure of The Transcriptional Regulator Prfa-L140F Mutant From Listeria Monocytogenes, PDB code: 6qw1 was solved by M.Hall, C.Grundstrom, S.Hansen, K.Brannstrom, J.Johansson, A.E.Sauer-Eriksson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.40 / 1.84
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	47.634, 88.806, 115.439, 90.00, 90.00, 90.00
R / Rfree (%)	18.1 / 24.1

The binding sites of Sodium atom in the The Transcriptional Regulator Prfa-L140F Mutant From Listeria Monocytogenes (pdb code 6qw1). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the The Transcriptional Regulator Prfa-L140F Mutant From Listeria Monocytogenes, PDB code: 6qw1:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the The Transcriptional Regulator Prfa-L140F Mutant From Listeria Monocytogenes


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-L140F Mutant From Listeria Monocytogenes within 5.0Å range: probe atom residue distance (Å) B Occ A:Na305 b:23.2 occ:1.00 O A:HOH413 2.3 29.9 1.0 O A:HOH450 2.3 26.6 1.0 O A:ASN30 2.3 20.3 1.0 O A:HOH500 2.4 17.3 1.0 OE1 A:GLU36 2.5 26.8 1.0 CD A:GLU36 3.4 25.7 1.0 C A:ASN30 3.5 17.7 1.0 O A:HOH447 3.6 29.1 1.0 OE2 A:GLU36 3.6 27.4 1.0 O A:ASP33 4.0 31.4 1.0 OG A:SER71 4.1 21.5 1.0 CA A:GLN31 4.2 20.8 1.0 N A:GLN31 4.2 18.8 1.0 CB A:SER71 4.3 17.1 1.0 N A:ASN30 4.3 19.7 1.0 O A:GLN35 4.3 30.5 1.0 CD1 A:PHE29 4.4 22.5 1.0 CB A:ASP33 4.5 29.5 1.0 O A:HOH493 4.5 26.5 1.0 C A:GLN31 4.5 31.9 1.0 O A:TYR83 4.5 18.2 1.0 CA A:ASN30 4.5 18.4 1.0 O A:HOH428 4.6 21.4 1.0 N A:ASP33 4.6 28.8 1.0 O A:GLN31 4.8 24.4 1.0 CG A:GLU36 4.9 26.5 1.0 CB A:PHE29 4.9 18.5 1.0 C A:ASP33 4.9 33.1 1.0 N A:TRP32 4.9 23.8 1.0 CA A:ASP33 4.9 30.2 1.0 CG A:PHE29 5.0 22.2 1.0

Sodium binding site 2 out of 3 in the The Transcriptional Regulator Prfa-L140F Mutant From Listeria Monocytogenes


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-L140F Mutant From Listeria Monocytogenes within 5.0Å range: probe atom residue distance (Å) B Occ A:Na306 b:46.9 occ:1.00 O A:ASN237 2.4 42.2 1.0 O A:HOH454 2.4 50.7 1.0 O A:GLY234 2.4 31.9 1.0 C A:ASN237 3.1 45.5 1.0 C A:GLY234 3.5 28.3 1.0 OXT A:ASN237 3.7 52.9 1.0 CA A:GLY234 3.8 26.0 1.0 CA A:ASN237 4.1 34.7 1.0 N A:ASN237 4.1 27.3 1.0 O A:HOH434 4.2 63.5 1.0 CB A:ASN237 4.5 30.3 1.0 N A:LYS235 4.6 30.8 1.0 C A:LYS235 4.9 46.2 1.0

Sodium binding site 3 out of 3 in the The Transcriptional Regulator Prfa-L140F Mutant From Listeria Monocytogenes


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of The Transcriptional Regulator Prfa-L140F Mutant From Listeria Monocytogenes within 5.0Å range: probe atom residue distance (Å) B Occ B:Na304 b:28.3 occ:1.00 O B:HOH405 2.2 35.7 1.0 O B:HOH458 2.3 22.8 1.0 O B:HOH437 2.4 24.6 1.0 O B:ASN30 2.5 24.9 1.0 OE1 B:GLU36 2.6 24.0 1.0 CD B:GLU36 3.5 25.9 1.0 C B:ASN30 3.5 17.8 1.0 O B:ASP33 3.6 38.4 1.0 O B:HOH436 3.6 36.5 1.0 OE2 B:GLU36 3.7 27.8 1.0 CB B:ASP33 4.2 39.9 1.0 OG B:SER71 4.2 22.9 1.0 O B:GLN35 4.3 26.2 1.0 N B:ASN30 4.3 19.5 1.0 CB B:SER71 4.3 22.3 1.0 N B:GLN31 4.3 19.3 1.0 O B:HOH450 4.3 24.4 1.0 CA B:GLN31 4.3 19.9 1.0 O B:TYR83 4.4 20.5 1.0 CD1 B:PHE29 4.4 22.6 1.0 N B:ASP33 4.5 30.0 1.0 CA B:ASN30 4.5 21.4 1.0 O B:HOH466 4.6 25.2 1.0 C B:ASP33 4.6 39.9 1.0 CA B:ASP33 4.7 30.5 1.0 C B:GLN31 4.7 27.4 1.0 CB B:PHE29 4.8 24.4 1.0 CG B:PHE29 4.9 23.4 1.0 CG B:GLU36 5.0 23.1 1.0

S.Hansen, M.Hall, C.Grundstrom, K.Brannstrom, A.E.Sauer-Eriksson, J.Johansson. A Novel Growth Based Selection Strategy Identifies New Constitutively Active Variants of the Major Virulence Regulator Prfa Inlisteria Monocytogenes. J.Bacteriol. 2020.
ISSN: ESSN 1098-5530
PubMed: 32179627
DOI: 10.1128/JB.00115-20