Sodium in PDB 6qvy: The Transcriptional Regulator Prfa-A94V Mutant From Listeria Monocytogenes

The structure of The Transcriptional Regulator Prfa-A94V Mutant From Listeria Monocytogenes, PDB code: 6qvy 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)	48.51 / 1.69
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	47.516, 88.571, 115.955, 90.00, 90.00, 90.00
R / Rfree (%)	14.9 / 20.7

The binding sites of Sodium atom in the The Transcriptional Regulator Prfa-A94V Mutant From Listeria Monocytogenes (pdb code 6qvy). 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-A94V Mutant From Listeria Monocytogenes, PDB code: 6qvy:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the The Transcriptional Regulator Prfa-A94V 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-A94V Mutant From Listeria Monocytogenes within 5.0Å range: probe atom residue distance (Å) B Occ A:Na304 b:21.0 occ:1.00 O A:HOH403 2.2 30.4 1.0 O A:HOH452 2.3 24.5 1.0 O A:HOH466 2.4 19.0 1.0 O A:ASN30 2.5 17.7 1.0 OE1 A:GLU36 2.6 22.2 1.0 CD A:GLU36 3.5 23.1 1.0 O A:HOH458 3.5 30.1 1.0 OE2 A:GLU36 3.6 22.5 1.0 C A:ASN30 3.6 16.9 1.0 O A:ASP33 3.9 32.0 1.0 OG A:SER71 4.1 16.5 1.0 O A:GLN35 4.2 24.7 1.0 CB A:ASP33 4.2 30.6 1.0 CA A:GLN31 4.3 20.5 1.0 CB A:SER71 4.3 16.2 1.0 N A:ASN30 4.4 17.8 1.0 CD1 A:PHE29 4.4 16.6 1.0 N A:GLN31 4.4 17.4 1.0 O A:HOH472 4.4 20.3 1.0 O A:TYR83 4.5 17.2 1.0 N A:ASP33 4.6 24.5 1.0 O A:HOH433 4.6 19.3 1.0 C A:GLN31 4.6 24.5 1.0 CA A:ASN30 4.6 16.6 1.0 C A:ASP33 4.8 32.8 1.0 O A:HOH449 4.8 44.9 1.0 CB A:PHE29 4.8 17.9 1.0 CA A:ASP33 4.8 30.1 1.0 CG A:GLU36 4.9 20.8 1.0 CG A:PHE29 4.9 18.0 1.0 O A:GLN31 5.0 26.1 1.0

Sodium binding site 2 out of 3 in the The Transcriptional Regulator Prfa-A94V 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-A94V Mutant From Listeria Monocytogenes within 5.0Å range: probe atom residue distance (Å) B Occ A:Na305 b:51.4 occ:1.00 O A:ASN237 2.3 40.2 1.0 O A:HOH424 2.4 48.9 1.0 O A:GLY234 2.4 32.1 1.0 C A:ASN237 3.2 39.2 1.0 C A:GLY234 3.4 32.4 1.0 CA A:GLY234 3.8 28.7 1.0 OXT A:ASN237 3.9 44.5 1.0 CA A:ASN237 4.1 29.5 1.0 N A:ASN237 4.1 26.3 1.0 CB A:ASN237 4.4 28.5 1.0 O A:HOH491 4.5 53.0 1.0 N A:LYS235 4.6 32.2 1.0 C A:LYS235 5.0 33.8 1.0

Sodium binding site 3 out of 3 in the The Transcriptional Regulator Prfa-A94V 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-A94V Mutant From Listeria Monocytogenes within 5.0Å range: probe atom residue distance (Å) B Occ B:Na304 b:25.0 occ:1.00 O B:HOH425 2.4 23.4 1.0 O B:HOH461 2.5 21.1 1.0 O B:ASN30 2.5 17.7 1.0 O B:ASP33 2.6 25.3 1.0 OE1 B:GLU36 2.8 24.8 1.0 O B:HOH462 3.1 31.7 1.0 CD B:GLU36 3.5 24.5 1.0 OE2 B:GLU36 3.5 26.6 1.0 C B:ASN30 3.7 17.9 1.0 C B:ASP33 3.8 26.0 1.0 O B:GLN35 4.1 24.4 1.0 CB B:ASP33 4.1 28.9 1.0 N B:ASP33 4.2 23.5 1.0 O B:HOH485 4.2 36.1 1.0 CA B:ASP33 4.2 22.5 1.0 O B:HOH444 4.3 23.6 1.0 N B:ASN30 4.3 16.2 1.0 OG B:SER71 4.5 20.4 1.0 CA B:GLN31 4.5 18.6 1.0 N B:GLN31 4.5 17.0 1.0 O B:TYR83 4.5 18.1 1.0 CD1 B:PHE29 4.6 16.0 1.0 CA B:ASN30 4.6 15.8 1.0 O B:HOH441 4.7 22.1 1.0 CB B:SER71 4.7 19.9 1.0 C B:GLN31 4.7 19.4 1.0 CB B:PHE29 4.9 16.1 1.0 CG B:ASP33 4.9 25.6 1.0 N B:PRO34 4.9 27.8 1.0 C B:GLN35 4.9 21.9 1.0 CG B:GLU36 4.9 22.9 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