Sodium in PDB 6qvz: The Transcriptional Regulator Prfa-L140H Mutant From Listeria Monocytogenes

The structure of The Transcriptional Regulator Prfa-L140H Mutant From Listeria Monocytogenes, PDB code: 6qvz 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)	44.22 / 2.71
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	47.821, 88.465, 116.090, 90.00, 90.00, 90.00
R / Rfree (%)	18.8 / 25.4

The binding sites of Sodium atom in the The Transcriptional Regulator Prfa-L140H Mutant From Listeria Monocytogenes (pdb code 6qvz). 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-L140H Mutant From Listeria Monocytogenes, PDB code: 6qvz:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the The Transcriptional Regulator Prfa-L140H 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-L140H Mutant From Listeria Monocytogenes within 5.0Å range: probe atom residue distance (Å) B Occ A:Na303 b:38.3 occ:1.00 O A:HOH418 2.4 42.7 1.0 O A:HOH420 2.4 39.6 1.0 O A:HOH434 2.4 22.1 1.0 O A:ASN30 2.6 28.0 1.0 OE1 A:GLU36 2.8 34.1 1.0 CD A:GLU36 3.7 39.0 1.0 C A:ASN30 3.7 25.4 1.0 OE2 A:GLU36 3.8 42.8 1.0 O A:ASP33 3.9 37.7 1.0 OG A:SER71 4.0 21.8 1.0 CB A:SER71 4.2 32.5 1.0 CD1 A:PHE29 4.2 27.4 1.0 O A:GLN35 4.3 39.6 1.0 CA A:GLN31 4.3 26.0 1.0 N A:GLN31 4.5 18.9 1.0 N A:ASN30 4.5 23.5 1.0 C A:GLN31 4.6 28.2 1.0 O A:HOH419 4.6 23.6 1.0 O A:HOH465 4.6 24.5 1.0 CB A:ASP33 4.7 35.4 1.0 O A:TYR83 4.7 20.3 1.0 CA A:ASN30 4.7 28.2 1.0 CB A:PHE29 4.8 26.0 1.0 C A:ASP33 4.8 35.6 1.0 N A:ASP33 4.9 34.9 1.0 CG A:PHE29 4.9 29.3 1.0 O A:GLN31 4.9 36.6 1.0 CE1 A:PHE29 4.9 28.4 1.0 CA A:GLU36 4.9 33.5 1.0

Sodium binding site 2 out of 3 in the The Transcriptional Regulator Prfa-L140H 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-L140H Mutant From Listeria Monocytogenes within 5.0Å range: probe atom residue distance (Å) B Occ A:Na304 b:62.5 occ:1.00 O A:ASN237 2.4 56.8 1.0 O A:HOH430 2.6 52.7 1.0 O A:GLY234 2.6 48.4 1.0 C A:ASN237 3.4 57.2 1.0 C A:GLY234 3.6 45.0 1.0 OXT A:ASN237 3.9 57.6 1.0 CA A:GLY234 4.0 41.9 1.0 CA A:ASN237 4.4 47.0 1.0 N A:ASN237 4.5 39.3 1.0 N A:LYS235 4.8 47.7 1.0 O A:HOH424 4.8 46.8 1.0 CB A:ASN237 4.9 46.4 1.0

Sodium binding site 3 out of 3 in the The Transcriptional Regulator Prfa-L140H 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-L140H Mutant From Listeria Monocytogenes within 5.0Å range: probe atom residue distance (Å) B Occ B:Na303 b:33.8 occ:1.00 O B:HOH413 2.3 24.7 1.0 O B:HOH403 2.4 39.7 1.0 O B:ASN30 2.5 20.9 1.0 O B:HOH429 2.6 40.8 1.0 OE1 B:GLU36 2.9 35.4 1.0 OE2 B:GLU36 3.3 38.2 1.0 O B:HOH406 3.5 34.1 1.0 CD B:GLU36 3.5 38.8 1.0 O B:ASP33 3.5 45.4 1.0 C B:ASN30 3.6 22.0 1.0 CA B:GLN31 4.1 25.3 1.0 N B:GLN31 4.3 24.1 1.0 O B:TYR83 4.3 29.1 1.0 N B:ASN30 4.4 22.7 1.0 CB B:SER71 4.4 34.8 1.0 C B:GLN31 4.4 27.7 1.0 OG B:SER71 4.4 34.3 1.0 O B:GLN35 4.5 32.7 1.0 CD1 B:PHE29 4.5 34.4 1.0 O B:HOH420 4.5 25.2 1.0 C B:ASP33 4.5 41.8 1.0 N B:ASP33 4.6 32.3 1.0 CA B:ASN30 4.6 25.0 1.0 CB B:ASP33 4.6 44.1 1.0 O B:GLN31 4.7 32.5 1.0 CB B:PHE29 4.8 29.4 1.0 CA B:ASP33 4.9 36.0 1.0 O B:HOH423 4.9 30.8 1.0 CG B:GLU36 4.9 40.7 1.0 CG B:PHE29 5.0 32.6 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