Sodium in PDB 6eut: The Transcriptional Regulator Prfa From Listeria Monocytogenes in Complex with A Ring-Fused 2-Pyridone (KSK67)

The structure of The Transcriptional Regulator Prfa From Listeria Monocytogenes in Complex with A Ring-Fused 2-Pyridone (KSK67), PDB code: 6eut was solved by A.Begum, M.Hall, C.Grundstrom, M.Kulen, M.Lindgren, J.Johansson, F.Almqvist, U.H.Sauer, A.E.Sauer-Eriksson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.34 / 1.90
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	47.934, 88.710, 116.788, 90.00, 90.00, 90.00
R / Rfree (%)	17.9 / 22.8

The binding sites of Sodium atom in the The Transcriptional Regulator Prfa From Listeria Monocytogenes in Complex with A Ring-Fused 2-Pyridone (KSK67) (pdb code 6eut). 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 A Ring-Fused 2-Pyridone (KSK67), PDB code: 6eut:
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 A Ring-Fused 2-Pyridone (KSK67)


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 A Ring-Fused 2-Pyridone (KSK67) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na302 b:22.5 occ:1.00 O A:HOH404 2.2 34.7 1.0 O A:HOH464 2.3 23.4 1.0 O A:ASN30 2.4 20.3 1.0 O A:HOH438 2.5 20.4 1.0 OE1 A:GLU36 2.8 26.8 1.0 O A:HOH429 3.6 34.3 1.0 C A:ASN30 3.6 14.8 1.0 CD A:GLU36 3.6 28.1 1.0 O A:ASP33 3.7 33.4 1.0 OE2 A:GLU36 3.7 27.2 1.0 OG A:SER71 4.2 21.3 1.0 O A:GLN35 4.3 26.6 1.0 CB A:ASP33 4.3 29.4 1.0 CA A:GLN31 4.3 23.5 1.0 N A:ASN30 4.3 19.8 1.0 N A:GLN31 4.4 18.6 1.0 O A:HOH489 4.4 22.4 1.0 CB A:SER71 4.4 20.1 1.0 N A:ASP33 4.4 27.6 1.0 O A:TYR83 4.5 20.5 1.0 CD1 A:PHE29 4.5 20.1 1.0 C A:GLN31 4.6 34.2 1.0 C A:ASP33 4.6 35.4 1.0 CA A:ASN30 4.6 18.7 1.0 CA A:ASP33 4.7 29.1 1.0 O A:HOH428 4.7 22.0 1.0 O A:GLN31 4.9 28.7 1.0 CB A:PHE29 4.9 20.2 1.0 N A:TRP32 4.9 28.1 1.0 CG A:GLU36 5.0 21.6 1.0

Sodium binding site 2 out of 2 in the The Transcriptional Regulator Prfa From Listeria Monocytogenes in Complex with A Ring-Fused 2-Pyridone (KSK67)


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 A Ring-Fused 2-Pyridone (KSK67) within 5.0Å range: probe atom residue distance (Å) B Occ B:Na302 b:31.2 occ:1.00 O B:HOH402 2.2 40.0 1.0 O B:HOH433 2.4 26.8 1.0 O B:HOH454 2.5 22.4 1.0 O B:ASN30 2.6 20.7 1.0 OE1 B:GLU36 2.9 25.4 1.0 O B:ASP33 3.3 36.8 1.0 O B:HOH423 3.5 42.2 1.0 C B:ASN30 3.6 15.1 1.0 OE2 B:GLU36 3.7 30.1 1.0 CD B:GLU36 3.7 26.6 1.0 CB B:ASP33 4.1 36.7 1.0 O B:GLN35 4.2 27.9 1.0 OG B:SER71 4.2 22.7 1.0 C B:ASP33 4.3 35.0 1.0 N B:ASN30 4.4 21.3 1.0 CA B:GLN31 4.4 20.3 1.0 N B:ASP33 4.4 28.1 1.0 O B:HOH431 4.4 26.7 1.0 O B:TYR83 4.4 19.5 1.0 N B:GLN31 4.4 22.3 1.0 CB B:SER71 4.5 23.2 1.0 CD1 B:PHE29 4.5 20.7 1.0 CA B:ASP33 4.5 24.9 1.0 CA B:ASN30 4.6 20.2 1.0 O B:HOH444 4.7 23.7 1.0 C B:GLN31 4.7 30.9 1.0 CB B:PHE29 4.8 25.1 1.0 CG B:PHE29 5.0 23.2 1.0

M.Kulen, M.Lindgren, S.Hansen, A.G.Cairns, C.Grundstrom, A.Begum, I.Van Der Lingen, K.Brannstrom, M.Hall, U.H.Sauer, J.Johansson, A.E.Sauer-Eriksson, F.Almqvist. Structure-Based Design of Inhibitors Targeting Prfa, the Master Virulence Regulator of Listeria Monocytogenes. J. Med. Chem. V. 61 4165 2018.
ISSN: ISSN 1520-4804
PubMed: 29667825
DOI: 10.1021/ACS.JMEDCHEM.8B00289