Sodium in PDB 6euz: The Transcriptional Regulator Prfa From Listeria Monocytogenes in Complex with A Ring-Fused 2-Pyridone (MK37)

The structure of The Transcriptional Regulator Prfa From Listeria Monocytogenes in Complex with A Ring-Fused 2-Pyridone (MK37), PDB code: 6euz 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)	44.52 / 1.95
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	48.109, 89.048, 116.231, 90.00, 90.00, 90.00
R / Rfree (%)	19.2 / 23.6

The binding sites of Sodium atom in the The Transcriptional Regulator Prfa From Listeria Monocytogenes in Complex with A Ring-Fused 2-Pyridone (MK37) (pdb code 6euz). 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 (MK37), PDB code: 6euz:
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 (MK37)


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 (MK37) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na303 b:24.8 occ:1.00 O A:HOH404 2.3 34.2 1.0 O A:HOH438 2.3 26.2 1.0 O A:HOH455 2.4 17.7 1.0 O A:ASN30 2.5 24.5 1.0 OE1 A:GLU36 2.6 27.3 1.0 CD A:GLU36 3.5 27.1 1.0 O A:HOH423 3.5 33.4 1.0 C A:ASN30 3.6 18.4 1.0 OE2 A:GLU36 3.6 28.9 1.0 O A:ASP33 4.0 32.1 1.0 OG A:SER71 4.0 19.6 1.0 CB A:SER71 4.3 16.3 1.0 CA A:GLN31 4.3 23.0 1.0 O A:GLN35 4.3 27.7 1.0 N A:ASN30 4.3 25.3 1.0 O A:HOH469 4.3 23.0 1.0 N A:GLN31 4.3 19.5 1.0 CD1 A:PHE29 4.4 22.8 1.0 CB A:ASP33 4.4 29.3 1.0 O A:TYR83 4.5 19.1 1.0 CA A:ASN30 4.6 17.2 1.0 O A:HOH424 4.6 21.6 1.0 C A:GLN31 4.6 34.8 1.0 N A:ASP33 4.7 34.4 1.0 CB A:PHE29 4.7 21.7 1.0 C A:ASP33 4.8 35.1 1.0 CG A:PHE29 4.9 17.7 1.0 CG A:GLU36 4.9 25.8 1.0 O A:GLN31 4.9 30.7 1.0 CA A:ASP33 4.9 27.6 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 (MK37)


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 (MK37) within 5.0Å range: probe atom residue distance (Å) B Occ B:Na303 b:31.3 occ:1.00 O B:HOH404 2.2 30.7 1.0 O B:HOH428 2.4 22.9 1.0 O B:HOH440 2.4 20.0 1.0 O B:ASN30 2.5 25.1 1.0 OE1 B:GLU36 2.8 25.2 1.0 O B:HOH452 3.4 37.7 1.0 CD B:GLU36 3.5 23.6 1.0 OE2 B:GLU36 3.6 30.8 1.0 C B:ASN30 3.6 20.2 1.0 O B:ASP33 3.6 37.2 1.0 OG B:SER71 4.2 24.3 1.0 CB B:ASP33 4.2 35.2 1.0 O B:GLN35 4.2 28.1 1.0 CA B:GLN31 4.3 19.2 1.0 N B:ASN30 4.4 21.4 1.0 N B:GLN31 4.4 19.3 1.0 CB B:SER71 4.4 20.2 1.0 O B:TYR83 4.4 19.6 1.0 CD1 B:PHE29 4.4 20.7 1.0 N B:ASP33 4.4 27.7 1.0 O B:HOH456 4.5 23.5 1.0 C B:ASP33 4.5 36.1 1.0 CA B:ASN30 4.6 27.8 1.0 O B:HOH427 4.6 23.2 1.0 CA B:ASP33 4.6 27.8 1.0 C B:GLN31 4.6 30.6 1.0 CB B:PHE29 4.9 24.6 1.0 CG B:GLU36 5.0 24.7 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