Sodium in PDB 6exk: The Transcriptional Regulator Prfa From Listeria Monocytogenes in Complex with A Ring-Fused 2-Pyridone (MK206) - Unfolded Hth Motif

The structure of The Transcriptional Regulator Prfa From Listeria Monocytogenes in Complex with A Ring-Fused 2-Pyridone (MK206) - Unfolded Hth Motif, PDB code: 6exk was solved by M.Hall, C.Grundstrom, A.Begum, 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)	47.90 / 2.10
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	92.152, 112.326, 47.895, 90.00, 90.00, 90.00
R / Rfree (%)	19.5 / 24.9

The binding sites of Sodium atom in the The Transcriptional Regulator Prfa From Listeria Monocytogenes in Complex with A Ring-Fused 2-Pyridone (MK206) - Unfolded Hth Motif (pdb code 6exk). 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 (MK206) - Unfolded Hth Motif, PDB code: 6exk:
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 (MK206) - Unfolded Hth Motif


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 (MK206) - Unfolded Hth Motif within 5.0Å range: probe atom residue distance (Å) B Occ A:Na302 b:43.0 occ:1.00 O A:HOH405 2.2 54.7 1.0 O A:ASN30 2.4 39.5 1.0 O A:HOH423 2.4 35.8 1.0 O A:HOH418 2.5 48.6 1.0 OE1 A:GLU36 2.6 39.2 1.0 C A:ASN30 3.5 30.8 1.0 CD A:GLU36 3.5 43.9 1.0 O A:ASP33 3.6 54.6 1.0 OE2 A:GLU36 3.6 51.1 1.0 OG A:SER71 4.1 39.0 1.0 CA A:GLN31 4.2 40.1 1.0 N A:GLN31 4.3 34.1 1.0 O A:GLN35 4.3 40.9 1.0 N A:ASN30 4.3 35.1 1.0 O A:TYR83 4.3 35.2 1.0 CD1 A:PHE29 4.3 34.3 1.0 O A:HOH424 4.4 40.4 1.0 CB A:SER71 4.4 40.2 1.0 O A:HOH417 4.5 36.3 1.0 CB A:ASP33 4.5 51.7 1.0 C A:GLN31 4.5 48.8 1.0 CA A:ASN30 4.6 32.4 1.0 C A:ASP33 4.6 59.9 1.0 N A:ASP33 4.6 43.6 1.0 CB A:PHE29 4.8 42.0 1.0 O A:GLN31 4.8 37.8 1.0 CA A:ASP33 4.8 43.8 1.0 N A:TRP32 4.9 47.5 1.0 CG A:PHE29 4.9 30.0 1.0 CG A:GLU36 5.0 40.8 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 (MK206) - Unfolded Hth Motif


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 (MK206) - Unfolded Hth Motif within 5.0Å range: probe atom residue distance (Å) B Occ B:Na302 b:43.3 occ:1.00 O B:HOH408 2.3 48.6 1.0 O B:HOH434 2.3 45.8 1.0 O B:ASN30 2.4 35.4 1.0 O B:HOH427 2.5 43.5 1.0 OE1 B:GLU36 2.6 41.9 1.0 CD B:GLU36 3.5 42.8 1.0 C B:ASN30 3.5 29.7 1.0 OE2 B:GLU36 3.6 42.4 1.0 O B:HOH412 3.6 45.0 1.0 O B:ASP33 4.1 56.0 1.0 OG B:SER71 4.1 35.8 1.0 CB B:ASP33 4.1 44.0 1.0 O B:GLN35 4.2 40.6 1.0 CA B:GLN31 4.2 37.6 1.0 N B:GLN31 4.3 36.1 1.0 N B:ASN30 4.3 33.1 1.0 CB B:SER71 4.4 47.9 1.0 O B:HOH435 4.4 40.3 1.0 O B:TYR83 4.5 38.0 1.0 C B:GLN31 4.5 45.6 1.0 N B:ASP33 4.5 36.4 1.0 CA B:ASN30 4.5 33.6 1.0 CD1 B:PHE29 4.6 34.4 1.0 O B:HOH409 4.7 34.6 1.0 CA B:ASP33 4.7 41.6 1.0 O B:GLN31 4.8 45.0 1.0 C B:ASP33 4.8 52.4 1.0 CB B:PHE29 4.9 47.2 1.0 N B:TRP32 4.9 46.9 1.0 CG B:GLU36 4.9 35.7 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