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

The structure of The Transcriptional Regulator Prfa From Listeria Monocytogenes in Complex with A Ring-Fused 2-Pyridone (MK206) - Folded Hth Motif, PDB code: 6exl 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)	43.90 / 1.90
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	47.749, 87.795, 116.183, 90.00, 90.00, 90.00
R / Rfree (%)	17.3 / 22.5

The binding sites of Sodium atom in the The Transcriptional Regulator Prfa From Listeria Monocytogenes in Complex with A Ring-Fused 2-Pyridone (MK206) - Folded Hth Motif (pdb code 6exl). 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 From Listeria Monocytogenes in Complex with A Ring-Fused 2-Pyridone (MK206) - Folded Hth Motif, PDB code: 6exl:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the The Transcriptional Regulator Prfa From Listeria Monocytogenes in Complex with A Ring-Fused 2-Pyridone (MK206) - Folded 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) - Folded Hth Motif within 5.0Å range: probe atom residue distance (Å) B Occ A:Na302 b:21.0 occ:1.00 O A:HOH403 2.1 27.7 1.0 O A:HOH487 2.4 21.4 1.0 O A:ASN30 2.4 18.7 1.0 O A:HOH494 2.4 18.0 1.0 OE1 A:GLU36 2.6 26.3 1.0 O A:HOH489 3.1 32.1 1.0 CD A:GLU36 3.4 25.1 1.0 OE2 A:GLU36 3.4 24.9 1.0 C A:ASN30 3.6 13.2 1.0 O A:ASP33 3.7 31.3 1.0 OG A:SER71 4.2 15.7 1.0 CB A:ASP33 4.3 31.3 1.0 O A:GLN35 4.3 23.3 1.0 CA A:GLN31 4.3 21.5 1.0 CB A:SER71 4.3 20.8 1.0 N A:GLN31 4.4 15.5 1.0 N A:ASN30 4.4 17.3 1.0 N A:ASP33 4.5 26.6 1.0 O A:HOH516 4.5 18.5 1.0 CD1 A:PHE29 4.5 16.1 1.0 O A:TYR83 4.5 17.2 1.0 C A:GLN31 4.5 29.8 1.0 O A:HOH419 4.5 18.4 1.0 C A:ASP33 4.6 33.2 1.0 CA A:ASN30 4.6 17.6 1.0 CA A:ASP33 4.7 28.5 1.0 CG A:GLU36 4.9 19.5 1.0 O A:GLN31 4.9 28.3 1.0 N A:TRP32 4.9 26.1 1.0 CB A:PHE29 4.9 14.9 1.0

Sodium binding site 2 out of 3 in the The Transcriptional Regulator Prfa From Listeria Monocytogenes in Complex with A Ring-Fused 2-Pyridone (MK206) - Folded 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) - Folded Hth Motif within 5.0Å range: probe atom residue distance (Å) B Occ A:Na303 b:35.4 occ:1.00 O A:GLY234 2.3 25.0 1.0 O A:ASN237 2.4 36.5 1.0 O A:HOH478 2.4 43.1 1.0 C A:ASN237 3.2 40.7 1.0 C A:GLY234 3.3 17.4 1.0 OXT A:ASN237 3.8 43.2 1.0 CA A:GLY234 3.8 19.9 1.0 N A:ASN237 4.0 21.2 1.0 CA A:ASN237 4.1 25.3 1.0 O A:HOH504 4.3 44.7 1.0 N A:LYS235 4.5 23.0 1.0 CB A:ASN237 4.5 25.2 1.0 O A:HOH536 4.5 42.1 1.0 C A:LYS235 4.8 35.3 1.0 CA A:LYS235 4.8 29.3 1.0 O A:LYS235 4.9 29.1 1.0 O A:HOH546 5.0 44.3 1.0

Sodium binding site 3 out of 3 in the The Transcriptional Regulator Prfa From Listeria Monocytogenes in Complex with A Ring-Fused 2-Pyridone (MK206) - Folded Hth Motif


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 From Listeria Monocytogenes in Complex with A Ring-Fused 2-Pyridone (MK206) - Folded Hth Motif within 5.0Å range: probe atom residue distance (Å) B Occ B:Na302 b:30.1 occ:1.00 O B:HOH426 2.4 27.2 1.0 O B:HOH460 2.5 19.4 1.0 O B:ASN30 2.6 17.7 1.0 OE1 B:GLU36 2.7 20.5 1.0 O B:HOH434 3.1 34.4 1.0 O B:ASP33 3.3 37.6 1.0 CD B:GLU36 3.5 24.8 1.0 OE2 B:GLU36 3.5 23.2 1.0 C B:ASN30 3.7 17.6 1.0 CB B:ASP33 4.0 29.6 1.0 O B:GLN35 4.1 23.8 1.0 C B:ASP33 4.3 33.4 1.0 OG B:SER71 4.3 18.5 1.0 N B:ASP33 4.4 27.2 1.0 CA B:GLN31 4.4 21.8 1.0 N B:ASN30 4.4 17.4 1.0 CB B:SER71 4.4 17.9 1.0 O B:HOH445 4.5 24.9 1.0 O B:TYR83 4.5 15.6 1.0 CA B:ASP33 4.5 23.9 1.0 N B:GLN31 4.5 19.6 1.0 CD1 B:PHE29 4.5 16.4 1.0 O B:HOH441 4.7 18.2 1.0 C B:GLN31 4.7 28.5 1.0 CA B:ASN30 4.7 15.1 1.0 CG B:GLU36 4.9 23.0 1.0 CB B:PHE29 5.0 20.0 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