Sodium in PDB 6euu: The Transcriptional Regulator Prfa From Listeria Monocytogenes in Complex with A Ring-Fused 2-Pyridone (KSK29)

The structure of The Transcriptional Regulator Prfa From Listeria Monocytogenes in Complex with A Ring-Fused 2-Pyridone (KSK29), PDB code: 6euu 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)	45.50 / 2.60
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	55.537, 81.180, 59.198, 90.00, 111.88, 90.00
R / Rfree (%)	21.3 / 27.1

The binding sites of Sodium atom in the The Transcriptional Regulator Prfa From Listeria Monocytogenes in Complex with A Ring-Fused 2-Pyridone (KSK29) (pdb code 6euu). 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 (KSK29), PDB code: 6euu:
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 (KSK29)


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 (KSK29) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na301 b:92.8 occ:1.00 CB A:SER71 2.3 63.4 1.0 O A:HOH404 2.4 64.4 1.0 OG A:SER71 2.4 60.0 1.0 O A:HOH405 2.4 54.4 1.0 OE1 A:GLU36 3.1 69.7 1.0 CA A:SER71 3.7 47.3 1.0 CD A:GLU36 3.8 79.3 1.0 CD1 A:PHE29 3.8 72.7 1.0 CE1 A:PHE29 3.9 60.1 1.0 OE2 A:GLU36 4.0 85.8 1.0 O A:SER71 4.1 53.6 1.0 C A:SER71 4.1 57.5 1.0 O A:GLN35 4.2 70.0 1.0 CA A:GLU36 4.4 76.2 1.0 CG A:PHE29 4.4 63.0 1.0 CZ A:PHE29 4.6 67.6 1.0 N A:TYR37 4.6 67.0 1.0 O A:ASN30 4.7 40.8 1.0 N A:SER71 4.8 59.8 1.0 CD1 A:TYR37 4.8 67.0 1.0 O A:ASP33 4.8 75.7 1.0 CB A:GLU36 4.9 72.8 1.0 CG A:GLU36 5.0 75.7 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 (KSK29)


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 (KSK29) within 5.0Å range: probe atom residue distance (Å) B Occ B:Na302 b:87.4 occ:1.00 O B:HOH402 2.3 66.2 1.0 O B:HOH401 2.4 45.9 1.0 O B:GLY81 3.6 79.7 1.0 O B:ASN30 3.6 59.7 1.0 CA B:GLN31 3.8 61.0 1.0 O B:GLN31 4.0 61.6 1.0 O B:TYR83 4.0 60.5 1.0 O B:ASP33 4.0 74.5 1.0 C B:GLN31 4.1 65.2 1.0 OG B:SER79 4.3 56.1 1.0 CD1 B:PHE29 4.3 56.5 1.0 C B:ASN30 4.3 59.1 1.0 CB B:SER71 4.3 69.2 1.0 CE1 B:PHE29 4.3 69.7 1.0 N B:TYR83 4.4 51.7 1.0 N B:GLN31 4.5 56.6 1.0 OG B:SER71 4.7 68.0 1.0 C B:GLY81 4.7 78.8 1.0 CA B:TYR82 4.8 77.2 1.0 CB B:GLN31 4.9 69.8 1.0 O B:SER71 4.9 57.7 1.0 C B:TYR83 5.0 58.4 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