Sodium in PDB 6exm: The Transcriptional Regulator Prfa From Listeria Monocytogenes in Complex with A Ring-Fused 2-Pyridone (MK202)

The structure of The Transcriptional Regulator Prfa From Listeria Monocytogenes in Complex with A Ring-Fused 2-Pyridone (MK202), PDB code: 6exm was solved by C.Grundstrom, A.Begum, M.Hall, 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)	48.53 / 1.60
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	47.729, 88.647, 115.997, 90.00, 90.00, 90.00
R / Rfree (%)	18.2 / 21.7

The binding sites of Sodium atom in the The Transcriptional Regulator Prfa From Listeria Monocytogenes in Complex with A Ring-Fused 2-Pyridone (MK202) (pdb code 6exm). 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 (MK202), PDB code: 6exm:
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 (MK202)


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 (MK202) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na302 b:18.6 occ:1.00 O A:HOH423 2.3 25.3 1.0 O A:HOH484 2.3 20.4 1.0 O A:ASN30 2.4 18.0 1.0 O A:HOH488 2.4 16.4 1.0 OE1 A:GLU36 2.5 19.4 1.0 CD A:GLU36 3.4 22.8 1.0 OE2 A:GLU36 3.5 23.2 1.0 C A:ASN30 3.6 13.9 1.0 O A:HOH444 3.6 24.7 1.0 OG A:SER71 4.1 16.5 1.0 O A:ASP33 4.1 28.0 1.0 CA A:GLN31 4.2 16.6 1.0 O A:GLN35 4.2 20.9 1.0 CB A:ASP33 4.3 27.4 1.0 CB A:SER71 4.3 16.2 1.0 N A:GLN31 4.3 16.5 1.0 N A:ASN30 4.3 15.7 1.0 CD1 A:PHE29 4.4 15.3 1.0 O A:HOH472 4.4 20.6 1.0 O A:TYR83 4.5 16.6 1.0 CA A:ASN30 4.5 13.6 1.0 C A:GLN31 4.6 20.3 1.0 N A:ASP33 4.6 23.8 1.0 O A:HOH445 4.6 19.1 1.0 CB A:PHE29 4.8 16.1 1.0 CG A:GLU36 4.8 20.2 1.0 CA A:ASP33 4.8 25.1 1.0 C A:ASP33 4.9 26.4 1.0 N A:TRP32 4.9 19.4 1.0 CG A:PHE29 4.9 16.4 1.0 O A:GLN31 5.0 23.5 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 (MK202)


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 (MK202) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na303 b:34.5 occ:1.00 O A:ASN237 2.3 32.2 1.0 O A:GLY234 2.4 25.2 1.0 O A:HOH539 2.8 42.7 1.0 C A:ASN237 3.1 41.8 1.0 C A:GLY234 3.4 27.1 1.0 OXT A:ASN237 3.6 46.0 1.0 CA A:GLY234 3.9 25.5 1.0 CA A:ASN237 4.1 25.2 1.0 N A:ASN237 4.1 23.4 1.0 CB A:ASN237 4.5 24.9 1.0 O A:HOH511 4.6 47.1 1.0 N A:LYS235 4.6 26.8 1.0 O A:HOH552 4.6 49.0 1.0 C A:LYS235 4.9 37.1 1.0 CA A:LYS235 5.0 28.8 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 (MK202)


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 (MK202) within 5.0Å range: probe atom residue distance (Å) B Occ B:Na302 b:24.4 occ:1.00 O B:HOH401 2.3 33.5 1.0 O B:HOH443 2.4 21.9 1.0 O B:HOH466 2.4 20.3 1.0 O B:ASN30 2.5 18.4 1.0 OE1 B:GLU36 2.7 20.3 1.0 O B:ASP33 3.4 34.0 1.0 O B:HOH454 3.5 29.3 1.0 CD B:GLU36 3.5 19.4 1.0 OE2 B:GLU36 3.6 21.8 1.0 C B:ASN30 3.6 15.8 1.0 CB B:ASP33 4.1 31.1 1.0 O B:GLN35 4.2 22.7 1.0 OG B:SER71 4.3 19.3 1.0 N B:ASN30 4.3 15.5 1.0 C B:ASP33 4.4 28.6 1.0 O B:HOH477 4.4 38.5 1.0 O B:HOH435 4.4 20.6 1.0 N B:ASP33 4.4 24.1 1.0 CA B:GLN31 4.4 18.2 1.0 O B:TYR83 4.4 15.0 1.0 CB B:SER71 4.4 16.6 1.0 CD1 B:PHE29 4.5 14.0 1.0 N B:GLN31 4.5 19.1 1.0 CA B:ASP33 4.5 22.6 1.0 CA B:ASN30 4.6 14.5 1.0 O B:HOH448 4.6 20.2 1.0 C B:GLN31 4.7 20.2 1.0 CB B:PHE29 4.8 19.4 1.0 CG B:PHE29 4.9 17.8 1.0 CG B:GLU36 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