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Sodium in PDB 6hck: The Transcriptional Regulator Prfa From Listeria Monocytogenes in Complex with Dipeptide Leu-Leu

Protein crystallography data

The structure of The Transcriptional Regulator Prfa From Listeria Monocytogenes in Complex with Dipeptide Leu-Leu, PDB code: 6hck was solved by C.Grundstrom, M.Oelker, E.Krypotou, M.Scortti, B.F.Luisi, J.Vazquez-Boland, A.E.Sauer-Eriksson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.36 / 2.70
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 47.948, 87.394, 116.883, 90.00, 90.00, 90.00
R / Rfree (%) 20.9 / 27

Sodium Binding Sites:

The binding sites of Sodium atom in the The Transcriptional Regulator Prfa From Listeria Monocytogenes in Complex with Dipeptide Leu-Leu (pdb code 6hck). 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 Dipeptide Leu-Leu, PDB code: 6hck:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 6hck

Go back to Sodium Binding Sites List in 6hck
Sodium binding site 1 out of 2 in the The Transcriptional Regulator Prfa From Listeria Monocytogenes in Complex with Dipeptide Leu-Leu


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 Dipeptide Leu-Leu within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na303

b:45.8
occ:1.00
O A:ASP33 2.5 55.8 1.0
O A:HOH425 2.6 50.4 1.0
O A:HOH412 2.7 42.0 1.0
OE1 A:GLU36 2.9 43.9 1.0
O A:ASN30 2.9 33.9 1.0
OE2 A:GLU36 3.1 48.3 1.0
CD A:GLU36 3.3 47.8 1.0
C A:ASP33 3.5 50.8 1.0
N A:ASP33 3.7 37.5 1.0
O A:GLN35 3.8 50.6 1.0
CB A:ASP33 3.9 47.7 1.0
CA A:ASP33 3.9 44.6 1.0
C A:ASN30 4.1 32.5 1.0
C A:GLN31 4.3 36.4 1.0
O A:GLN31 4.4 48.3 1.0
CA A:GLN31 4.4 39.2 1.0
N A:TRP32 4.6 37.4 1.0
C A:TRP32 4.7 41.0 1.0
CG A:GLU36 4.7 46.7 1.0
C A:GLN35 4.7 51.4 1.0
N A:GLN31 4.7 31.4 1.0
N A:PRO34 4.7 56.4 1.0
OG A:SER71 4.8 36.6 1.0
CG A:ASP33 4.9 52.0 1.0

Sodium binding site 2 out of 2 in 6hck

Go back to Sodium Binding Sites List in 6hck
Sodium binding site 2 out of 2 in the The Transcriptional Regulator Prfa From Listeria Monocytogenes in Complex with Dipeptide Leu-Leu


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 Dipeptide Leu-Leu within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na301

b:43.2
occ:1.00
OE1 B:GLU36 2.8 40.5 1.0
O B:ASN30 2.8 38.6 1.0
O B:HOH404 3.0 43.3 1.0
O B:HOH403 3.1 49.1 1.0
O B:ASP33 3.1 53.6 1.0
CD B:GLU36 3.6 55.9 1.0
O B:GLN35 3.6 47.7 1.0
OE2 B:GLU36 3.7 43.6 1.0
O B:HOH406 3.8 45.4 1.0
CB B:ASP33 3.8 42.3 1.0
OG B:SER71 3.9 41.2 1.0
C B:ASN30 4.0 37.1 1.0
C B:ASP33 4.0 51.0 1.0
CA B:ASP33 4.3 48.7 1.0
N B:ASP33 4.3 37.4 1.0
N B:ASN30 4.4 34.8 1.0
CB B:SER71 4.4 36.2 1.0
CB B:PHE29 4.5 40.7 1.0
C B:GLN35 4.6 46.1 1.0
CD1 B:PHE29 4.6 36.0 1.0
CA B:GLU36 4.6 50.9 1.0
CG B:ASP33 4.7 52.8 1.0
CA B:ASN30 4.8 40.2 1.0
N B:GLN31 4.9 31.6 1.0
CG B:PHE29 4.9 35.0 1.0
CA B:GLN31 4.9 41.0 1.0
CG B:GLU36 4.9 58.0 1.0
O B:TYR83 5.0 31.4 1.0

Reference:

E.Krypotou, M.Scortti, C.Grundstrom, M.Oelker, B.F.Luisi, A.E.Sauer-Eriksson, J.Vazquez-Boland. Control of Bacterial Virulence Through the Peptide Signature of the Habitat. Cell Rep V. 26 1815 2019.
ISSN: ESSN 2211-1247
PubMed: 30759392
DOI: 10.1016/J.CELREP.2019.01.073
Page generated: Tue Dec 15 12:20:06 2020

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