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Sodium in PDB 5lrr: The Transcriptional Regulator Prfa From Listeria Monocytogenes in Complex with Glutathione

Protein crystallography data

The structure of The Transcriptional Regulator Prfa From Listeria Monocytogenes in Complex with Glutathione, PDB code: 5lrr was solved by M.Hall, C.Grundstrom, A.Begum, M.Lindberg, U.H.Sauer, F.Almqvist, J.Johansson, A.E.Sauer-Eriksson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.54 / 2.17
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 116.265, 184.227, 100.457, 90.00, 90.00, 90.00
R / Rfree (%) 20.8 / 24.1

Sodium Binding Sites:

The binding sites of Sodium atom in the The Transcriptional Regulator Prfa From Listeria Monocytogenes in Complex with Glutathione (pdb code 5lrr). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 5 binding sites of Sodium where determined in the The Transcriptional Regulator Prfa From Listeria Monocytogenes in Complex with Glutathione, PDB code: 5lrr:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in 5lrr

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Sodium binding site 1 out of 5 in the The Transcriptional Regulator Prfa From Listeria Monocytogenes in Complex with Glutathione


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 Glutathione within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na302

b:41.5
occ:1.00
 HG A:SER71 2.3 46.1 1.0
O A:HOH441 2.3 46.0 1.0
O A:GLN35 2.6 50.2 1.0
HA A:GLU36 2.6 55.1 1.0
HB2 A:PHE29 2.9 39.0 1.0
OG A:SER71 3.0 38.4 1.0
HD2 A:TYR37 3.0 55.7 1.0
HB2 A:SER71 3.1 47.5 1.0
HE2 A:TYR37 3.5 60.9 1.0
CB A:SER71 3.5 39.6 1.0
CA A:GLU36 3.6 45.9 1.0
CD2 A:TYR37 3.6 46.4 1.0
C A:GLN35 3.6 53.7 1.0
CB A:PHE29 3.7 32.5 1.0
HB3 A:SER71 3.7 47.5 1.0
O A:HOH414 3.8 44.8 1.0
HB3 A:PHE29 3.8 39.0 1.0
CE2 A:TYR37 3.8 50.7 1.0
HB3 A:ASP33 3.9 66.0 1.0
H A:TYR37 3.9 55.8 1.0
CG A:PHE29 3.9 34.1 1.0
HD1 A:PHE29 4.0 39.5 1.0
O A:HOH478 4.0 42.7 1.0
N A:GLU36 4.0 50.7 1.0
O A:HOH408 4.1 40.0 1.0
CD1 A:PHE29 4.1 32.9 1.0
HB3 A:GLU36 4.2 56.7 1.0
N A:TYR37 4.3 46.5 1.0
C A:GLU36 4.3 49.7 1.0
CB A:GLU36 4.4 47.2 1.0
O A:HOH402 4.5 45.5 1.0
CD2 A:PHE29 4.6 35.1 1.0
O A:ASN30 4.6 35.0 1.0
HB2 A:GLU36 4.7 56.7 1.0
CB A:ASP33 4.7 55.0 1.0
H A:ASN30 4.7 41.5 1.0
CG A:TYR37 4.7 45.2 1.0
OD2 A:ASP33 4.7 51.5 1.0
CG A:ASP33 4.8 61.0 1.0
HD2 A:PHE29 4.8 42.2 1.0
HB2 A:TYR37 4.8 49.9 1.0
O A:ASP33 4.9 55.5 1.0
CE1 A:PHE29 4.9 33.5 1.0
H A:GLU36 4.9 60.8 1.0
CA A:SER71 4.9 36.0 1.0
O A:SER71 4.9 37.0 1.0
CA A:GLN35 5.0 60.7 1.0

Sodium binding site 2 out of 5 in 5lrr

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Sodium binding site 2 out of 5 in the The Transcriptional Regulator Prfa From Listeria Monocytogenes in Complex with Glutathione


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 Glutathione within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na302

b:56.9
occ:1.00
 O D:GLN35 2.3 68.9 1.0
HB2 D:PHE29 2.7 59.5 1.0
HB2 D:SER71 2.8 59.7 1.0
O D:HOH429 3.1 56.7 1.0
OG D:SER71 3.1 52.3 1.0
HD2 D:TYR37 3.2 82.8 1.0
CB D:SER71 3.3 49.7 1.0
HB3 D:SER71 3.4 59.7 1.0
O D:HOH421 3.4 54.3 1.0
CB D:PHE29 3.4 49.5 1.0
C D:GLN35 3.5 67.2 1.0
HD1 D:PHE29 3.5 58.7 1.0
HA D:GLU36 3.6 74.6 1.0
CG D:PHE29 3.6 50.0 1.0
CD1 D:PHE29 3.7 48.9 1.0
HB3 D:PHE29 3.7 59.5 1.0
HG D:SER71 3.8 62.7 1.0
HE2 D:TYR37 3.9 81.1 1.0
CD2 D:TYR37 3.9 69.0 1.0
O D:HOH401 4.0 49.5 1.0
H D:ASN30 4.0 62.0 1.0
O D:ASN30 4.1 54.0 1.0
HB2 D:GLN35 4.1 86.8 1.0
H D:GLN35 4.1 87.9 1.0
H D:TYR37 4.2 67.9 1.0
CE2 D:TYR37 4.2 67.6 1.0
N D:GLU36 4.4 64.5 1.0
CA D:GLU36 4.4 62.2 1.0
CD2 D:PHE29 4.4 48.5 1.0
O D:ASP33 4.5 75.3 1.0
CA D:GLN35 4.5 72.1 1.0
CE1 D:PHE29 4.5 48.1 1.0
N D:GLN35 4.6 73.3 1.0
N D:ASN30 4.6 51.6 1.0
CB D:GLN35 4.7 72.3 1.0
N D:TYR37 4.7 56.6 1.0
CA D:PHE29 4.7 50.3 1.0
CA D:SER71 4.8 48.2 1.0
HD2 D:PHE29 4.8 58.2 1.0
HB3 D:GLN35 4.8 86.8 1.0
HB2 D:TYR37 4.8 73.1 1.0
O D:SER71 4.9 47.4 1.0
HA D:PHE29 4.9 60.4 1.0
HE1 D:PHE29 4.9 57.8 1.0
C D:GLU36 4.9 62.5 1.0
HG3 D:GLU36 5.0 73.2 1.0
CG D:TYR37 5.0 65.9 1.0

Sodium binding site 3 out of 5 in 5lrr

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Sodium binding site 3 out of 5 in the The Transcriptional Regulator Prfa From Listeria Monocytogenes in Complex with Glutathione


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 Glutathione within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na302

b:41.7
occ:1.00
 O E:HOH419 2.5 37.1 1.0
O E:ASP33 2.5 41.2 1.0
O E:HOH412 2.5 42.0 1.0
O E:ASN30 2.6 32.9 1.0
O E:HOH407 2.7 45.1 1.0
OE1 E:GLU36 2.8 45.4 1.0
HB3 E:ASP33 3.4 49.3 1.0
HA E:GLN31 3.4 44.0 1.0
H E:ASP33 3.5 52.8 1.0
OE2 E:GLU36 3.5 43.2 1.0
CD E:GLU36 3.5 45.1 1.0
C E:ASN30 3.6 36.7 1.0
C E:ASP33 3.6 40.7 1.0
H E:ASN30 4.0 39.5 1.0
HB2 E:PHE29 4.0 42.0 1.0
HB2 E:SER71 4.1 47.0 1.0
CA E:GLN31 4.1 36.6 1.0
N E:ASP33 4.1 44.0 1.0
HA E:GLU36 4.2 51.5 1.0
O E:GLN35 4.2 40.4 1.0
CB E:ASP33 4.2 41.1 1.0
CA E:ASP33 4.2 40.1 1.0
HD1 E:PHE29 4.2 41.1 1.0
N E:GLN31 4.3 34.8 1.0
O E:HOH422 4.4 44.4 1.0
C E:GLN31 4.4 39.7 1.0
HA E:PRO34 4.4 53.0 1.0
N E:ASN30 4.4 32.9 1.0
O E:HOH453 4.5 46.3 1.0
O E:HOH465 4.6 34.5 1.0
HG E:SER71 4.6 45.3 1.0
O E:TYR83 4.6 37.8 1.0
OG E:SER71 4.6 37.7 1.0
O E:HOH436 4.7 49.6 1.0
CA E:ASN30 4.7 35.0 1.0
O E:GLN31 4.7 42.0 1.0
N E:PRO34 4.7 44.0 1.0
CD1 E:PHE29 4.8 34.2 1.0
CB E:SER71 4.8 39.2 1.0
HB2 E:ASP33 4.8 49.3 1.0
C E:GLN35 4.9 43.8 1.0
CA E:PRO34 4.9 44.2 1.0
N E:TRP32 4.9 37.5 1.0
CB E:PHE29 4.9 35.0 1.0
CG E:GLU36 5.0 43.1 1.0

Sodium binding site 4 out of 5 in 5lrr

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Sodium binding site 4 out of 5 in the The Transcriptional Regulator Prfa From Listeria Monocytogenes in Complex with Glutathione


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of The Transcriptional Regulator Prfa From Listeria Monocytogenes in Complex with Glutathione within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Na302

b:37.6
occ:1.00
 HG F:SER71 2.0 45.8 1.0
HD2 F:TYR37 2.5 48.1 1.0
OG F:SER71 2.8 38.2 1.0
O F:HOH407 2.9 36.3 1.0
O F:GLN35 3.0 43.9 1.0
HB2 F:SER71 3.0 44.1 1.0
HE2 F:TYR37 3.2 49.5 1.0
CD2 F:TYR37 3.2 40.1 1.0
HA F:GLU36 3.3 49.1 1.0
CB F:SER71 3.3 36.8 1.0
HB2 F:PHE29 3.3 46.9 1.0
HB3 F:SER71 3.4 44.1 1.0
CE2 F:TYR37 3.6 41.3 1.0
HD1 F:PHE29 3.6 53.2 1.0
CD1 F:PHE29 3.6 44.3 1.0
CG F:PHE29 3.7 40.3 1.0
HB3 F:ASP33 3.7 43.0 1.0
H F:TYR37 3.8 45.2 1.0
CB F:PHE29 3.9 39.1 1.0
O F:HOH422 4.0 38.6 1.0
C F:GLN35 4.1 43.5 1.0
HB3 F:PHE29 4.1 46.9 1.0
CA F:GLU36 4.2 40.9 1.0
CE1 F:PHE29 4.2 40.2 1.0
N F:TYR37 4.3 37.7 1.0
O F:HOH408 4.3 27.4 1.0
HB2 F:TYR37 4.4 48.9 1.0
CD2 F:PHE29 4.4 38.7 1.0
O F:ASP33 4.4 37.4 1.0
CG F:TYR37 4.4 41.8 1.0
O F:HOH424 4.5 38.8 1.0
HE1 F:PHE29 4.5 48.2 1.0
N F:GLU36 4.6 39.0 1.0
C F:GLU36 4.6 40.3 1.0
CB F:ASP33 4.6 35.8 1.0
O F:ASN30 4.7 39.3 1.0
HG3 F:GLU36 4.7 47.1 1.0
CZ F:PHE29 4.8 37.1 1.0
HD2 F:PHE29 4.8 46.4 1.0
CA F:SER71 4.8 36.9 1.0
CB F:TYR37 4.8 40.8 1.0
CE2 F:PHE29 4.8 36.9 1.0
CG F:ASP33 4.9 35.2 1.0
CZ F:TYR37 4.9 43.8 1.0

Sodium binding site 5 out of 5 in 5lrr

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Sodium binding site 5 out of 5 in the The Transcriptional Regulator Prfa From Listeria Monocytogenes in Complex with Glutathione


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of The Transcriptional Regulator Prfa From Listeria Monocytogenes in Complex with Glutathione within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Na302

b:43.6
occ:1.00
 O H:HOH421 2.7 36.1 1.0
O H:ASP33 2.8 43.8 1.0
O H:ASN30 2.8 38.9 1.0
O H:HOH411 2.9 38.9 1.0
HB3 H:ASP33 3.1 52.1 1.0
HA H:GLN31 3.3 45.1 1.0
O H:GLN31 3.3 38.4 1.0
O H:HOH426 3.5 42.8 1.0
H H:ASP33 3.5 50.3 1.0
C H:GLN31 3.6 39.1 1.0
O H:HOH406 3.6 33.6 1.0
C H:ASP33 3.8 42.6 1.0
N H:ASP33 3.8 41.9 1.0
HD1 H:PHE29 3.9 47.4 1.0
CA H:GLN31 3.9 37.6 1.0
C H:ASN30 3.9 36.3 1.0
CB H:ASP33 4.0 43.4 1.0
CA H:ASP33 4.1 41.4 1.0
HB2 H:SER71 4.2 45.2 1.0
N H:TRP32 4.4 41.1 1.0
N H:GLN31 4.4 34.4 1.0
HB2 H:ASP33 4.4 52.1 1.0
C H:TRP32 4.5 42.1 1.0
O H:TYR83 4.5 35.5 1.0
CD1 H:PHE29 4.5 39.5 1.0
HB2 H:PHE29 4.6 47.0 1.0
H H:TYR83 4.6 46.7 1.0
O H:GLN35 4.6 41.4 1.0
HG H:SER71 4.6 48.6 1.0
H H:TRP32 4.8 49.4 1.0
HE1 H:PHE29 4.9 48.8 1.0
H H:ASN30 4.9 47.0 1.0
CB H:SER71 4.9 37.7 1.0
CA H:TRP32 4.9 40.9 1.0
HA H:TYR82 4.9 45.3 1.0

Reference:

M.Hall, C.Grundstrom, A.Begum, M.J.Lindberg, U.H.Sauer, F.Almqvist, J.Johansson, A.E.Sauer-Eriksson. Structural Basis For Glutathione-Mediated Activation of the Virulence Regulatory Protein Prfa in Listeria. Proc. Natl. Acad. Sci. V. 113 14733 2016U.S.A..
ISSN: ESSN 1091-6490
PubMed: 27930316
DOI: 10.1073/PNAS.1614028114
Page generated: Mon Oct 7 22:23:52 2024

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