Atomistry » Sodium » PDB 2x5x-2xjq » 2xdj
Atomistry »
  Sodium »
    PDB 2x5x-2xjq »
      2xdj »

Sodium in PDB 2xdj: Crystal Structure of the N-Terminal Domain of E.Coli Ybgf

Protein crystallography data

The structure of Crystal Structure of the N-Terminal Domain of E.Coli Ybgf, PDB code: 2xdj was solved by A.M.Krachler, A.Sharma, C.Kleanthous, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.41 / 1.82
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 39.409, 40.870, 237.867, 90.00, 90.00, 90.00
R / Rfree (%) 22.524 / 27.447

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of the N-Terminal Domain of E.Coli Ybgf (pdb code 2xdj). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Crystal Structure of the N-Terminal Domain of E.Coli Ybgf, PDB code: 2xdj:

Sodium binding site 1 out of 1 in 2xdj

Go back to Sodium Binding Sites List in 2xdj
Sodium binding site 1 out of 1 in the Crystal Structure of the N-Terminal Domain of E.Coli Ybgf


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of the N-Terminal Domain of E.Coli Ybgf within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na1069

b:26.2
occ:1.00
NE2 C:GLN57 3.2 29.9 1.0
OE1 E:GLN57 3.3 34.9 1.0
OE1 D:GLN57 3.3 27.1 1.0
CG E:GLN57 3.3 28.4 1.0
CG C:GLN57 3.4 28.6 1.0
CG D:GLN57 3.7 27.1 1.0
CD E:GLN57 3.8 33.8 1.0
CD C:GLN57 3.8 33.8 1.0
CD D:GLN57 4.0 26.9 1.0
CD1 D:ILE60 4.0 35.8 1.0
CB D:GLN57 4.0 26.9 1.0
CD1 E:ILE60 4.0 25.8 1.0
CD1 C:ILE60 4.0 26.7 1.0
CA D:GLN57 4.2 28.3 1.0
CB E:GLN57 4.4 26.6 1.0
CB C:GLN57 4.4 22.6 1.0
CA E:GLN57 4.7 25.9 1.0
CA C:GLN57 4.7 23.1 1.0
CG2 D:ILE60 4.7 28.0 1.0
CB D:ILE60 4.8 28.1 1.0
N D:GLN57 4.9 28.1 1.0

Reference:

A.M.Krachler, A.Sharma, A.Cauldwell, G.Papadakos, C.Kleanthous. Tola Modulates the Oligomeric Status of Ybgf in the Bacterial Periplasm. J.Mol.Biol. V. 403 270 2010.
ISSN: ISSN 0022-2836
PubMed: 20816983
DOI: 10.1016/J.JMB.2010.08.050
Page generated: Mon Oct 7 05:09:45 2024

Last articles

Ca in 2W1S
Ca in 2W0D
Ca in 2W0Q
Ca in 2W1Q
Ca in 2W0C
Ca in 2W08
Ca in 2VZR
Ca in 2VZQ
Ca in 2VZP
Ca in 2VYP
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy