Atomistry » Sodium » PDB 5nbj-5npk » 5nib
Atomistry »
  Sodium »
    PDB 5nbj-5npk »
      5nib »

Sodium in PDB 5nib: Ligand Complex of Rorg Lbd

Protein crystallography data

The structure of Ligand Complex of Rorg Lbd, PDB code: 5nib was solved by Y.Xue, A.Aagaard, F.Narjes, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.94 / 1.82
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 62.140, 62.140, 158.250, 90.00, 90.00, 90.00
R / Rfree (%) 19.2 / 22.7

Sodium Binding Sites:

The binding sites of Sodium atom in the Ligand Complex of Rorg Lbd (pdb code 5nib). 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 Ligand Complex of Rorg Lbd, PDB code: 5nib:

Sodium binding site 1 out of 1 in 5nib

Go back to Sodium Binding Sites List in 5nib
Sodium binding site 1 out of 1 in the Ligand Complex of Rorg Lbd


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Ligand Complex of Rorg Lbd within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na602

b:41.5
occ:1.00
O A:CYS366 2.3 30.1 1.0
O A:TYR369 2.4 32.0 1.0
OG A:SER408 2.6 42.6 1.0
O A:HOH779 2.8 39.6 1.0
O A:HOH844 2.8 49.7 1.0
C A:CYS366 3.4 31.0 1.0
C A:TYR369 3.5 34.4 1.0
CB A:SER408 3.5 35.0 1.0
O A:HOH717 4.1 53.0 1.0
N A:TYR369 4.1 31.5 1.0
CA A:TYR369 4.1 30.9 1.0
CA A:SER408 4.2 32.4 1.0
CB A:TYR369 4.2 30.8 1.0
N A:ARG367 4.3 26.2 1.0
CA A:CYS366 4.4 27.9 1.0
CA A:ARG367 4.4 27.6 1.0
C A:ARG367 4.4 33.6 1.0
CD2 A:TYR369 4.4 32.5 1.0
O A:ARG367 4.5 34.1 1.0
O A:HOH869 4.6 57.0 1.0
N A:ASN370 4.6 32.2 1.0
CB A:CYS366 4.7 28.6 1.0
NH1 A:ARG296 4.7 66.2 1.0
O A:HOH785 4.8 43.8 1.0
CG A:TYR369 4.8 31.8 1.0
N A:ALA371 5.0 35.2 1.0
CA A:ASN370 5.0 32.3 1.0

Reference:

F.Narjes, Y.Xue, S.Von Berg, J.Malmberg, A.Llinas, R.I.Olsson, J.Jirholt, H.Grindebacke, A.Leffler, N.Hossain, M.Lepisto, L.Thunberg, H.Leek, A.Aagaard, J.Mcpheat, E.L.Hansson, E.Back, S.Tangefjord, R.Chen, Y.Xiong, G.Hongbin, T.G.Hansson. Potent and Orally Bioavailable Inverse Agonists of Ror Gamma T Resulting From Structure-Based Design. J. Med. Chem. V. 61 7796 2018.
ISSN: ISSN 1520-4804
PubMed: 30095900
DOI: 10.1021/ACS.JMEDCHEM.8B00783
Page generated: Tue Dec 15 11:21:00 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy