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Sodium in PDB 5y8z: Crystal Structure Analysis of the BRD4

Protein crystallography data

The structure of Crystal Structure Analysis of the BRD4, PDB code: 5y8z was solved by Y.Xu, Y.Zhang, M.Song, C.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.03 / 1.84
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 39.480, 48.270, 77.890, 90.00, 90.00, 90.00
R / Rfree (%) 16.8 / 18.5

Other elements in 5y8z:

The structure of Crystal Structure Analysis of the BRD4 also contains other interesting chemical elements:

Bromine (Br) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure Analysis of the BRD4 (pdb code 5y8z). 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 Analysis of the BRD4, PDB code: 5y8z:

Sodium binding site 1 out of 1 in 5y8z

Go back to Sodium Binding Sites List in 5y8z
Sodium binding site 1 out of 1 in the Crystal Structure Analysis of the BRD4


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure Analysis of the BRD4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na206

b:23.7
occ:1.00
O A:HOH370 2.2 26.8 1.0
O A:HOH343 2.3 32.8 1.0
O A:HOH372 2.3 31.3 1.0
O A:ASN140 2.4 16.5 1.0
O A:TYR137 2.5 14.6 1.0
O A:ILE138 2.7 12.3 1.0
C A:ILE138 3.3 14.2 1.0
C A:ASN140 3.6 16.5 1.0
CA A:ILE138 3.6 14.9 1.0
C A:TYR137 3.6 14.9 1.0
O A:HOH337 3.7 21.8 1.0
N A:ILE138 4.1 14.4 1.0
N A:ASN140 4.1 13.4 1.0
N A:TYR139 4.2 12.5 1.0
C A:TYR139 4.4 14.2 1.0
CA A:ASN140 4.5 15.3 1.0
N A:LYS141 4.5 17.9 1.0
CA A:LYS141 4.6 20.2 1.0
O A:TYR139 4.7 13.8 1.0
CD A:LYS141 4.8 31.2 1.0
CA A:TYR139 4.8 13.3 1.0
O A:HOH349 4.8 38.3 1.0
CA A:TYR137 4.9 13.8 1.0
NZ A:LYS141 4.9 37.5 1.0

Reference:

M.Zhang, Y.Zhang, M.Song, X.Xue, J.Wang, C.Wang, C.Zhang, C.Li, Q.Xiang, L.Zou, X.Wu, C.Wu, B.Dong, W.Xue, Y.Zhou, H.Chen, D.Wu, K.Ding, Y.Xu. Structure-Based Discovery and Optimization of Benzo[ D]Isoxazole Derivatives As Potent and Selective Bet Inhibitors For Potential Treatment of Castration-Resistant Prostate Cancer (Crpc) J. Med. Chem. V. 61 3037 2018.
ISSN: ISSN 1520-4804
PubMed: 29566488
DOI: 10.1021/ACS.JMEDCHEM.8B00103
Page generated: Tue Oct 8 01:21:45 2024

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