Sodium in PDB 5y8w: Crystal Structure Analysis of the BRD4

The structure of Crystal Structure Analysis of the BRD4, PDB code: 5y8w 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)	40.96 / 1.76
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	38.970, 48.200, 77.680, 90.00, 90.00, 90.00
R / Rfree (%)	18.9 / 23.6

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

Bromine

(Br)

1 atom

The binding sites of Sodium atom in the Crystal Structure Analysis of the BRD4 (pdb code 5y8w). 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: 5y8w:

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:Na208 b:29.0 occ:1.00 O A:HOH360 2.2 34.4 1.0 O A:HOH357 2.3 36.5 1.0 O A:ASN140 2.3 24.3 1.0 O A:HOH356 2.4 33.7 1.0 O A:TYR137 2.5 20.1 1.0 O A:ILE138 2.5 21.4 1.0 C A:ILE138 3.2 22.0 1.0 C A:ASN140 3.5 23.0 1.0 C A:TYR137 3.6 22.7 1.0 CA A:ILE138 3.6 22.7 1.0 O A:HOH314 3.8 36.7 1.0 N A:ASN140 4.0 20.5 1.0 N A:ILE138 4.1 23.6 1.0 N A:TYR139 4.2 20.0 1.0 C A:TYR139 4.2 20.8 1.0 CA A:ASN140 4.3 21.4 1.0 N A:LYS141 4.4 25.6 1.0 CA A:LYS141 4.5 28.2 1.0 NZ A:LYS141 4.6 46.9 1.0 O A:TYR139 4.6 19.2 1.0 CA A:TYR139 4.7 20.2 1.0 CD A:LYS141 4.8 42.3 1.0 CA A:TYR137 4.9 21.2 1.0 CB A:ILE138 5.0 22.6 1.0

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