Sodium in PDB 7usi: BRD2-BD1 in Complex with MDP5

The structure of BRD2-BD1 in Complex with MDP5, PDB code: 7usi was solved by T.D.Jayasinghe, D.R.Ronning, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.56 / 2.50
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	63.81, 149.872, 63.819, 90, 112.27, 90
R / Rfree (%)	20.1 / 25

The structure of BRD2-BD1 in Complex with MDP5 also contains other interesting chemical elements:

Chlorine

(Cl)

6 atoms

The binding sites of Sodium atom in the BRD2-BD1 in Complex with MDP5 (pdb code 7usi). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the BRD2-BD1 in Complex with MDP5, PDB code: 7usi:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the BRD2-BD1 in Complex with MDP5


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of BRD2-BD1 in Complex with MDP5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na213 b:65.0 occ:1.00 OD1 A:ASP161 3.3 64.5 1.0 CG A:ASP161 4.0 64.6 1.0 CB A:ASP161 4.3 51.9 1.0 CG A:MET165 4.3 45.4 1.0 CZ A:PHE95 4.4 44.9 1.0 CE1 A:PHE95 4.4 45.3 1.0 SD A:MET165 4.6 47.0 1.0 O A:ASP161 4.7 45.6 1.0 CA A:ASP161 4.9 54.4 1.0 OD2 A:ASP161 4.9 63.1 1.0 CD2 A:LEU164 5.0 70.4 1.0

Sodium binding site 2 out of 2 in the BRD2-BD1 in Complex with MDP5


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of BRD2-BD1 in Complex with MDP5 within 5.0Å range: probe atom residue distance (Å) B Occ E:Na213 b:73.0 occ:1.00 OD2 E:ASP161 3.1 66.4 1.0 N E:ASP161 3.3 66.3 1.0 CG E:ASP161 3.6 66.5 1.0 CB E:ASP161 3.9 63.0 1.0 CA E:ASP160 4.0 64.7 1.0 C E:ASP160 4.2 60.7 1.0 OD1 E:ASP160 4.3 77.3 1.0 CA E:ASP161 4.3 59.2 1.0 OD1 E:ASP161 4.5 61.7 1.0 CB E:ASP160 4.6 66.1 1.0 CG E:ASP160 4.8 71.4 1.0 O E:THR159 4.9 60.8 1.0

B.Sethi, V.Kumar, T.D.Jayasinghe, Y.Dong, D.R.Ronning, H.A.Zhong, D.W.Coulter, R.I.Mahato. Targeting BRD4 and PI3K Signaling Pathways For the Treatment of Medulloblastoma. J Control Release V. 354 80 2023.
ISSN: ISSN 1873-4995
PubMed: 36599397
DOI: 10.1016/J.JCONREL.2022.12.055