Sodium in PDB 7la9: Crystal Structure of the First Bromodomain (BD1) of Human BRD4 (BRD4- 1) in Complex with Bivalent Inhibitor Nc-III-49-1

The structure of Crystal Structure of the First Bromodomain (BD1) of Human BRD4 (BRD4- 1) in Complex with Bivalent Inhibitor Nc-III-49-1, PDB code: 7la9 was solved by M.R.Karim, E.Schonbrunn, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.36 / 2.20
Space group	P 31
Cell size a, b, c (Å), α, β, γ (°)	114.126, 114.126, 94.834, 90, 90, 120
R / Rfree (%)	18.5 / 20.8

The structure of Crystal Structure of the First Bromodomain (BD1) of Human BRD4 (BRD4- 1) in Complex with Bivalent Inhibitor Nc-III-49-1 also contains other interesting chemical elements:

Chlorine

(Cl)

8 atoms

The binding sites of Sodium atom in the Crystal Structure of the First Bromodomain (BD1) of Human BRD4 (BRD4- 1) in Complex with Bivalent Inhibitor Nc-III-49-1 (pdb code 7la9). 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 First Bromodomain (BD1) of Human BRD4 (BRD4- 1) in Complex with Bivalent Inhibitor Nc-III-49-1, PDB code: 7la9:

Sodium binding site 1 out of 1 in the Crystal Structure of the First Bromodomain (BD1) of Human BRD4 (BRD4- 1) in Complex with Bivalent Inhibitor Nc-III-49-1


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 First Bromodomain (BD1) of Human BRD4 (BRD4- 1) in Complex with Bivalent Inhibitor Nc-III-49-1 within 5.0Å range: probe atom residue distance (Å) B Occ C:Na206 b:63.6 occ:1.00 OG1 C:THR134 2.7 50.0 1.0 OD1 C:ASN135 2.9 55.0 1.0 O C:HOH334 3.2 64.8 1.0 N C:ASN135 3.6 48.5 1.0 O C:HOH307 3.6 57.8 1.0 CB C:THR134 3.6 52.7 1.0 C C:THR134 3.8 51.7 1.0 CG C:ASN135 3.9 49.9 1.0 CA C:ASN135 4.1 51.2 1.0 O C:THR131 4.2 47.9 1.0 O C:THR134 4.3 49.6 1.0 CA C:THR134 4.3 51.4 1.0 O C:HOH317 4.4 51.6 1.0 CG2 C:THR131 4.5 52.1 1.0 O C:HOH324 4.6 63.5 1.0 CB C:ASN135 4.6 50.5 1.0 CA C:THR131 4.6 51.5 1.0 C C:THR131 4.9 48.9 1.0 ND2 C:ASN135 4.9 48.3 1.0 CG2 C:THR134 4.9 47.2 1.0 CG2 C:ILE138 5.0 52.6 1.0

X.Guan, N.Cheryala, R.M.Karim, A.Chan, N.Berndt, J.Qi, G.I.Georg, E.Schonbrunn. Bivalent Bet Bromodomain Inhibitors Confer Increased Potency and Selectivity For Brdt Via Protein Conformational Plasticity. J.Med.Chem. V. 65 10441 2022.
ISSN: ISSN 0022-2623
PubMed: 35867655
DOI: 10.1021/ACS.JMEDCHEM.2C00453