Sodium in PDB 5dw1: X-Ray Crystal Structure of Human BRD2(BD2) in Complex with RVX297 to 1.55 A Resolution

The structure of X-Ray Crystal Structure of Human BRD2(BD2) in Complex with RVX297 to 1.55 A Resolution, PDB code: 5dw1 was solved by A.White, E.Fontano, R.K.Suto, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 1.55
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	56.289, 57.318, 62.033, 62.09, 72.08, 66.08
R / Rfree (%)	15.9 / 19.5

The binding sites of Sodium atom in the X-Ray Crystal Structure of Human BRD2(BD2) in Complex with RVX297 to 1.55 A Resolution (pdb code 5dw1). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the X-Ray Crystal Structure of Human BRD2(BD2) in Complex with RVX297 to 1.55 A Resolution, PDB code: 5dw1:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the X-Ray Crystal Structure of Human BRD2(BD2) in Complex with RVX297 to 1.55 A Resolution


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of X-Ray Crystal Structure of Human BRD2(BD2) in Complex with RVX297 to 1.55 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ C:Na502 b:38.1 occ:1.00 O C:HOH679 2.3 32.0 1.0 O C:HOH712 2.3 50.7 1.0 O C:HOH719 2.4 49.4 1.0 OD1 C:ASP377 2.4 25.5 1.0 OG C:SER379 2.5 33.3 1.0 CG C:ASP377 3.3 29.6 1.0 CB C:SER379 3.7 28.6 1.0 O C:HOH753 3.8 52.1 1.0 OD2 C:ASP377 3.8 28.6 1.0 N C:SER379 4.0 23.5 1.0 O C:HOH733 4.2 47.8 1.0 O C:HOH607 4.3 40.3 1.0 O C:HOH638 4.4 27.1 1.0 CA C:SER379 4.4 25.7 1.0 CA C:ASP377 4.4 19.9 1.0 CB C:ASP377 4.5 23.4 1.0 C C:ASP377 4.5 20.7 1.0 N C:ALA378 4.6 21.0 1.0 N C:ALA380 4.7 27.4 1.0

Sodium binding site 2 out of 2 in the X-Ray Crystal Structure of Human BRD2(BD2) in Complex with RVX297 to 1.55 A Resolution


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of X-Ray Crystal Structure of Human BRD2(BD2) in Complex with RVX297 to 1.55 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ D:Na502 b:30.7 occ:1.00 O D:HOH683 2.3 31.6 1.0 O D:GLY382 2.4 25.4 1.0 C D:GLY382 3.4 24.9 1.0 CA D:GLY382 4.0 25.6 1.0 O D:HOH671 4.2 31.3 1.0 C13 D:5GD501 4.2 24.4 1.0 N D:LEU383 4.4 24.4 1.0 ND1 D:HIS384 4.5 28.2 1.0 C12 D:5GD501 4.7 21.9 1.0 O D:LEU381 4.7 23.9 1.0 CA D:LEU383 4.8 22.5 1.0

O.A.Kharenko, E.M.Gesner, R.G.Patel, K.Norek, A.White, E.Fontano, R.K.Suto, P.R.Young, K.G.Mclure, H.C.Hansen. Rvx-297- A Novel BD2 Selective Inhibitor of Bet Bromodomains. Biochem.Biophys.Res.Commun. V. 477 62 2016.
ISSN: ESSN 1090-2104
PubMed: 27282480
DOI: 10.1016/J.BBRC.2016.06.021