Sodium in PDB 6y7k: Structure of the BRD9 Bromodomain and Compound 27

The structure of Structure of the BRD9 Bromodomain and Compound 27, PDB code: 6y7k was solved by L.Diaz-Saez, T.Krojer, S.Picaud, F.Von Delft, P.Filippakopoulos, C.H.Arrowsmith, A.Edwards, C.Bountra, K.V.M.Huber, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	53.14 / 1.20
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	108.888, 41.67, 30.19, 90, 102.58, 90
R / Rfree (%)	12.2 / 15.8

The binding sites of Sodium atom in the Structure of the BRD9 Bromodomain and Compound 27 (pdb code 6y7k). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Structure of the BRD9 Bromodomain and Compound 27, PDB code: 6y7k:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Structure of the BRD9 Bromodomain and Compound 27


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of the BRD9 Bromodomain and Compound 27 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na703 b:16.3 occ:1.00 O A:HOH889 2.8 12.5 1.0 OD1 A:ASN211 2.9 7.3 1.0 O A:HOH939 3.0 20.2 1.0 N A:HIS179 3.1 7.6 1.0 O A:HIS179 3.5 7.7 1.0 CB A:HIS179 3.5 9.4 0.5 CB A:HIS179 3.5 9.6 0.5 N A:LYS178 3.6 8.3 1.0 CA A:HIS179 3.6 8.2 1.0 CG2 A:ILE177 3.8 9.1 1.0 CG A:ASN211 3.8 6.9 1.0 C A:HIS179 3.8 7.9 1.0 CD1 A:LEU207 3.9 7.9 1.0 CD2 A:HIS179 3.9 13.7 0.5 O A:HOH867 4.0 24.3 1.0 ND1 A:HIS179 4.0 14.6 0.5 CG A:HIS179 4.0 11.1 0.5 ND2 A:ASN211 4.1 6.8 1.0 C A:LYS178 4.1 8.5 1.0 CG A:HIS179 4.2 11.4 0.5 CA A:LYS178 4.3 9.5 0.5 C A:ILE177 4.3 8.6 1.0 CA A:LYS178 4.3 9.4 0.5 CA A:ILE177 4.4 8.4 1.0 CB A:LYS178 4.6 12.3 0.5 CB A:ILE177 4.7 8.1 1.0 CB A:LYS178 4.7 12.2 0.5 CD1 A:ILE177 4.8 10.0 1.0 N A:PRO180 4.9 8.3 1.0 O A:HOH958 4.9 25.9 1.0

Sodium binding site 2 out of 2 in the Structure of the BRD9 Bromodomain and Compound 27


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of the BRD9 Bromodomain and Compound 27 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na704 b:24.1 occ:1.00 NH1 A:ARG241 2.9 23.3 0.5 O A:HOH907 2.9 42.9 1.0 NE2 A:HIS147 3.1 14.9 1.0 NH1 A:ARG241 3.3 12.9 0.5 NH2 A:ARG241 3.4 17.1 0.5 CG A:MET236 3.6 11.6 0.5 SD A:MET236 3.7 13.2 0.5 CZ A:ARG241 3.7 17.0 0.5 CE1 A:HIS147 4.0 14.5 1.0 CD2 A:HIS147 4.0 12.4 1.0 CG A:MET236 4.0 10.4 0.5 CZ A:ARG241 4.1 26.4 0.5 CG A:GLN151 4.4 14.2 1.0 CE1 A:PHE148 4.6 9.7 1.0 SD A:MET236 4.6 10.6 0.5 NH2 A:ARG241 4.6 26.8 0.5 CD1 A:PHE148 4.6 8.7 1.0 O A:HOH955 4.7 32.4 1.0 CB A:MET236 4.9 10.7 0.5

L.Diaz-Saez, T.Krojer, S.Picaud, F.Von Delft, P.Filippakopoulos, C.H.Arrowsmith, A.Edwards, C.Bountra, K.V.M.Huber. Structure of the BRD9 Bromodomain To Be Published.