Sodium in PDB 6ajv: Crystal Structure of BRD4 in Complex with Isoliquiritigenin and Dmso (Cocktail No. 3)

The structure of Crystal Structure of BRD4 in Complex with Isoliquiritigenin and Dmso (Cocktail No. 3), PDB code: 6ajv was solved by T.Yokoyama, K.Matsumoto, Y.Nabeshima, M.Mizuguchi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.07 / 1.45
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	33.784, 47.147, 78.060, 90.00, 90.00, 90.00
R / Rfree (%)	18.9 / 22.7

The binding sites of Sodium atom in the Crystal Structure of BRD4 in Complex with Isoliquiritigenin and Dmso (Cocktail No. 3) (pdb code 6ajv). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Crystal Structure of BRD4 in Complex with Isoliquiritigenin and Dmso (Cocktail No. 3), PDB code: 6ajv:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Crystal Structure of BRD4 in Complex with Isoliquiritigenin and Dmso (Cocktail No. 3)


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 BRD4 in Complex with Isoliquiritigenin and Dmso (Cocktail No. 3) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na201 b:27.3 occ:1.00 O A:VAL90 2.3 23.1 1.0 OD1 A:ASN93 2.4 29.0 1.0 CG A:ASN93 3.4 25.4 1.0 C A:VAL90 3.4 21.5 1.0 ND2 A:ASN93 3.8 30.0 1.0 O A:LYS91 4.0 20.1 1.0 CA A:LYS91 4.1 20.9 1.0 N A:LYS91 4.2 22.0 1.0 CG1 A:VAL90 4.2 29.1 1.0 C A:LYS91 4.2 20.1 1.0 CA A:VAL90 4.4 24.2 1.0 N A:ASN93 4.5 23.2 1.0 CB A:ASN93 4.6 24.6 1.0 CA A:ASN93 4.6 20.2 1.0 CB A:VAL90 4.9 25.3 1.0

Sodium binding site 2 out of 3 in the Crystal Structure of BRD4 in Complex with Isoliquiritigenin and Dmso (Cocktail No. 3)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of BRD4 in Complex with Isoliquiritigenin and Dmso (Cocktail No. 3) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na204 b:23.3 occ:1.00 O A:LYS160 2.2 24.2 1.0 OH A:TYR65 2.2 30.6 1.0 O A:GLU163 2.3 25.3 1.0 O A:HOH364 2.4 24.0 1.0 O A:HOH370 2.4 25.7 1.0 O A:HOH409 3.0 27.9 1.0 CZ A:TYR65 3.2 25.9 1.0 C A:LYS160 3.3 23.1 1.0 C A:GLU163 3.4 25.1 1.0 CE2 A:TYR65 3.5 23.9 1.0 N A:GLU163 3.9 29.2 1.0 CA A:LYS160 4.0 24.6 1.0 CA A:GLU163 4.0 28.2 1.0 CB A:GLU163 4.1 28.9 1.0 CE1 A:TYR65 4.4 28.6 1.0 N A:ILE161 4.4 23.5 1.0 O A:GLN159 4.5 22.6 1.0 N A:LEU164 4.5 28.4 1.0 CA A:ILE161 4.6 23.2 1.0 N A:ASN162 4.7 26.0 1.0 C A:ILE161 4.8 26.9 1.0 O A:HOH396 4.8 33.4 1.0 O A:HOH414 4.8 35.0 1.0 CB A:LYS160 4.8 27.3 1.0 CD2 A:TYR65 4.8 21.8 1.0 CA A:LEU164 5.0 28.7 1.0

Sodium binding site 3 out of 3 in the Crystal Structure of BRD4 in Complex with Isoliquiritigenin and Dmso (Cocktail No. 3)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of BRD4 in Complex with Isoliquiritigenin and Dmso (Cocktail No. 3) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na205 b:72.3 occ:1.00 O A:HOH392 2.4 42.4 1.0 N A:TYR119 2.9 18.3 1.0 O A:TYR119 3.0 20.7 1.0 OD1 A:ASN117 3.2 40.1 1.0 CB A:TYR119 3.3 17.6 1.0 CA A:TYR119 3.4 19.2 1.0 O A:ARG58 3.5 28.5 1.0 CD1 A:LEU63 3.5 19.9 1.0 C A:TYR119 3.5 19.0 1.0 C A:ASN117 3.5 29.5 1.0 N A:TYR118 3.5 22.5 1.0 CA A:ASN117 3.6 28.7 1.0 C A:TYR118 4.0 18.9 1.0 CD2 A:TYR119 4.0 16.3 1.0 CG A:TYR119 4.1 14.2 1.0 O A:ASN117 4.2 39.3 1.0 CG A:ASN117 4.2 39.1 1.0 CG A:LEU63 4.3 19.1 1.0 CD2 A:LEU63 4.3 18.0 1.0 CA A:TYR118 4.3 19.8 1.0 CB A:ASN117 4.5 29.5 1.0 CB A:LEU63 4.5 19.7 1.0 O A:ARG113 4.5 21.6 1.0 N A:ASN117 4.6 29.6 1.0 C A:ARG58 4.6 25.4 1.0 N A:TRP120 4.8 17.2 1.0 OE1 A:GLN59 4.8 69.6 1.0 O A:LEU114 4.8 24.4 1.0 N A:ARG58 5.0 23.1 1.0 O A:TYR118 5.0 20.2 1.0

T.Yokoyama, K.Matsumoto, A.Ostermann, T.E.Schrader, Y.Nabeshima, M.Mizuguchi. Structural and Thermodynamic Characterization of the Binding of Isoliquiritigenin to the First Bromodomain of BRD4. Febs J. V. 286 1656 2019.
ISSN: ISSN 1742-464X
PubMed: 30565859
DOI: 10.1111/FEBS.14736