Sodium in PDB 6g0e: BRD4 (BD1) in Complex with Apsc-Derived Ligands

The structure of BRD4 (BD1) in Complex with Apsc-Derived Ligands, PDB code: 6g0e was solved by J.Pretzel, L.Humbeck, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.15 / 1.61
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	34.482, 46.749, 78.347, 90.00, 90.00, 90.00
R / Rfree (%)	23.3 / 26.1

The binding sites of Sodium atom in the BRD4 (BD1) in Complex with Apsc-Derived Ligands (pdb code 6g0e). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the BRD4 (BD1) in Complex with Apsc-Derived Ligands, PDB code: 6g0e:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the BRD4 (BD1) in Complex with Apsc-Derived Ligands


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of BRD4 (BD1) in Complex with Apsc-Derived Ligands within 5.0Å range: probe atom residue distance (Å) B Occ A:Na204 b:37.2 occ:1.00 O A:ASN140 2.4 32.5 1.0 O A:ILE138 2.6 34.3 1.0 O A:TYR137 2.6 30.3 1.0 C A:ILE138 3.2 32.9 1.0 C A:ASN140 3.6 29.2 1.0 CA A:ILE138 3.6 31.2 1.0 C A:TYR137 3.7 33.2 1.0 N A:ASN140 4.0 29.1 1.0 N A:ILE138 4.1 32.8 1.0 N A:TYR139 4.2 29.2 1.0 C A:TYR139 4.3 31.5 1.0 CA A:ASN140 4.4 28.7 1.0 N A:LYS141 4.5 33.5 1.0 CA A:LYS141 4.5 34.8 1.0 CA A:TYR139 4.7 28.0 1.0 O A:TYR139 4.7 29.4 1.0 CG A:LYS141 4.8 44.6 1.0 CA A:TYR137 4.9 28.7 1.0

Sodium binding site 2 out of 2 in the BRD4 (BD1) in Complex with Apsc-Derived Ligands


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of BRD4 (BD1) in Complex with Apsc-Derived Ligands within 5.0Å range: probe atom residue distance (Å) B Occ A:Na205 b:36.5 occ:1.00 OH A:TYR65 2.4 37.1 1.0 O A:LYS160 2.4 33.9 1.0 O A:GLU163 2.4 34.8 1.0 O A:HOH303 2.7 44.5 1.0 CZ A:TYR65 3.2 36.2 1.0 C A:LYS160 3.4 36.1 1.0 CE2 A:TYR65 3.5 37.7 1.0 C A:GLU163 3.5 40.5 1.0 N A:GLU163 4.0 36.0 1.0 CA A:LYS160 4.1 35.8 1.0 CA A:GLU163 4.1 35.6 1.0 CB A:GLU163 4.2 38.6 1.0 CE1 A:TYR65 4.4 37.1 1.0 O A:GLN159 4.5 34.9 1.0 N A:ILE161 4.5 32.4 1.0 O A:HOH339 4.5 41.7 1.0 O A:HOH332 4.6 41.6 1.0 N A:LEU164 4.6 38.2 1.0 CD2 A:TYR65 4.8 31.5 1.0 CA A:ILE161 4.8 37.6 1.0 CB A:LYS160 4.9 41.4 1.0 N A:ASN162 4.9 34.5 1.0 CA A:LEU164 5.0 41.7 1.0 C A:ILE161 5.0 39.3 1.0

L.Humbeck, J.Pretzel, S.Spitzer, O.Koch. Discovery of An Unexpected Similarity in Ligand Binding Between BRD4 and Ppargamma Chemrxiv 2019.
DOI: 10.26434/CHEMRXIV.11472618