Sodium in PDB 6ajz: Joint Nentron and X-Ray Structure of BRD4 in Complex with Colchicin

The structure of Joint Nentron and X-Ray Structure of BRD4 in Complex with Colchicin, PDB code: 6ajz was solved by T.Yokoyama, A.Ostermann, T.E.Schrader, Y.Nabeshima, M.Mizuguchi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	N/A / 1.30
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	36.763, 47.101, 79.052, 90.00, 90.00, 90.00
R / Rfree (%)	20.4 / 23.5

The binding sites of Sodium atom in the Joint Nentron and X-Ray Structure of BRD4 in Complex with Colchicin (pdb code 6ajz). 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 Joint Nentron and X-Ray Structure of BRD4 in Complex with Colchicin, PDB code: 6ajz:

Sodium binding site 1 out of 1 in the Joint Nentron and X-Ray Structure of BRD4 in Complex with Colchicin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Joint Nentron and X-Ray Structure of BRD4 in Complex with Colchicin within 5.0Å range: probe atom residue distance (Å) B Occ A:Na201 b:28.3 occ:1.00 O A:ASN140 2.2 26.3 1.0 O A:DOD399 2.3 32.6 1.0 O A:TYR137 2.4 24.8 1.0 O A:ILE138 2.5 24.2 1.0 D1 A:DOD399 2.8 37.8 1.0 HA A:ILE138 3.0 26.9 1.0 D2 A:DOD399 3.0 37.4 1.0 C A:ILE138 3.1 23.0 1.0 D2 A:DOD370 3.2 34.4 1.0 C A:ASN140 3.5 23.8 1.0 D1 A:DOD370 3.5 38.2 1.0 CA A:ILE138 3.5 22.9 1.0 C A:TYR137 3.5 22.4 1.0 HA A:LYS141 3.7 30.9 1.0 D A:ASN140 3.8 23.5 1.0 H A:ASN140 3.8 23.5 0.0 O A:DOD370 3.8 33.0 1.0 N A:ASN140 3.9 21.8 1.0 N A:ILE138 4.0 22.3 1.0 O A:DOD337 4.0 35.8 1.0 N A:TYR139 4.1 23.0 1.0 C A:TYR139 4.2 21.7 1.0 HG2 A:LYS141 4.3 36.0 1.0 CA A:ASN140 4.3 22.0 1.0 HD3 A:PRO142 4.4 35.8 1.0 N A:LYS141 4.4 25.2 1.0 CA A:LYS141 4.5 26.9 1.0 CA A:TYR139 4.6 21.3 1.0 H A:TYR139 4.7 23.0 0.3 D A:TYR139 4.7 23.0 0.7 O A:TYR139 4.7 23.5 1.0 HA A:TYR137 4.7 26.7 1.0 CA A:TYR137 4.8 20.9 1.0 HA A:TYR139 4.8 25.0 1.0 H A:ILE138 4.8 22.1 0.3 D A:ILE138 4.8 22.1 0.7 HA A:ASN140 4.9 27.2 1.0 CB A:ILE138 4.9 25.4 1.0 HG22 A:ILE138 5.0 25.5 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