Sodium in PDB 8cza: Crystal Structure of the First Bromodomain (BD1) of Human Brdt Bound to Gxh-IV-075

The structure of Crystal Structure of the First Bromodomain (BD1) of Human Brdt Bound to Gxh-IV-075, PDB code: 8cza was solved by A.Chan, E.Schonbrunn, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.40 / 2.96
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	94.801, 175.737, 143.071, 90, 90, 90
R / Rfree (%)	20.4 / 26.8

The structure of Crystal Structure of the First Bromodomain (BD1) of Human Brdt Bound to Gxh-IV-075 also contains other interesting chemical elements:

Fluorine	(F)	6 atoms
Chlorine	(Cl)	3 atoms

The binding sites of Sodium atom in the Crystal Structure of the First Bromodomain (BD1) of Human Brdt Bound to Gxh-IV-075 (pdb code 8cza). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of the First Bromodomain (BD1) of Human Brdt Bound to Gxh-IV-075, PDB code: 8cza:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of the First Bromodomain (BD1) of Human Brdt Bound to Gxh-IV-075


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 the First Bromodomain (BD1) of Human Brdt Bound to Gxh-IV-075 within 5.0Å range: probe atom residue distance (Å) B Occ C:Na202 b:36.2 occ:0.50 O C:LEU107 2.5 58.5 1.0 O C:TYR106 2.8 50.2 1.0 HA C:LEU107 3.1 73.0 1.0 O C:ASN109 3.1 55.9 1.0 C C:LEU107 3.2 60.7 1.0 CA C:LEU107 3.6 60.9 1.0 C C:TYR106 3.8 54.5 1.0 C C:ASN109 3.9 56.0 1.0 H C:ASN109 4.1 63.7 1.0 HA C:LYS110 4.1 82.2 1.0 N C:ASN109 4.2 53.0 1.0 N C:LEU107 4.2 59.5 1.0 N C:TYR108 4.2 59.2 1.0 C C:TYR108 4.4 56.9 1.0 N C:LYS110 4.6 61.1 1.0 CA C:ASN109 4.7 55.2 1.0 CA C:TYR108 4.8 57.8 1.0 HA C:TYR108 4.8 69.4 1.0 H C:TYR108 4.8 71.1 1.0 CA C:LYS110 4.9 68.5 1.0 HD23 C:LEU107 4.9 71.2 1.0 HB3 C:LEU107 4.9 74.5 1.0 CB C:LEU107 4.9 62.1 1.0 O C:TYR108 4.9 59.4 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of the First Bromodomain (BD1) of Human Brdt Bound to Gxh-IV-075


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 the First Bromodomain (BD1) of Human Brdt Bound to Gxh-IV-075 within 5.0Å range: probe atom residue distance (Å) B Occ D:Na201 b:41.4 occ:0.50 O D:ASN109 2.5 63.4 1.0 O D:LEU107 2.7 63.8 1.0 O D:TYR106 2.7 57.5 1.0 H D:ASN109 3.5 53.9 1.0 C D:LEU107 3.5 59.0 1.0 C D:ASN109 3.6 57.4 1.0 HA D:LEU107 3.6 61.5 1.0 N D:ASN109 3.8 44.9 1.0 C D:TYR106 3.8 53.5 1.0 CA D:LEU107 4.0 51.2 1.0 HD3 D:PRO111 4.1 66.5 1.0 CA D:ASN109 4.3 55.2 1.0 HA D:LYS110 4.4 69.8 1.0 N D:LEU107 4.4 45.1 1.0 C D:TYR108 4.5 48.9 1.0 N D:TYR108 4.5 56.9 1.0 HG3 D:PRO111 4.5 69.2 1.0 HD12 D:LEU107 4.6 74.0 1.0 N D:LYS110 4.6 63.3 1.0 CA D:LYS110 4.9 58.1 1.0 CD D:PRO111 4.9 55.4 1.0 HA D:ASN109 4.9 66.2 1.0 HA D:TYR106 5.0 61.7 1.0 CA D:TYR108 5.0 52.3 1.0

X.Guan, N.Cheryala, R.M.Karim, A.Chan, N.Berndt, J.Qi, G.I.Georg, E.Schonbrunn. Bivalent Bet Bromodomain Inhibitors Confer Increased Potency and Selectivity For Brdt Via Protein Conformational Plasticity. J.Med.Chem. V. 65 10441 2022.
ISSN: ISSN 0022-2623
PubMed: 35867655
DOI: 10.1021/ACS.JMEDCHEM.2C00453