Sodium in PDB 7rjq: Crystal Structure of Human Bromodomain Containing Protein 4 (BRD4) in Complex with ILF3

The structure of Crystal Structure of Human Bromodomain Containing Protein 4 (BRD4) in Complex with ILF3, PDB code: 7rjq was solved by E.Fedorov, K.Islam, A.Ghosh, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	23.44 / 1.72
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	43.741, 57.115, 123.096, 90, 90, 90
R / Rfree (%)	17.9 / 22.3

The structure of Crystal Structure of Human Bromodomain Containing Protein 4 (BRD4) in Complex with ILF3 also contains other interesting chemical elements:

Chlorine

(Cl)

3 atoms

The binding sites of Sodium atom in the Crystal Structure of Human Bromodomain Containing Protein 4 (BRD4) in Complex with ILF3 (pdb code 7rjq). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 5 binding sites of Sodium where determined in the Crystal Structure of Human Bromodomain Containing Protein 4 (BRD4) in Complex with ILF3, PDB code: 7rjq:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in the Crystal Structure of Human Bromodomain Containing Protein 4 (BRD4) in Complex with ILF3


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 Human Bromodomain Containing Protein 4 (BRD4) in Complex with ILF3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na201 b:44.3 occ:1.00 N A:ASN61 3.0 23.2 1.0 OD1 A:ASN61 3.2 57.0 1.0 CA A:THR60 3.5 19.9 1.0 C A:THR60 3.7 24.8 1.0 CB A:THR60 3.8 26.5 1.0 CG A:ASN61 3.9 55.2 1.0 CB A:ASN61 4.0 39.6 1.0 CA A:ASN61 4.1 27.2 1.0 CG2 A:THR60 4.6 24.4 1.0 O A:GLN59 4.7 26.2 1.0 N A:THR60 4.8 21.0 1.0 OG1 A:THR60 4.9 26.2 1.0 O A:THR60 5.0 22.1 1.0

Sodium binding site 2 out of 5 in the Crystal Structure of Human Bromodomain Containing Protein 4 (BRD4) in Complex with ILF3


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 Human Bromodomain Containing Protein 4 (BRD4) in Complex with ILF3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na202 b:33.7 occ:1.00 N A:GLN59 3.3 23.8 1.0 CB A:ARG58 3.7 26.2 1.0 CA A:ARG58 3.8 22.7 1.0 O A:GLN59 3.9 26.2 1.0 C A:ARG58 4.0 20.6 1.0 CA A:GLN59 4.2 29.3 1.0 CB A:GLN59 4.2 34.2 1.0 C A:GLN59 4.5 25.9 1.0 CG A:ARG58 4.7 26.6 1.0 O A:LYS57 5.0 20.6 1.0

Sodium binding site 3 out of 5 in the Crystal Structure of Human Bromodomain Containing Protein 4 (BRD4) in Complex with ILF3


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 Human Bromodomain Containing Protein 4 (BRD4) in Complex with ILF3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na203 b:62.9 occ:0.50 CZ2 A:TRP81 4.4 31.1 1.0 CD1 B:LEU104 4.7 21.5 1.0 CH2 A:TRP81 4.7 32.1 1.0

Sodium binding site 4 out of 5 in the Crystal Structure of Human Bromodomain Containing Protein 4 (BRD4) in Complex with ILF3


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of Human Bromodomain Containing Protein 4 (BRD4) in Complex with ILF3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na204 b:45.0 occ:1.00 O A:HOH373 3.2 38.7 1.0 ND2 A:ASN121 3.3 20.4 1.0 OD1 A:ASN121 3.6 21.3 1.0 CG A:ASN121 3.9 19.7 1.0 CB A:GLN123 4.1 22.1 1.0 CG A:GLU124 4.4 24.1 1.0 N A:GLU124 4.6 17.1 1.0 CG A:GLN123 4.8 42.7 1.0 C A:GLN123 5.0 17.5 1.0

Sodium binding site 5 out of 5 in the Crystal Structure of Human Bromodomain Containing Protein 4 (BRD4) in Complex with ILF3


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Crystal Structure of Human Bromodomain Containing Protein 4 (BRD4) in Complex with ILF3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na205 b:31.0 occ:1.00 OH A:TYR139 2.7 25.4 1.0 N A:ASP96 3.1 19.0 1.0 CB A:ASP96 3.2 22.7 1.0 CA A:LEU94 3.4 18.5 1.0 C A:LEU94 3.4 18.5 1.0 CA A:ASP96 3.6 19.2 1.0 CB A:LEU94 3.6 16.2 1.0 N A:PRO95 3.7 22.9 1.0 CD A:PRO95 3.8 23.4 1.0 N A:TYR97 3.8 15.5 1.0 CZ A:TYR139 3.8 22.1 1.0 O A:LEU94 3.9 19.4 1.0 CG A:ASP96 3.9 48.3 1.0 C A:ASP96 4.0 16.7 1.0 OD2 A:ASP96 4.1 62.2 1.0 CD2 A:LEU94 4.1 25.2 1.0 O B:HOH302 4.1 31.8 1.0 CE1 A:TYR139 4.1 19.2 1.0 C A:PRO95 4.2 22.9 1.0 CG A:PRO95 4.5 26.2 1.0 CG A:LEU94 4.5 21.6 1.0 CA A:PRO95 4.5 25.3 1.0 CA A:TYR97 4.7 16.3 1.0 N A:LEU94 4.7 18.4 1.0 OD1 A:ASP96 4.8 52.0 1.0 O A:ASN93 4.9 22.4 1.0 O A:ASP96 5.0 19.2 1.0

S.Wagner, E.Fedorov, B.Sudhamalla, H.N.Jnawali, R.Debiec, A.Ghosh, K.Islam. Uncovering the Bromodomain Interactome Using Site-Specific Azide-Acetyllysine Photochemistry, Proteomic Profiling and Structural Characterization To Be Published.