Nickel in PDB 3oni: Crystal Structure of the Second Bromodomain of Human BRD2 in Complex with the Inhibitor JQ1

The structure of Crystal Structure of the Second Bromodomain of Human BRD2 in Complex with the Inhibitor JQ1, PDB code: 3oni was solved by P.Filippakopoulos, S.Picaud, O.Fedorov, F.Von Delft, C.H.Arrowsmith, A.M.Edwards, J.Weigelt, C.Bountra, J.E.Bradner, Structural Genomicsconsortium (Sgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.16 / 1.61
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	52.600, 71.710, 31.970, 90.00, 90.00, 90.00
R / Rfree (%)	14.8 / 18.4

The structure of Crystal Structure of the Second Bromodomain of Human BRD2 in Complex with the Inhibitor JQ1 also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Nickel atom in the Crystal Structure of the Second Bromodomain of Human BRD2 in Complex with the Inhibitor JQ1 (pdb code 3oni). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the Crystal Structure of the Second Bromodomain of Human BRD2 in Complex with the Inhibitor JQ1, PDB code: 3oni:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in the Crystal Structure of the Second Bromodomain of Human BRD2 in Complex with the Inhibitor JQ1


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Crystal Structure of the Second Bromodomain of Human BRD2 in Complex with the Inhibitor JQ1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni456 b:19.6 occ:0.50 O A:HOH15 3.1 12.9 1.0 NH1 A:ARG419 3.2 9.0 1.0 CD A:ARG419 3.8 8.7 1.0 CA A:ALA416 4.1 6.1 1.0 CZ A:ARG419 4.3 6.8 1.0 CB A:ALA416 4.3 5.3 1.0 N A:ALA416 4.4 6.3 1.0 NE A:ARG419 4.5 8.5 1.0 O A:HOH68 4.5 21.4 1.0 O A:HOH73 4.6 20.2 1.0 O A:HOH13 4.7 11.9 1.0 C A:ALA415 4.8 5.8 1.0 O A:ALA415 5.0 6.0 1.0

Nickel binding site 2 out of 2 in the Crystal Structure of the Second Bromodomain of Human BRD2 in Complex with the Inhibitor JQ1


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Crystal Structure of the Second Bromodomain of Human BRD2 in Complex with the Inhibitor JQ1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni2 b:22.8 occ:1.00 O A:HOH131 2.6 29.8 1.0 O A:ARG406 2.9 10.9 1.0 O A:HOH87 3.2 24.6 1.0 C A:ARG406 4.0 10.9 1.0 CB A:ARG406 4.0 12.2 1.0 O A:HOH125 4.0 33.9 1.0 CG A:ARG409 4.1 16.6 1.0 O A:TYR408 4.3 16.2 1.0 CA A:ARG406 4.5 8.6 1.0 O A:ASP407 4.6 10.7 1.0 O A:HOH36 4.6 10.1 1.0 CA A:ARG409 4.7 14.1 1.0 NE A:ARG409 4.8 17.7 1.0 CD A:ARG409 4.8 14.5 1.0 C A:TYR408 4.9 11.4 1.0 CB A:ARG409 4.9 12.9 1.0 C A:ASP407 5.0 10.7 1.0

P.Filippakopoulos, J.Qi, S.Picaud, Y.Shen, W.B.Smith, O.Fedorov, E.M.Morse, T.Keates, T.T.Hickman, I.Felletar, M.Philpott, S.Munro, M.R.Mckeown, Y.Wang, A.L.Christie, N.West, M.J.Cameron, B.Schwartz, T.D.Heightman, N.La Thangue, C.A.French, O.Wiest, A.L.Kung, S.Knapp, J.E.Bradner. Selective Inhibition of Bet Bromodomains. Nature V. 468 1067 2010.
ISSN: ISSN 0028-0836
PubMed: 20871596
DOI: 10.1038/NATURE09504