Nickel in PDB 5n16: First Bromodomain (BD1) From Candida Albicans BDF1 Bound to A Dibenzothiazepinone (Compound 1)

The structure of First Bromodomain (BD1) From Candida Albicans BDF1 Bound to A Dibenzothiazepinone (Compound 1), PDB code: 5n16 was solved by F.Mietton, E.Ferri, M.Champleboux, N.Zala, D.Maubon, Y.Zhou, M.Harbut, D.Spittler, C.Garnaud, M.Courcon, M.Chauvel, C.D'enfert, B.A.Kashemirov, M.Hull, M.Cornet, C.E.Mckenna, J.Govin, C.Petosa, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.74 / 1.76
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	75.435, 77.292, 102.593, 90.00, 90.00, 90.00
R / Rfree (%)	17.9 / 21.5

The binding sites of Nickel atom in the First Bromodomain (BD1) From Candida Albicans BDF1 Bound to A Dibenzothiazepinone (Compound 1) (pdb code 5n16). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 5 binding sites of Nickel where determined in the First Bromodomain (BD1) From Candida Albicans BDF1 Bound to A Dibenzothiazepinone (Compound 1), PDB code: 5n16:
Jump to Nickel binding site number: 1; 2; 3; 4; 5;

Nickel binding site 1 out of 5 in the First Bromodomain (BD1) From Candida Albicans BDF1 Bound to A Dibenzothiazepinone (Compound 1)


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of First Bromodomain (BD1) From Candida Albicans BDF1 Bound to A Dibenzothiazepinone (Compound 1) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni402 b:31.4 occ:1.00 O A:HOH621 1.8 27.2 1.0 N A:GLY192 1.9 34.6 1.0 O A:HOH640 2.1 35.1 1.0 O A:HOH542 2.1 31.9 1.0 CA A:GLY192 2.8 27.1 1.0 O A:GLY192 3.4 30.9 1.0 C A:GLY192 3.5 31.6 1.0 O A:HOH623 3.8 43.5 1.0 O A:PRO246 3.9 25.0 1.0 O A:HOH518 3.9 43.9 1.0 CB A:PRO246 4.2 22.3 1.0 N A:ALA193 4.6 27.0 1.0 C A:PRO246 4.6 21.4 1.0 CA A:PRO246 4.7 23.2 1.0

Nickel binding site 2 out of 5 in the First Bromodomain (BD1) From Candida Albicans BDF1 Bound to A Dibenzothiazepinone (Compound 1)


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of First Bromodomain (BD1) From Candida Albicans BDF1 Bound to A Dibenzothiazepinone (Compound 1) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni403 b:78.2 occ:1.00 O A:HOH613 3.1 35.7 1.0 NH2 C:ARG227 3.2 35.7 1.0 N A:LYS318 3.2 43.2 1.0 O C:HOH558 3.6 34.8 1.0 CA A:PRO317 3.7 43.9 1.0 CD C:LYS223 3.9 43.8 1.0 C A:PRO317 4.0 43.0 1.0 CB A:PRO317 4.0 40.3 1.0 CB A:LYS318 4.0 54.3 1.0 CZ C:ARG227 4.1 31.3 1.0 NE C:ARG227 4.2 34.6 1.0 CA A:LYS318 4.2 47.4 1.0 O C:HOH580 4.6 54.9 1.0 CG C:LYS223 4.6 32.2 1.0 CB C:LYS223 4.7 24.6 1.0 NE2 A:GLN214 4.7 33.0 1.0 CE C:LYS223 4.8 55.8 1.0 NZ C:LYS223 4.9 68.8 1.0 N A:PRO317 5.0 41.1 1.0

Nickel binding site 3 out of 5 in the First Bromodomain (BD1) From Candida Albicans BDF1 Bound to A Dibenzothiazepinone (Compound 1)


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of First Bromodomain (BD1) From Candida Albicans BDF1 Bound to A Dibenzothiazepinone (Compound 1) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni401 b:31.4 occ:1.00 O B:HOH542 1.9 34.3 1.0 O B:HOH505 1.9 37.5 1.0 N B:GLY192 2.0 31.5 1.0 O B:HOH651 2.3 40.5 1.0 O B:HOH667 2.3 41.5 1.0 CA B:GLY192 2.9 22.8 1.0 O B:GLY192 3.3 32.2 1.0 C B:GLY192 3.4 31.5 1.0 O B:HOH637 3.7 35.4 1.0 O B:PRO246 3.9 23.7 1.0 O B:HOH544 3.9 42.0 1.0 CB B:PRO246 4.2 25.2 1.0 O B:HOH599 4.2 48.4 1.0 O B:HOH666 4.3 53.3 1.0 N B:ALA193 4.5 25.3 1.0 C B:PRO246 4.7 24.4 1.0 O B:ALA193 4.7 25.4 1.0 CA B:PRO246 4.7 25.6 1.0

Nickel binding site 4 out of 5 in the First Bromodomain (BD1) From Candida Albicans BDF1 Bound to A Dibenzothiazepinone (Compound 1)


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of First Bromodomain (BD1) From Candida Albicans BDF1 Bound to A Dibenzothiazepinone (Compound 1) within 5.0Å range: probe atom residue distance (Å) B Occ C:Ni403 b:30.3 occ:1.00 O C:HOH607 1.9 33.5 1.0 N C:GLY192 1.9 28.2 1.0 O C:HOH505 2.0 31.2 1.0 O C:HOH614 2.3 39.1 1.0 CA C:GLY192 2.8 28.8 1.0 O C:GLY192 3.3 31.7 1.0 C C:GLY192 3.4 31.8 1.0 O C:HOH626 3.7 37.1 1.0 O C:PRO246 3.8 25.3 1.0 O C:HOH603 4.0 44.0 1.0 CB C:PRO246 4.4 22.1 1.0 N C:ALA193 4.5 31.2 1.0 C C:PRO246 4.7 18.7 1.0 O C:ALA193 4.7 30.0 1.0 CA C:PRO246 4.8 20.9 1.0

Nickel binding site 5 out of 5 in the First Bromodomain (BD1) From Candida Albicans BDF1 Bound to A Dibenzothiazepinone (Compound 1)


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 5 of First Bromodomain (BD1) From Candida Albicans BDF1 Bound to A Dibenzothiazepinone (Compound 1) within 5.0Å range: probe atom residue distance (Å) B Occ D:Ni402 b:29.4 occ:1.00 N D:GLY192 2.0 31.2 1.0 O D:HOH526 2.1 30.8 1.0 O D:HOH644 2.2 35.9 1.0 O D:HOH662 2.3 45.6 1.0 CA D:GLY192 3.0 20.9 1.0 O D:GLY192 3.5 27.5 1.0 C D:GLY192 3.6 25.3 1.0 O D:HOH628 3.8 39.5 1.0 O D:HOH668 3.9 31.9 1.0 O D:PRO246 4.0 25.4 1.0 CB D:PRO246 4.2 19.8 1.0 N D:ALA193 4.7 23.3 1.0 C D:PRO246 4.7 18.5 1.0 CA D:PRO246 4.8 19.9 1.0

F.Mietton, E.Ferri, M.Champleboux, N.Zala, D.Maubon, Y.Zhou, M.Harbut, D.Spittler, C.Garnaud, M.Courcon, M.Chauvel, C.D'enfert, B.A.Kashemirov, M.Hull, M.Cornet, C.E.Mckenna, J.Govin, C.Petosa. Selective Bet Bromodomain Inhibition As An Antifungal Therapeutic Strategy. Nat Commun V. 8 15482 2017.
ISSN: ESSN 2041-1723
PubMed: 28516956
DOI: 10.1038/NCOMMS15482