Nickel in PDB 5f5a: Crystal Structure of Human JMJD2D Complexed with KDOAM16

The structure of Crystal Structure of Human JMJD2D Complexed with KDOAM16, PDB code: 5f5a was solved by T.Krojer, M.Vollmar, L.Crawley, A.R.Bradley, A.Szykowska, G.F.Ruda, H.Yang, N.Burgess-Brown, P.Brennan, C.Bountra, C.H.Arrowsmith, A.Edwards, U.Oppermann, F.Von Delft, Structural Genomics Consortium (Sgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.40 / 1.41
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	71.280, 71.280, 150.360, 90.00, 90.00, 90.00
R / Rfree (%)	13.1 / 16.5

The structure of Crystal Structure of Human JMJD2D Complexed with KDOAM16 also contains other interesting chemical elements:

Zinc

(Zn)

1 atom

The binding sites of Nickel atom in the Crystal Structure of Human JMJD2D Complexed with KDOAM16 (pdb code 5f5a). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total only one binding site of Nickel was determined in the Crystal Structure of Human JMJD2D Complexed with KDOAM16, PDB code: 5f5a:

Nickel binding site 1 out of 1 in the Crystal Structure of Human JMJD2D Complexed with KDOAM16


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 Human JMJD2D Complexed with KDOAM16 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni402 b:12.7 occ:0.52 OE2 A:GLU194 2.0 18.8 1.0 O A:HOH529 2.2 26.5 1.0 N A:5V0403 2.2 20.1 0.8 NE2 A:HIS280 2.2 13.3 1.0 N1 A:5V0403 2.3 21.7 0.8 NE2 A:HIS192 2.4 18.5 1.0 C A:5V0403 3.0 21.9 0.8 C1 A:5V0403 3.0 21.5 0.8 CE1 A:HIS280 3.0 13.8 1.0 CD A:GLU194 3.1 12.6 1.0 C7 A:5V0403 3.1 23.2 0.8 C5 A:5V0403 3.2 19.3 0.8 CE1 A:HIS192 3.2 17.5 1.0 CD2 A:HIS280 3.4 12.5 1.0 OE1 A:GLU194 3.4 15.1 1.0 CD2 A:HIS192 3.5 17.4 1.0 ND1 A:HIS280 4.2 12.5 1.0 OG A:SER200 4.2 15.0 0.8 C2 A:5V0403 4.4 20.6 0.8 ND1 A:HIS192 4.4 15.8 1.0 CG A:GLU194 4.4 11.6 1.0 CG A:HIS280 4.4 10.5 1.0 C4 A:5V0403 4.5 15.7 0.8 C8 A:5V0403 4.5 19.4 0.8 CG A:HIS192 4.6 13.6 1.0 OD1 A:ASN202 4.8 11.2 0.3 O A:HOH766 4.8 49.3 1.0 CB A:SER200 4.9 11.7 0.2 CB A:SER200 4.9 12.6 0.8 OG A:SER200 4.9 12.4 0.2 OG1 A:THR274 5.0 15.5 1.0 C3 A:5V0403 5.0 19.6 0.8

V.Bavetsias, R.M.Lanigan, G.F.Ruda, B.Atrash, M.G.Mclaughlin, A.Tumber, N.Y.Mok, Y.V.Le Bihan, S.Dempster, K.J.Boxall, F.Jeganathan, S.B.Hatch, P.Savitsky, S.Velupillai, T.Krojer, K.S.England, J.Sejberg, C.Thai, A.Donovan, A.Pal, G.Scozzafava, J.M.Bennett, A.Kawamura, C.Johansson, A.Szykowska, C.Gileadi, N.A.Burgess-Brown, F.Von Delft, U.Oppermann, Z.Walters, J.Shipley, F.I.Raynaud, S.M.Westaway, R.K.Prinjha, O.Fedorov, R.Burke, C.J.Schofield, I.M.Westwood, C.Bountra, S.Muller, R.L.Van Montfort, P.E.Brennan, J.Blagg. 8-Substituted Pyrido[3,4-D]Pyrimidin-4(3H)-One Derivatives As Potent, Cell Permeable, KDM4 (JMJD2) and KDM5 (JARID1) Histone Lysine Demethylase Inhibitors. J.Med.Chem. V. 59 1388 2016.
ISSN: ISSN 0022-2623
PubMed: 26741168
DOI: 10.1021/ACS.JMEDCHEM.5B01635