Nickel in PDB 4ai9: JMJD2A Complexed with Daminozide

The structure of JMJD2A Complexed with Daminozide, PDB code: 4ai9 was solved by R.Chowdhury, C.J.Schofield, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.62 / 2.25
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	100.476, 149.752, 57.533, 90.00, 90.00, 90.00
R / Rfree (%)	21.6 / 23.7

The structure of JMJD2A Complexed with Daminozide also contains other interesting chemical elements:

Chlorine	(Cl)	2 atoms
Zinc	(Zn)	2 atoms

The binding sites of Nickel atom in the JMJD2A Complexed with Daminozide (pdb code 4ai9). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the JMJD2A Complexed with Daminozide, PDB code: 4ai9:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in the JMJD2A Complexed with Daminozide


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of JMJD2A Complexed with Daminozide within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni501 b:42.5 occ:1.00 OE2 A:GLU190 2.1 39.2 1.0 NE2 A:HIS188 2.2 25.6 1.0 O01 A:DZA605 2.3 55.5 1.0 NE2 A:HIS276 2.3 31.5 1.0 N04 A:DZA605 2.3 61.7 1.0 O A:HOH2159 2.6 53.9 1.0 C05 A:DZA605 2.8 59.0 1.0 C02 A:DZA605 3.0 58.4 1.0 CE1 A:HIS188 3.0 27.8 1.0 N03 A:DZA605 3.0 60.2 1.0 CD A:GLU190 3.1 36.8 1.0 CE1 A:HIS276 3.2 29.7 1.0 C06 A:DZA605 3.2 63.1 1.0 CD2 A:HIS188 3.2 25.8 1.0 CD2 A:HIS276 3.3 29.1 1.0 OE1 A:GLU190 3.5 35.1 1.0 ND1 A:HIS188 4.2 26.9 1.0 CG A:HIS188 4.3 24.1 1.0 ND1 A:HIS276 4.4 28.9 1.0 O A:HOH2069 4.4 52.9 1.0 CG A:HIS276 4.5 26.9 1.0 C07 A:DZA605 4.5 59.4 1.0 CG A:GLU190 4.5 34.7 1.0 OG A:SER196 4.6 36.8 1.0

Nickel binding site 2 out of 2 in the JMJD2A Complexed with Daminozide


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of JMJD2A Complexed with Daminozide within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni501 b:37.3 occ:1.00 NE2 B:HIS276 2.1 26.6 1.0 OE2 B:GLU190 2.1 31.2 1.0 O01 B:DZA603 2.2 65.0 1.0 N04 B:DZA603 2.2 68.2 1.0 NE2 B:HIS188 2.3 27.2 1.0 O B:HOH2182 2.5 33.8 1.0 C06 B:DZA603 2.6 66.1 1.0 C02 B:DZA603 2.8 68.9 1.0 N03 B:DZA603 2.9 68.8 1.0 CE1 B:HIS188 3.0 28.6 1.0 CE1 B:HIS276 3.0 22.5 1.0 CD2 B:HIS276 3.1 23.7 1.0 C05 B:DZA603 3.2 67.6 1.0 CD B:GLU190 3.3 29.1 1.0 CD2 B:HIS188 3.4 27.8 1.0 OE1 B:GLU190 3.7 26.3 1.0 ND1 B:HIS276 4.2 25.7 1.0 ND1 B:HIS188 4.2 30.6 1.0 CG B:HIS276 4.2 25.2 1.0 C07 B:DZA603 4.4 68.9 1.0 CG B:HIS188 4.4 26.8 1.0 OG B:SER196 4.5 34.1 1.0 CG B:GLU190 4.5 27.5 1.0 CG2 B:THR270 4.9 29.8 1.0 C08 B:DZA603 5.0 69.3 1.0

N.R.Rose, E.C.Woon, A.Tumber, L.J.Walport, R.Chowdhury, X.S.Li, O.N.King, C.Lejeune, S.S.Ng, T.Krojer, M.C.Chan, A.M.Rydzik, R.J.Hopkinson, K.H.Che, M.Daniel, C.Strain-Damerell, C.Gileadi, G.Kochan, I.K.Leung, J.Dunford, K.K.Yeoh, P.J.Ratcliffe, N.Burgess-Brown, F.Von Delft, S.Muller, B.Marsden, P.E.Brennan, M.A.Mcdonough, U.Oppermann, R.J.Klose, C.J.Schofield, A.Kawamura. Plant Growth Regulator Daminozide Is A Selective Inhibitor of Human KDM2/7 Histone Demethylases. J. Med. Chem. V. 55 6639 2012.
ISSN: ISSN 1520-4804
PubMed: 22724510
DOI: 10.1021/JM300677J