Nickel in PDB 4ura: Crystal Structure of Human JMJD2A in Complex with Compound 14A

The structure of Crystal Structure of Human JMJD2A in Complex with Compound 14A, PDB code: 4ura was solved by T.Krojer, K.S.England, M.Vollmar, L.Crawley, E.Williams, E.Riesebos, A.Szykowska, N.Burgess-Brown, U.Oppermann, P.E.Brennan, C.Bountra, C.H.Arrowsmith, A.Edwards, F.Von Delft, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	60.13 / 2.23
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	101.040, 149.660, 57.860, 90.00, 90.00, 90.00
R / Rfree (%)	20.7 / 25.9

The structure of Crystal Structure of Human JMJD2A in Complex with Compound 14A also contains other interesting chemical elements:

Zinc

(Zn)

2 atoms

The binding sites of Nickel atom in the Crystal Structure of Human JMJD2A in Complex with Compound 14A (pdb code 4ura). 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 Human JMJD2A in Complex with Compound 14A, PDB code: 4ura:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in the Crystal Structure of Human JMJD2A in Complex with Compound 14A


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 JMJD2A in Complex with Compound 14A within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni2501 b:42.9 occ:1.00 OE2 A:GLU190 2.4 35.4 1.0 NE2 A:HIS276 2.4 29.8 1.0 N7 A:LEL4000 2.4 36.4 0.8 NE2 A:HIS188 2.5 36.1 1.0 N3 A:LEL4000 2.6 33.5 0.8 O A:HOH2043 2.6 41.6 1.0 C1 A:LEL4000 3.2 31.4 0.8 CE1 A:HIS188 3.3 32.1 1.0 CD A:GLU190 3.3 35.5 1.0 CD2 A:HIS276 3.3 31.9 1.0 C6 A:LEL4000 3.3 39.1 0.8 C2 A:LEL4000 3.3 42.0 0.8 CE1 A:HIS276 3.4 29.6 1.0 CD2 A:HIS188 3.5 35.6 1.0 OE1 A:GLU190 3.5 31.3 1.0 N2 A:LEL4000 3.7 38.7 0.8 O2 A:EDO1353 4.0 41.1 1.0 O A:HOH2047 4.4 42.4 1.0 ND1 A:HIS188 4.4 33.4 1.0 OG A:SER196 4.5 31.0 1.0 CG A:HIS276 4.5 33.5 1.0 ND1 A:HIS276 4.5 33.4 1.0 CG A:HIS188 4.5 32.1 1.0 C A:LEL4000 4.6 36.5 0.8 C7 A:LEL4000 4.6 42.4 0.8 CG A:GLU190 4.7 31.1 1.0 C3 A:LEL4000 4.7 36.1 0.8 N1 A:LEL4000 4.7 36.4 0.8

Nickel binding site 2 out of 2 in the Crystal Structure of Human JMJD2A in Complex with Compound 14A


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 Human JMJD2A in Complex with Compound 14A within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni2501 b:46.6 occ:1.00 OE2 B:GLU190 2.4 37.1 1.0 N7 B:LEL4000 2.4 37.6 0.8 NE2 B:HIS188 2.5 31.2 1.0 N3 B:LEL4000 2.5 34.7 0.8 NE2 B:HIS276 2.5 30.2 1.0 O B:HOH2062 2.6 41.3 1.0 C6 B:LEL4000 3.2 40.0 0.8 C2 B:LEL4000 3.2 41.5 0.8 CD B:GLU190 3.3 38.3 1.0 CD2 B:HIS188 3.3 32.0 1.0 C1 B:LEL4000 3.4 32.2 0.8 CE1 B:HIS276 3.4 35.3 1.0 OE1 B:GLU190 3.4 37.0 1.0 CE1 B:HIS188 3.5 34.7 1.0 CD2 B:HIS276 3.6 34.9 1.0 N2 B:LEL4000 3.6 40.8 0.8 OG B:SER196 4.4 42.4 1.0 C7 B:LEL4000 4.5 42.3 0.8 CG B:HIS188 4.5 30.5 1.0 ND1 B:HIS276 4.5 31.8 1.0 ND1 B:HIS188 4.6 36.4 1.0 C3 B:LEL4000 4.6 35.8 0.8 N1 B:LEL4000 4.6 44.1 0.8 CG B:HIS276 4.7 32.4 1.0 CG B:GLU190 4.7 33.1 1.0 C B:LEL4000 4.7 36.1 0.8

K.S.England, A.Tumber, T.Krojer, G.Scozzafava, S.S.Ng, M.Daniel, A.Szykowska, K.Che, F.Von Delft, N.A.Burgess-Brown, A.Kawamura, C.J.Schofield, P.E.Brennan. Optimisation of A Triazolopyridine Based Histone Demethylase Inhibitor Yields A Potent and Selective KDM2A (FBXL11) Inhibitor. Medchemcomm V. 5 1879 2014.
ISSN: ISSN 2040-2503
PubMed: 26682034
DOI: 10.1039/C4MD00291A