Nickel in PDB 2wwj: Structure of JMJD2A Complexed with Inhibitor 10A

All present enzymatic activity of Structure of JMJD2A Complexed with Inhibitor 10A:
1.14.11.27;

The structure of Structure of JMJD2A Complexed with Inhibitor 10A, PDB code: 2wwj was solved by N.R.Rose, I.J.Clifton, U.Oppermann, M.A.Mcdonough, C.J.Schofield, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.97 / 2.60
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	101.330, 148.970, 57.110, 90.00, 90.00, 90.00
R / Rfree (%)	17.8 / 24.8

The structure of Structure of JMJD2A Complexed with Inhibitor 10A also contains other interesting chemical elements:

Zinc

(Zn)

2 atoms

The binding sites of Nickel atom in the Structure of JMJD2A Complexed with Inhibitor 10A (pdb code 2wwj). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the Structure of JMJD2A Complexed with Inhibitor 10A, PDB code: 2wwj:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in the Structure of JMJD2A Complexed with Inhibitor 10A


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Structure of JMJD2A Complexed with Inhibitor 10A within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni501 b:36.2 occ:1.00 O A:HOH2035 1.9 23.4 1.0 OE2 A:GLU190 2.0 22.3 1.0 NE2 A:HIS276 2.1 22.6 1.0 OAX A:Y281354 2.2 32.6 1.0 OAW A:Y281354 2.2 33.4 1.0 NE2 A:HIS188 2.3 18.1 1.0 CAR A:Y281354 2.9 41.4 1.0 CAS A:Y281354 3.0 43.7 1.0 CE1 A:HIS188 3.0 18.4 1.0 CD A:GLU190 3.0 19.6 1.0 CE1 A:HIS276 3.0 19.4 1.0 CD2 A:HIS276 3.2 21.0 1.0 OE1 A:GLU190 3.4 18.6 1.0 CD2 A:HIS188 3.4 16.6 1.0 ND1 A:HIS188 4.2 19.1 1.0 ND1 A:HIS276 4.2 22.4 1.0 OAY A:Y281354 4.2 28.2 1.0 N A:Y281354 4.2 38.3 1.0 OG A:SER196 4.3 19.4 1.0 CG A:HIS276 4.3 20.1 1.0 CG A:GLU190 4.4 19.2 1.0 CG A:HIS188 4.4 18.2 1.0 O A:HOH2058 4.7 80.2 1.0 CB A:SER196 4.8 18.6 1.0 CA A:Y281354 4.9 43.0 1.0 CD1 A:Y281354 4.9 45.9 1.0 CG2 A:THR270 4.9 18.0 1.0 CB A:Y281354 4.9 36.0 1.0

Nickel binding site 2 out of 2 in the Structure of JMJD2A Complexed with Inhibitor 10A


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Structure of JMJD2A Complexed with Inhibitor 10A within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni501 b:37.1 occ:1.00 NE2 B:HIS188 2.1 19.8 1.0 OE2 B:GLU190 2.1 30.2 1.0 NE2 B:HIS276 2.2 22.9 1.0 O B:HOH2073 2.2 28.5 1.0 OAX B:Y281354 2.2 23.4 1.0 OAW B:Y281354 2.3 23.6 1.0 CE1 B:HIS188 2.9 21.2 1.0 CAS B:Y281354 3.0 37.5 1.0 CAR B:Y281354 3.0 28.9 1.0 CE1 B:HIS276 3.0 25.5 1.0 CD2 B:HIS188 3.2 18.9 1.0 CD B:GLU190 3.2 23.5 1.0 CD2 B:HIS276 3.3 25.1 1.0 OE1 B:GLU190 3.6 23.5 1.0 ND1 B:HIS188 4.0 13.7 1.0 ND1 B:HIS276 4.2 27.8 1.0 OAY B:Y281354 4.2 30.8 1.0 CG B:HIS188 4.2 16.3 1.0 N B:Y281354 4.3 28.7 1.0 CG B:HIS276 4.3 26.3 1.0 OG B:SER196 4.4 20.9 1.0 CG B:GLU190 4.5 23.9 1.0 CD1 B:Y281354 4.9 30.0 1.0 CA B:Y281354 4.9 39.0 1.0 CB B:SER196 4.9 22.7 1.0 CB B:Y281354 5.0 21.0 1.0

N.R.Rose, E.C.Woon, G.L.Kingham, O.N.King, J.Mecinovic, I.J.Clifton, S.S.Ng, J.Talib-Hardy, U.Oppermann, M.A.Mcdonough, C.J.Schofield. Selective Inhibitors of the JMJD2 Histone Demethylases: Combined Nondenaturing Mass Spectrometric Screening and Crystallographic Approaches. J. Med. Chem. V. 53 1810 2010.
ISSN: ISSN 1520-4804
PubMed: 20088513
DOI: 10.1021/JM901680B