Nickel in PDB 3njy: Crystal Structure of JMJD2A Complexed with 5-Carboxy-8- Hydroxyquinoline

The structure of Crystal Structure of JMJD2A Complexed with 5-Carboxy-8- Hydroxyquinoline, PDB code: 3njy was solved by O.N.F.King, I.J.Clifton, M.Wang, D.J.Maloney, A.Jadhav, U.Oppermann, T.D.Heightman, A.Simeonov, 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)	37.68 / 2.60
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	100.550, 148.990, 56.910, 90.00, 90.00, 90.00
R / Rfree (%)	18 / 22.6

The structure of Crystal Structure of JMJD2A Complexed with 5-Carboxy-8- Hydroxyquinoline also contains other interesting chemical elements:

Zinc

(Zn)

2 atoms

The binding sites of Nickel atom in the Crystal Structure of JMJD2A Complexed with 5-Carboxy-8- Hydroxyquinoline (pdb code 3njy). 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 JMJD2A Complexed with 5-Carboxy-8- Hydroxyquinoline, PDB code: 3njy:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in the Crystal Structure of JMJD2A Complexed with 5-Carboxy-8- Hydroxyquinoline


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 JMJD2A Complexed with 5-Carboxy-8- Hydroxyquinoline within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni501 b:50.2 occ:1.00 OAC A:8XQ360 2.2 36.5 1.0 OE2 A:GLU190 2.2 39.5 1.0 NAI A:8XQ360 2.3 48.7 1.0 O A:HOH508 2.3 45.4 1.0 NE2 A:HIS188 2.4 35.3 1.0 OE1 A:GLU190 2.7 31.7 1.0 CD A:GLU190 2.8 32.1 1.0 CAK A:8XQ360 2.9 40.9 1.0 CAN A:8XQ360 3.0 45.7 1.0 CAE A:8XQ360 3.3 49.1 1.0 CE1 A:HIS188 3.3 33.4 1.0 CD2 A:HIS188 3.3 33.0 1.0 NE2 A:HIS276 3.6 32.8 1.0 O A:HOH440 3.6 38.9 1.0 CAF A:8XQ360 4.3 41.4 1.0 CG A:GLU190 4.3 24.4 1.0 CE1 A:HIS276 4.3 33.4 1.0 CAM A:8XQ360 4.3 47.4 1.0 O A:HOH504 4.3 63.4 1.0 NZ A:LYS241 4.4 71.8 1.0 ND1 A:HIS188 4.4 30.3 1.0 O A:HOH381 4.5 32.7 1.0 CG A:HIS188 4.5 26.6 1.0 CAD A:8XQ360 4.6 48.4 1.0 CD2 A:HIS276 4.6 31.8 1.0 O A:HOH461 4.8 53.3 1.0 CE A:LYS241 4.8 63.4 1.0 CA A:GLU190 4.9 22.9 1.0 CAH A:8XQ360 5.0 47.9 1.0

Nickel binding site 2 out of 2 in the Crystal Structure of JMJD2A Complexed with 5-Carboxy-8- Hydroxyquinoline


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 JMJD2A Complexed with 5-Carboxy-8- Hydroxyquinoline within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni501 b:46.5 occ:1.00 OAC B:8XQ360 2.0 30.3 1.0 NE2 B:HIS188 2.1 30.9 1.0 OE2 B:GLU190 2.2 45.3 1.0 NAI B:8XQ360 2.4 45.3 1.0 CAK B:8XQ360 2.8 36.0 1.0 O B:HOH466 2.9 47.2 1.0 CD B:GLU190 2.9 40.4 1.0 OE1 B:GLU190 2.9 40.2 1.0 CAN B:8XQ360 3.0 44.1 1.0 CE1 B:HIS188 3.1 32.0 1.0 CD2 B:HIS188 3.1 29.7 1.0 CAE B:8XQ360 3.4 45.2 1.0 NE2 B:HIS276 3.7 36.8 1.0 O B:HOH489 3.8 63.3 1.0 O B:HOH488 3.9 44.3 1.0 CAF B:8XQ360 4.1 35.6 1.0 ND1 B:HIS188 4.2 31.7 1.0 CE1 B:HIS276 4.3 35.0 1.0 CG B:HIS188 4.3 28.3 1.0 CG B:GLU190 4.3 34.7 1.0 CAM B:8XQ360 4.4 47.0 1.0 CAD B:8XQ360 4.7 45.1 1.0 O B:HOH406 4.8 36.2 1.0 CA B:GLU190 4.8 33.6 1.0 CD2 B:HIS276 4.8 35.5 1.0 NZ B:LYS241 4.9 64.3 1.0

O.N.F.King, X.S.Li, M.Sakurai, A.Kawamura, N.R.Rose, S.S.Ng, A.M.Quinn, G.Rai, B.T.Mott, P.Beswick, R.J.Klose, U.Oppermann, A.Jadhav, T.D.Heightman, D.J.Maloney, C.J.Schofield, A.Simeonov. Quantitative High-Throughput Screening Identifies 8-Hydroxyquinolines As Cell-Active Histone Demethylase Inhibitors Plos One V. 5 E1553 2010.
ISSN: ESSN 1932-6203
PubMed: 21124847
DOI: 10.1371/JOURNAL.PONE.0015535