Nickel in PDB 4bis: JMJD2A Complexed with 8-Hydroxyquinoline-4-Carboxylic Acid

The structure of JMJD2A Complexed with 8-Hydroxyquinoline-4-Carboxylic Acid, PDB code: 4bis was solved by R.Chowdhury, C.Thinnes, C.J.Schofield, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	60.187 / 2.49
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	100.690, 150.150, 57.450, 90.00, 90.00, 90.00
R / Rfree (%)	19.25 / 22.44

The structure of JMJD2A Complexed with 8-Hydroxyquinoline-4-Carboxylic Acid 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 8-Hydroxyquinoline-4-Carboxylic Acid (pdb code 4bis). 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 8-Hydroxyquinoline-4-Carboxylic Acid, PDB code: 4bis:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in the JMJD2A Complexed with 8-Hydroxyquinoline-4-Carboxylic Acid


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 8-Hydroxyquinoline-4-Carboxylic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni501 b:30.3 occ:1.00 O A:HOH2077 2.0 36.7 1.0 OE2 A:GLU190 2.1 20.0 1.0 OAC A:8HQ601 2.1 35.5 1.0 NE2 A:HIS276 2.2 21.6 1.0 NE2 A:HIS188 2.3 23.1 1.0 NAI A:8HQ601 2.3 36.5 1.0 CAK A:8HQ601 3.0 37.4 1.0 CAN A:8HQ601 3.0 36.7 1.0 CE1 A:HIS188 3.1 22.2 1.0 CD2 A:HIS276 3.2 21.9 1.0 CE1 A:HIS276 3.2 21.9 1.0 CD A:GLU190 3.2 19.4 1.0 CAE A:8HQ601 3.4 36.3 1.0 CD2 A:HIS188 3.4 22.4 1.0 OE1 A:GLU190 3.6 21.6 1.0 O A:HOH2083 4.1 47.1 1.0 ND1 A:HIS188 4.2 23.4 1.0 ND1 A:HIS276 4.3 22.9 1.0 CG A:HIS276 4.3 22.8 1.0 CAF A:8HQ601 4.3 37.3 1.0 O A:HOH2075 4.3 55.1 1.0 CAM A:8HQ601 4.4 37.5 1.0 CG A:HIS188 4.4 22.8 1.0 CG A:GLU190 4.5 20.3 1.0 O A:HOH2076 4.5 55.1 1.0 OG A:SER196 4.6 33.7 1.0 CAD A:8HQ601 4.6 38.9 1.0

Nickel binding site 2 out of 2 in the JMJD2A Complexed with 8-Hydroxyquinoline-4-Carboxylic Acid


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 8-Hydroxyquinoline-4-Carboxylic Acid within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni501 b:33.1 occ:1.00 OAC B:8HQ601 2.2 39.4 1.0 O B:HOH2085 2.2 39.6 1.0 OE2 B:GLU190 2.2 28.6 1.0 NE2 B:HIS188 2.2 20.4 1.0 NAI B:8HQ601 2.3 42.7 1.0 NE2 B:HIS276 2.3 25.6 1.0 CE1 B:HIS188 3.0 23.1 1.0 CAK B:8HQ601 3.0 45.1 1.0 CAN B:8HQ601 3.0 44.3 1.0 CD B:GLU190 3.2 27.8 1.0 CE1 B:HIS276 3.3 25.8 1.0 CD2 B:HIS276 3.3 25.0 1.0 CAE B:8HQ601 3.3 40.9 1.0 CD2 B:HIS188 3.4 21.7 1.0 OE1 B:GLU190 3.5 30.3 1.0 O B:HOH2089 4.1 36.8 1.0 ND1 B:HIS188 4.2 24.1 1.0 CAF B:8HQ601 4.3 45.4 1.0 CAM B:8HQ601 4.4 44.5 1.0 ND1 B:HIS276 4.4 24.9 1.0 CG B:HIS188 4.4 21.0 1.0 CG B:HIS276 4.4 24.5 1.0 CG B:GLU190 4.5 24.7 1.0 CAD B:8HQ601 4.6 43.1 1.0 OG B:SER196 4.6 28.2 1.0 NZ B:LYS241 4.9 37.4 1.0

R.J.Hopkinson, A.Tumber, C.Yapp, R.Chowdhury, W.Aik, K.H.Che, X.S.Li, J.B.L.Kristensen, O.N.F.King, M.C.Chan, K.K.Yeoh, H.Choi, L.J.Walport, C.C.Thinnes, J.T.Bush, C.Lejeune, A.M.Rydzik, N.R.Rose, E.A.Bagg, M.A.Mcdonough, T.J.Krojer, W.W.Yue, S.S.Ng, L.Olsen, P.E.Brennan, U.Oppermann, S. Muller, R.J.Klose, P.J.Ratcliffe, C.J.Schofield, A.Kawamura. 8-Hydroxyquinoline-5-Carboxylic Acid Is A Broad Spectrum 2-Oxoglutarate Oxygenase Inhibitor Which Causes Iron Translocation Chem.Rev. V. 4 3110 2013.
ISSN: ISSN 2041-6520
DOI: 10.1039/C3SC51122G