Zinc 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:

Nickel

(Ni)

2 atoms

The binding sites of Zinc 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 Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of JMJD2A Complexed with 5-Carboxy-8- Hydroxyquinoline, PDB code: 3njy:
Jump to Zinc binding site number: 1; 2;

Zinc 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 Zinc with other atoms in the Zn 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:Zn502 b:50.2 occ:1.00 NE2 A:HIS240 2.1 44.0 1.0 SG A:CYS306 2.2 44.4 1.0 SG A:CYS234 2.2 37.6 1.0 SG A:CYS308 2.5 48.9 1.0 CE1 A:HIS240 3.1 46.1 1.0 CD2 A:HIS240 3.1 41.1 1.0 CB A:CYS234 3.2 38.6 1.0 CB A:CYS308 3.4 49.6 1.0 CB A:CYS306 3.4 40.2 1.0 N A:CYS308 3.6 55.8 1.0 CA A:CYS306 4.0 45.6 1.0 CA A:CYS308 4.0 52.9 1.0 CG A:ARG309 4.0 53.7 1.0 N A:SER307 4.0 57.6 1.0 N A:ARG309 4.2 57.6 1.0 ND1 A:HIS240 4.2 43.0 1.0 C A:CYS306 4.2 50.8 1.0 CG A:HIS240 4.2 38.2 1.0 CD A:ARG309 4.4 59.7 1.0 C A:CYS308 4.4 54.8 1.0 CA A:CYS234 4.6 44.8 1.0 CB A:ARG309 4.6 53.8 1.0 C A:SER307 4.7 58.8 1.0 O A:ALA236 4.8 33.4 1.0 CA A:PHE237 4.9 34.8 1.0 NE A:ARG309 4.9 65.2 1.0 CA A:SER307 5.0 60.0 1.0

Zinc 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 Zinc with other atoms in the Zn 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:Zn502 b:46.9 occ:1.00 NE2 B:HIS240 2.1 45.6 1.0 SG B:CYS308 2.2 55.5 1.0 SG B:CYS234 2.3 40.8 1.0 SG B:CYS306 2.3 52.7 1.0 CD2 B:HIS240 3.1 43.5 1.0 CE1 B:HIS240 3.1 45.0 1.0 CB B:CYS234 3.4 42.6 1.0 CB B:CYS306 3.4 45.4 1.0 N B:CYS308 3.5 57.9 1.0 CB B:CYS308 3.6 52.0 1.0 CA B:CYS306 3.8 51.9 1.0 N B:SER307 3.9 60.4 1.0 CA B:CYS308 4.0 54.7 1.0 C B:CYS306 4.1 58.0 1.0 ND1 B:HIS240 4.2 41.1 1.0 CG B:HIS240 4.2 38.8 1.0 N B:ARG309 4.3 58.4 1.0 CG B:ARG309 4.3 57.2 1.0 O B:HOH443 4.4 48.5 1.0 C B:CYS308 4.5 56.6 1.0 O B:ALA236 4.6 41.9 1.0 C B:SER307 4.6 60.4 1.0 CA B:CYS234 4.7 48.8 1.0 CD B:ARG309 4.7 58.5 1.0 CA B:SER307 4.8 60.6 1.0 CA B:PHE237 4.8 39.4 1.0 C B:ALA236 4.9 41.9 1.0 O B:CYS306 4.9 60.6 1.0 CB B:ARG309 4.9 57.9 1.0 NE B:ARG309 5.0 60.6 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