Zinc in PDB 3pdq: Crystal Structure of JMJD2A Complexed with Bipyridyl Inhibitor

The structure of Crystal Structure of JMJD2A Complexed with Bipyridyl Inhibitor, PDB code: 3pdq was solved by O.N.F.King, K.-H.Chang, N.R.Rose, I.J.Clifton, 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)	45.47 / 1.99
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	100.770, 149.440, 57.300, 90.00, 90.00, 90.00
R / Rfree (%)	16.7 / 20.7

The structure of Crystal Structure of JMJD2A Complexed with Bipyridyl Inhibitor also contains other interesting chemical elements:

Nickel	(Ni)	2 atoms
Chlorine	(Cl)	5 atoms
Sodium	(Na)	2 atoms

The binding sites of Zinc atom in the Crystal Structure of JMJD2A Complexed with Bipyridyl Inhibitor (pdb code 3pdq). 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 Bipyridyl Inhibitor, PDB code: 3pdq:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of JMJD2A Complexed with Bipyridyl Inhibitor


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 Bipyridyl Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:25.3 occ:1.00 NE2 A:HIS240 2.1 26.2 1.0 SG A:CYS306 2.2 26.2 1.0 SG A:CYS234 2.3 24.3 1.0 SG A:CYS308 2.4 24.8 1.0 CE1 A:HIS240 3.0 27.4 1.0 CD2 A:HIS240 3.1 26.7 1.0 CB A:CYS234 3.2 27.3 1.0 CB A:CYS306 3.4 24.7 1.0 CB A:CYS308 3.4 33.4 1.0 N A:CYS308 3.7 41.9 1.0 CA A:CYS306 3.9 26.0 1.0 N A:SER307 4.0 35.4 1.0 CG A:ARG309 4.0 51.0 0.4 CA A:CYS308 4.0 39.4 1.0 CG A:ARG309 4.2 50.6 0.6 ND1 A:HIS240 4.2 26.4 1.0 C A:CYS306 4.2 31.3 1.0 CG A:HIS240 4.3 24.6 1.0 N A:ARG309 4.3 48.7 1.0 C A:CYS308 4.4 42.8 1.0 CA A:CYS234 4.6 34.7 1.0 O A:HOH583 4.6 39.9 1.0 C A:SER307 4.7 43.8 1.0 O A:ALA236 4.7 18.8 1.0 CB A:ARG309 4.8 52.0 0.4 CD A:ARG309 4.8 47.8 0.6 CB A:ARG309 4.8 51.9 0.6 CA A:PHE237 4.8 20.5 1.0 CA A:SER307 4.9 41.8 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of JMJD2A Complexed with Bipyridyl Inhibitor


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 Bipyridyl Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn502 b:28.4 occ:1.00 NE2 B:HIS240 2.2 24.8 1.0 SG B:CYS306 2.2 31.3 1.0 SG B:CYS234 2.3 28.4 1.0 SG B:CYS308 2.3 31.9 1.0 CE1 B:HIS240 3.2 29.3 1.0 CD2 B:HIS240 3.2 22.7 1.0 CB B:CYS234 3.2 31.9 1.0 CB B:CYS306 3.5 26.7 1.0 CB B:CYS308 3.5 41.5 1.0 N B:CYS308 3.6 45.7 1.0 CA B:CYS306 3.9 24.5 1.0 N B:SER307 3.9 39.5 1.0 CA B:CYS308 4.0 45.6 1.0 C B:CYS306 4.2 35.4 1.0 CG B:ARG309 4.2 63.2 1.0 ND1 B:HIS240 4.3 26.4 1.0 CG B:HIS240 4.3 23.2 1.0 N B:ARG309 4.4 58.2 1.0 O B:HOH595 4.5 38.7 1.0 CA B:CYS234 4.5 35.9 1.0 C B:CYS308 4.5 50.8 1.0 C B:SER307 4.7 51.3 1.0 CD B:ARG309 4.8 63.0 1.0 O B:ALA236 4.8 22.2 1.0 CA B:PHE237 4.8 24.2 1.0 O B:HOH419 4.9 36.3 1.0 CA B:SER307 4.9 50.0 1.0 NE B:ARG309 4.9 65.2 1.0 C B:ALA236 5.0 23.1 1.0

K.-H.Chang, O.N.F.King, A.Tumber, E.C.Woon, T.D.Heightman, M.A.Mcdonough, C.J.Schofield, N.R.Rose. Inhibition of Histone Demethylases By 4-Carboxy-2,2'-Bipyridyl Compounds Chemmedchem V. 6 759 2011.
ISSN: ISSN 1860-7179
PubMed: 21412984
DOI: 10.1002/CMDC.201100026