Nickel 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:

Zinc	(Zn)	2 atoms
Chlorine	(Cl)	5 atoms
Sodium	(Na)	2 atoms

The binding sites of Nickel 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 Nickel atom.
In total 2 binding sites of Nickel where determined in the Crystal Structure of JMJD2A Complexed with Bipyridyl Inhibitor, PDB code: 3pdq:
Jump to Nickel binding site number: 1; 2;

Nickel 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 Nickel with other atoms in the Ni 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:Ni501 b:24.0 occ:1.00 N19 A:KC6503 2.1 25.1 1.0 NE2 A:HIS276 2.1 16.7 1.0 OE2 A:GLU190 2.1 19.6 1.0 N06 A:KC6503 2.2 22.5 1.0 NE2 A:HIS188 2.2 24.9 1.0 O A:HOH513 2.3 28.1 1.0 C08 A:KC6503 2.8 36.0 1.0 C07 A:KC6503 2.9 34.1 1.0 CD A:GLU190 3.1 16.9 1.0 CE1 A:HIS276 3.1 18.4 1.0 CD2 A:HIS276 3.1 14.1 1.0 C18 A:KC6503 3.1 35.3 1.0 CE1 A:HIS188 3.2 21.1 1.0 CD2 A:HIS188 3.2 19.6 1.0 C05 A:KC6503 3.3 30.3 1.0 OE1 A:GLU190 3.4 19.5 1.0 C09 A:KC6503 4.2 42.6 1.0 ND1 A:HIS276 4.2 18.6 1.0 CG A:HIS276 4.2 18.2 1.0 ND1 A:HIS188 4.3 21.6 1.0 C20 A:KC6503 4.3 34.1 1.0 CG A:HIS188 4.3 19.6 1.0 CG A:GLU190 4.4 14.5 1.0 C17 A:KC6503 4.4 42.0 1.0 OG A:SER196 4.4 24.0 1.0 C04 A:KC6503 4.6 29.6 1.0 O A:HOH539 4.8 54.6 1.0 C10 A:KC6503 4.8 47.1 1.0 C03 A:KC6503 5.0 30.4 1.0 O A:HOH643 5.0 42.8 1.0

Nickel 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 Nickel with other atoms in the Ni 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:Ni501 b:24.8 occ:1.00 N19 B:KC6503 2.1 29.3 1.0 OE2 B:GLU190 2.2 22.4 1.0 N06 B:KC6503 2.2 22.4 1.0 O B:HOH458 2.2 25.7 1.0 NE2 B:HIS188 2.2 18.1 1.0 NE2 B:HIS276 2.2 16.3 1.0 C08 B:KC6503 2.9 41.3 1.0 C07 B:KC6503 2.9 35.1 1.0 CE1 B:HIS276 3.1 18.3 1.0 CE1 B:HIS188 3.1 18.8 1.0 CD B:GLU190 3.2 21.8 1.0 C18 B:KC6503 3.2 39.1 1.0 CD2 B:HIS188 3.2 19.6 1.0 C05 B:KC6503 3.3 27.4 1.0 CD2 B:HIS276 3.3 17.5 1.0 OE1 B:GLU190 3.5 21.3 1.0 C09 B:KC6503 4.2 45.4 1.0 ND1 B:HIS188 4.3 19.8 1.0 ND1 B:HIS276 4.3 18.2 1.0 C20 B:KC6503 4.3 36.5 1.0 CG B:HIS188 4.3 19.8 1.0 CG B:HIS276 4.4 18.5 1.0 O B:HOH467 4.4 44.1 1.0 OG B:SER196 4.4 24.6 1.0 C17 B:KC6503 4.5 45.0 1.0 CG B:GLU190 4.5 20.3 1.0 C04 B:KC6503 4.5 27.0 1.0 C10 B:KC6503 4.9 51.0 1.0 C03 B:KC6503 5.0 33.4 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