Zinc in PDB 5a3t: Crystal Structure of Human Plu-1 (JARID1B) in Complex with KDM5-C49 (2-(((2-((2-(Dimethylamino)Ethyl)(Ethyl)Amino)-2- Oxoethyl)Amino)Methyl) Isonicotinic Acid).

The structure of Crystal Structure of Human Plu-1 (JARID1B) in Complex with KDM5-C49 (2-(((2-((2-(Dimethylamino)Ethyl)(Ethyl)Amino)-2- Oxoethyl)Amino)Methyl) Isonicotinic Acid)., PDB code: 5a3t was solved by V.Srikannathasan, C.Johansson, C.Gileadi, J.Kopec, C.Strain-Damerell, K.Kupinska, N.A.Burgessbrown, F.Von Delft, C.H.Arrowsmith, C.Bountra, A.M.Edwards, U.Oppermann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	122.85 / 1.90
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	141.852, 141.852, 151.509, 90.00, 90.00, 120.00
R / Rfree (%)	19.944 / 22.039

The structure of Crystal Structure of Human Plu-1 (JARID1B) in Complex with KDM5-C49 (2-(((2-((2-(Dimethylamino)Ethyl)(Ethyl)Amino)-2- Oxoethyl)Amino)Methyl) Isonicotinic Acid). also contains other interesting chemical elements:

Nickel	(Ni)	1 atom
Manganese	(Mn)	1 atom

The binding sites of Zinc atom in the Crystal Structure of Human Plu-1 (JARID1B) in Complex with KDM5-C49 (2-(((2-((2-(Dimethylamino)Ethyl)(Ethyl)Amino)-2- Oxoethyl)Amino)Methyl) Isonicotinic Acid). (pdb code 5a3t). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total only one binding site of Zinc was determined in the Crystal Structure of Human Plu-1 (JARID1B) in Complex with KDM5-C49 (2-(((2-((2-(Dimethylamino)Ethyl)(Ethyl)Amino)-2- Oxoethyl)Amino)Methyl) Isonicotinic Acid)., PDB code: 5a3t:

Zinc binding site 1 out of 1 in the Crystal Structure of Human Plu-1 (JARID1B) in Complex with KDM5-C49 (2-(((2-((2-(Dimethylamino)Ethyl)(Ethyl)Amino)-2- Oxoethyl)Amino)Methyl) Isonicotinic Acid).


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 Human Plu-1 (JARID1B) in Complex with KDM5-C49 (2-(((2-((2-(Dimethylamino)Ethyl)(Ethyl)Amino)-2- Oxoethyl)Amino)Methyl) Isonicotinic Acid). within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1754 b:33.4 occ:1.00 SG A:CYS692 2.0 33.4 1.0 SG A:CYS715 2.2 35.4 1.0 ND1 A:HIS718 2.2 43.5 1.0 SG A:CYS695 2.4 33.9 1.0 CE1 A:HIS718 3.1 43.7 1.0 CB A:CYS692 3.1 32.6 1.0 CG A:HIS718 3.3 41.4 1.0 CB A:CYS715 3.4 33.3 1.0 CB A:CYS695 3.4 34.1 1.0 CB A:HIS718 3.7 39.5 1.0 N A:CYS695 3.9 37.4 1.0 N A:CYS715 3.9 30.9 1.0 CA A:CYS715 4.1 31.7 1.0 CA A:CYS695 4.2 35.9 1.0 NE2 A:HIS718 4.2 42.5 1.0 CG2 A:THR697 4.3 34.2 1.0 CD2 A:HIS718 4.4 41.9 1.0 CA A:CYS692 4.6 33.4 1.0 CB A:LYS694 4.6 41.4 1.0 O A:CYS715 4.6 32.8 1.0 N A:HIS718 4.6 36.9 1.0 C A:CYS715 4.6 31.8 1.0 CA A:HIS718 4.8 38.0 1.0 CG A:ARG619 4.9 44.7 1.0 C A:CYS695 4.9 35.3 1.0 CB A:HIS717 4.9 36.6 1.0 C A:LYS694 5.0 41.6 1.0

C.Johansson, S.Velupillai, A.Tumber, A.Szykowska, E.S.Hookway, R.P.Nowak, C.Strain-Damerell, C.Gileadi, M.Philpott, N.Burgess-Brown, N.Wu, J.Kopec, A.Nuzzi, H.Steuber, U.Egner, V.Badock, S.Munro, N.B.Lathangue, S.Westaway, J.Brown, N.Athanasou, R.Prinjha, P.E.Brennan, U.Oppermann. Structural Analysis of Human KDM5B Guides Histone Demethylase Inhibitor Development. Nat.Chem.Biol. V. 12 539 2016.
ISSN: ISSN 1552-4450
PubMed: 27214403
DOI: 10.1038/NCHEMBIO.2087