Zinc in PDB 5a3w: Crystal Structure of Human Plu-1 (JARID1B) in Complex with Pyridine-2, 6-Dicarboxylic Acid (Pdca)

The structure of Crystal Structure of Human Plu-1 (JARID1B) in Complex with Pyridine-2, 6-Dicarboxylic Acid (Pdca), PDB code: 5a3w was solved by V.Srikannathasan, C.Johansson, C.Gileadi, J.Kopec, C.Strain-Damerell, K.Kupinska, N.A.Burgess-Brown, 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)	19.85 / 2.00
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	142.102, 142.102, 152.256, 90.00, 90.00, 120.00
R / Rfree (%)	18.4 / 21.6

The structure of Crystal Structure of Human Plu-1 (JARID1B) in Complex with Pyridine-2, 6-Dicarboxylic Acid (Pdca) also contains other interesting chemical elements:

Manganese	(Mn)	1 atom
Sodium	(Na)	1 atom

The binding sites of Zinc atom in the Crystal Structure of Human Plu-1 (JARID1B) in Complex with Pyridine-2, 6-Dicarboxylic Acid (Pdca) (pdb code 5a3w). 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 Human Plu-1 (JARID1B) in Complex with Pyridine-2, 6-Dicarboxylic Acid (Pdca), PDB code: 5a3w:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of Human Plu-1 (JARID1B) in Complex with Pyridine-2, 6-Dicarboxylic Acid (Pdca)


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 Pyridine-2, 6-Dicarboxylic Acid (Pdca) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1754 b:27.6 occ:1.00 ND1 A:HIS718 2.1 30.5 1.0 SG A:CYS715 2.3 27.5 1.0 SG A:CYS692 2.3 26.7 1.0 SG A:CYS695 2.3 27.8 1.0 CE1 A:HIS718 2.9 29.1 1.0 CB A:CYS692 3.2 22.8 1.0 CG A:HIS718 3.3 31.8 1.0 CB A:CYS695 3.4 23.9 1.0 CB A:CYS715 3.5 26.0 1.0 CB A:HIS718 3.8 31.7 1.0 N A:CYS695 3.8 33.5 1.0 N A:CYS715 3.9 25.2 1.0 NE2 A:HIS718 4.1 34.8 1.0 CA A:CYS695 4.2 26.9 1.0 CA A:CYS715 4.2 26.9 1.0 CD2 A:HIS718 4.3 31.0 1.0 CG2 A:THR697 4.4 25.4 1.0 N A:HIS718 4.6 28.4 1.0 CB A:LYS694 4.6 29.8 1.0 CA A:CYS692 4.6 29.1 1.0 C A:CYS715 4.7 24.6 1.0 CD A:ARG619 4.7 32.8 0.8 O A:CYS715 4.7 25.4 1.0 CB A:HIS717 4.8 26.5 1.0 CA A:HIS718 4.8 31.5 1.0 C A:CYS695 4.8 24.4 1.0 C A:LYS694 4.9 37.1 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Human Plu-1 (JARID1B) in Complex with Pyridine-2, 6-Dicarboxylic Acid (Pdca)


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 Human Plu-1 (JARID1B) in Complex with Pyridine-2, 6-Dicarboxylic Acid (Pdca) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1755 b:46.5 occ:1.00 SG A:CYS723 2.3 38.7 1.0 SG A:CYS706 2.4 35.4 1.0 CB A:CYS708 2.5 50.8 1.0 SG A:CYS725 2.5 41.1 1.0 SG A:CYS708 2.6 55.8 1.0 CB A:CYS725 3.2 35.8 1.0 CB A:CYS706 3.3 30.1 1.0 CB A:CYS723 3.4 37.2 1.0 CA A:CYS708 3.9 43.1 1.0 N A:CYS725 4.1 38.6 1.0 N A:CYS708 4.2 38.9 1.0 CA A:CYS725 4.3 36.2 1.0 CE1 A:TYR730 4.3 33.6 1.0 C A:CYS708 4.6 54.0 1.0 CA A:CYS706 4.7 31.3 1.0 CA A:CYS723 4.8 35.6 1.0 N A:LYS709 4.8 45.1 1.0 C A:CYS706 4.9 36.0 1.0 N A:SER724 4.9 39.5 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