Zinc in PDB 5fun: Crystal Structure of Human JARID1B in Complex with GSK467

The structure of Crystal Structure of Human JARID1B in Complex with GSK467, PDB code: 5fun was solved by V.Srikannathasan, C.Johansson, C.Gileadi, J.Kopec, F.Von Delft, C.H.Arrowsmith, C.Bountra, A.Edwards, P.Brennan, U.Oppermann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.898 / 2.30
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	142.842, 142.842, 152.011, 90.00, 90.00, 120.00
R / Rfree (%)	18.05 / 21.17

The structure of Crystal Structure of Human JARID1B in Complex with GSK467 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 JARID1B in Complex with GSK467 (pdb code 5fun). 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 JARID1B in Complex with GSK467, PDB code: 5fun:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of Human JARID1B in Complex with GSK467


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 JARID1B in Complex with GSK467 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1754 b:45.8 occ:1.00 ND1 A:HIS718 2.1 40.9 1.0 SG A:CYS695 2.3 47.0 1.0 SG A:CYS715 2.3 46.1 1.0 SG A:CYS692 2.4 40.0 1.0 CE1 A:HIS718 2.8 43.0 1.0 CB A:CYS692 3.2 41.0 1.0 CG A:HIS718 3.3 44.8 1.0 CB A:CYS695 3.4 47.2 1.0 CB A:CYS715 3.5 41.0 1.0 N A:CYS695 3.7 52.1 1.0 CB A:HIS718 3.8 41.2 1.0 N A:CYS715 3.9 40.1 1.0 NE2 A:HIS718 4.0 52.0 1.0 CA A:CYS695 4.2 45.1 1.0 CA A:CYS715 4.2 45.5 1.0 CG2 A:THR697 4.3 36.5 1.0 CD2 A:HIS718 4.3 41.6 1.0 CB A:LYS694 4.4 55.9 1.0 N A:HIS718 4.6 53.5 1.0 CA A:CYS692 4.6 41.8 1.0 CD A:ARG619 4.7 55.3 0.8 C A:CYS715 4.8 41.6 1.0 O A:CYS715 4.8 38.3 1.0 C A:LYS694 4.8 54.8 1.0 CB A:HIS717 4.8 41.5 1.0 C A:CYS695 4.8 46.5 1.0 CA A:HIS718 4.9 50.3 1.0 CA A:LYS694 5.0 55.1 1.0 N A:LYS694 5.0 52.9 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Human JARID1B in Complex with GSK467


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 JARID1B in Complex with GSK467 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1755 b:70.0 occ:1.00 SG A:CYS708 2.0 0.5 1.0 SG A:CYS723 2.4 61.4 1.0 SG A:CYS725 2.4 66.0 1.0 CB A:CYS708 2.8 78.6 1.0 CB A:CYS725 3.0 53.3 1.0 SG A:CYS706 3.0 61.0 1.0 CB A:CYS723 3.3 57.7 1.0 CB A:CYS706 3.8 48.3 1.0 N A:CYS725 4.0 69.4 1.0 CA A:CYS725 4.1 67.6 1.0 CA A:CYS708 4.2 69.4 1.0 CE1 A:TYR730 4.2 59.3 1.0 N A:CYS708 4.4 60.7 1.0 CA A:CYS723 4.7 54.2 1.0 N A:SER724 4.8 65.7 1.0 CD1 A:TYR730 5.0 50.4 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