Zinc in PDB 5fpu: Crystal Structure of Human JARID1B in Complex with GSKJ1

The structure of Crystal Structure of Human JARID1B in Complex with GSKJ1, PDB code: 5fpu was solved by V.Srikannathasan, R.Nowak, C.Johansson, C.Gileadi, F.Von Delft, C.H.Arrowsmith, C.Bountra, A.Edwards, U.Oppermann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	64.60 / 2.24
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	141.660, 141.660, 151.980, 90.00, 90.00, 120.00
R / Rfree (%)	19 / 22.1

The structure of Crystal Structure of Human JARID1B in Complex with GSKJ1 also contains other interesting chemical elements:

Manganese

(Mn)

2 atoms

The binding sites of Zinc atom in the Crystal Structure of Human JARID1B in Complex with GSKJ1 (pdb code 5fpu). 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 GSKJ1, PDB code: 5fpu:
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 GSKJ1


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 GSKJ1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1754 b:32.3 occ:1.00 ND1 A:HIS718 2.2 34.2 1.0 SG A:CYS715 2.3 31.6 1.0 SG A:CYS692 2.3 32.0 1.0 SG A:CYS695 2.3 30.8 1.0 CE1 A:HIS718 3.0 33.5 1.0 CB A:CYS692 3.2 29.8 1.0 CG A:HIS718 3.3 41.2 1.0 CB A:CYS695 3.4 29.2 1.0 CB A:CYS715 3.5 28.1 1.0 CB A:HIS718 3.8 37.4 1.0 N A:CYS695 3.8 34.5 1.0 N A:CYS715 3.8 32.1 1.0 CA A:CYS715 4.2 31.1 1.0 NE2 A:HIS718 4.2 44.1 1.0 CA A:CYS695 4.2 38.6 1.0 CD2 A:HIS718 4.4 40.4 1.0 CG2 A:THR697 4.4 27.0 1.0 N A:HIS718 4.6 36.9 1.0 CB A:LYS694 4.6 32.7 1.0 O A:CYS715 4.6 31.4 1.0 CA A:CYS692 4.6 28.7 1.0 C A:CYS715 4.6 31.7 1.0 CB A:HIS717 4.8 34.9 1.0 CD A:ARG619 4.8 39.1 0.6 CA A:HIS718 4.8 35.8 1.0 CG A:ARG619 4.9 40.1 0.4 C A:CYS695 4.9 32.3 1.0 C A:LYS694 4.9 43.0 1.0 CD A:ARG619 5.0 34.4 0.4 C A:VAL714 5.0 35.3 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Human JARID1B in Complex with GSKJ1


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 GSKJ1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1755 b:74.1 occ:1.00 SG A:CYS723 2.4 48.1 1.0 CB A:CYS708 2.5 67.8 1.0 SG A:CYS706 2.7 44.7 1.0 SG A:CYS708 3.1 1.0 1.0 SG A:CYS725 3.1 85.6 1.0 CB A:CYS723 3.3 41.6 1.0 CB A:CYS725 3.3 42.2 1.0 CB A:CYS706 3.6 34.5 1.0 CA A:CYS708 3.8 64.3 1.0 N A:CYS708 4.0 57.0 1.0 C A:CYS708 4.3 63.4 1.0 N A:CYS725 4.3 48.7 1.0 N A:LYS709 4.3 55.7 1.0 CE1 A:TYR730 4.4 51.6 1.0 CA A:CYS725 4.5 53.5 1.0 CA A:CYS723 4.7 37.3 1.0 CG A:LYS709 4.8 60.4 1.0 CA A:CYS706 4.9 37.5 1.0 N A:SER724 4.9 47.5 1.0 C A:CYS706 5.0 39.2 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