Zinc in PDB 5fup: Crystal Structure of Human JARID1B in Complex with 2-Oxoglutarate.

The structure of Crystal Structure of Human JARID1B in Complex with 2-Oxoglutarate., PDB code: 5fup was solved by R.Nowak, V.Srikannathasan, C.Johansson, C.Gileadi, K.Kupinska, C.Strain-Damerell, A.Szykowska, R.Talon, F.Von Delft, N.A.Burgess-Brown, 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)	71.17 / 2.15
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	142.340, 142.340, 152.260, 90.00, 90.00, 120.00
R / Rfree (%)	18.3 / 22.7

The structure of Crystal Structure of Human JARID1B in Complex with 2-Oxoglutarate. also contains other interesting chemical elements:

Manganese	(Mn)	2 atoms
Chlorine	(Cl)	1 atom

The binding sites of Zinc atom in the Crystal Structure of Human JARID1B in Complex with 2-Oxoglutarate. (pdb code 5fup). 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 2-Oxoglutarate., PDB code: 5fup:
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 2-Oxoglutarate.


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 2-Oxoglutarate. within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1755 b:29.7 occ:1.00 ND1 A:HIS718 2.1 38.1 1.0 SG A:CYS692 2.2 28.2 1.0 SG A:CYS715 2.3 30.4 1.0 SG A:CYS695 2.4 31.7 1.0 CE1 A:HIS718 2.9 39.1 1.0 CB A:CYS692 3.1 27.1 1.0 CG A:HIS718 3.2 40.7 1.0 CB A:CYS695 3.4 29.4 1.0 CB A:CYS715 3.5 26.1 1.0 CB A:HIS718 3.7 32.8 1.0 N A:CYS695 3.8 34.7 1.0 N A:CYS715 3.9 28.6 1.0 NE2 A:HIS718 4.1 42.9 1.0 CA A:CYS695 4.1 29.4 1.0 CA A:CYS715 4.2 26.4 1.0 CD2 A:HIS718 4.3 40.0 1.0 CG2 A:THR697 4.3 30.6 1.0 CB A:LYS694 4.5 31.7 1.0 N A:HIS718 4.5 32.2 1.0 CA A:CYS692 4.6 32.1 1.0 CD A:ARG619 4.7 38.8 1.0 C A:CYS715 4.7 23.7 1.0 O A:CYS715 4.7 27.9 1.0 CB A:HIS717 4.8 32.9 1.0 CA A:HIS718 4.8 36.1 1.0 C A:LYS694 4.8 41.1 1.0 C A:CYS695 4.8 32.9 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Human JARID1B in Complex with 2-Oxoglutarate.


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 2-Oxoglutarate. within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1756 b:54.0 occ:1.00 SG A:CYS723 2.3 45.0 1.0 CB A:CYS708 2.5 57.7 1.0 SG A:CYS706 2.5 39.9 1.0 SG A:CYS708 2.5 65.9 1.0 SG A:CYS725 2.6 49.1 1.0 CB A:CYS725 3.2 36.9 1.0 CB A:CYS706 3.4 39.1 1.0 CB A:CYS723 3.4 36.0 1.0 CA A:CYS708 3.9 52.3 1.0 N A:CYS725 4.1 47.1 1.0 CA A:CYS725 4.3 45.4 1.0 N A:CYS708 4.3 40.3 1.0 CE1 A:TYR730 4.4 39.4 1.0 C A:CYS708 4.5 59.8 1.0 N A:LYS709 4.7 51.1 1.0 CA A:CYS706 4.7 34.4 1.0 CA A:CYS723 4.7 34.1 1.0 CG A:LYS709 4.9 50.8 1.0 N A:SER724 4.9 44.7 1.0 C A:CYS706 4.9 39.0 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