Zinc in PDB 5fv3: Crystal Structure of Human JARID1B Construct C2 in Complex with N- Oxalylglycine.

The structure of Crystal Structure of Human JARID1B Construct C2 in Complex with N- Oxalylglycine., PDB code: 5fv3 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)	123.28 / 2.37
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	142.350, 142.350, 152.330, 90.00, 90.00, 120.00
R / Rfree (%)	19.4 / 23.5

The structure of Crystal Structure of Human JARID1B Construct C2 in Complex with N- Oxalylglycine. 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 Construct C2 in Complex with N- Oxalylglycine. (pdb code 5fv3). 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 JARID1B Construct C2 in Complex with N- Oxalylglycine., PDB code: 5fv3:

Zinc binding site 1 out of 1 in the Crystal Structure of Human JARID1B Construct C2 in Complex with N- Oxalylglycine.


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 Construct C2 in Complex with N- Oxalylglycine. within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1754 b:39.1 occ:1.00 ND1 A:HIS718 2.3 43.9 1.0 SG A:CYS692 2.3 39.9 1.0 SG A:CYS715 2.3 43.9 1.0 SG A:CYS695 2.4 49.3 1.0 CE1 A:HIS718 3.1 55.9 1.0 CB A:CYS692 3.1 48.1 1.0 CG A:HIS718 3.4 57.9 1.0 CB A:CYS715 3.4 38.9 1.0 CB A:CYS695 3.5 53.2 1.0 CB A:HIS718 3.8 41.7 1.0 N A:CYS715 3.8 47.3 1.0 N A:CYS695 3.8 60.9 1.0 CA A:CYS715 4.1 40.5 1.0 CA A:CYS695 4.2 53.8 1.0 CG2 A:THR697 4.2 37.7 1.0 NE2 A:HIS718 4.3 66.0 1.0 CD2 A:HIS718 4.4 56.8 1.0 CB A:LYS694 4.5 48.7 1.0 CD A:ARG619 4.6 57.6 1.0 CA A:CYS692 4.6 37.4 1.0 N A:HIS718 4.6 41.4 1.0 C A:CYS715 4.7 43.1 1.0 O A:CYS715 4.7 43.8 1.0 C A:CYS695 4.9 53.6 1.0 CA A:HIS718 4.9 40.2 1.0 C A:LYS694 4.9 50.3 1.0 C A:VAL714 4.9 37.8 1.0 CB A:HIS717 5.0 35.3 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