Zinc in PDB 5a3n: Crystal Structure of Human Plu-1 (JARID1B) in Complex with KDOAM25A

The structure of Crystal Structure of Human Plu-1 (JARID1B) in Complex with KDOAM25A, PDB code: 5a3n was solved by V.Srikannathasan, C.Johansson, C.Gileadi, A.Nuzzi, G.F.Ruda, J.Kopec, F.Vondelft, 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)	122.87 / 2.00
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	141.874, 141.874, 151.865, 90.00, 90.00, 120.00
R / Rfree (%)	18.3 / 20.3

The structure of Crystal Structure of Human Plu-1 (JARID1B) in Complex with KDOAM25A also contains other interesting chemical elements:

Manganese

(Mn)

3 atoms

The binding sites of Zinc atom in the Crystal Structure of Human Plu-1 (JARID1B) in Complex with KDOAM25A (pdb code 5a3n). 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 KDOAM25A, PDB code: 5a3n:
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 KDOAM25A


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 KDOAM25A within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1754 b:27.8 occ:1.00 SG A:CYS692 2.1 27.9 1.0 ND1 A:HIS718 2.3 35.8 1.0 SG A:CYS715 2.3 28.5 1.0 SG A:CYS695 2.4 28.0 1.0 CE1 A:HIS718 3.1 35.7 1.0 CB A:CYS692 3.1 29.3 1.0 CG A:HIS718 3.3 34.8 1.0 CB A:CYS695 3.4 28.8 1.0 CB A:CYS715 3.4 27.4 1.0 CB A:HIS718 3.7 32.7 1.0 N A:CYS695 3.8 31.9 1.0 N A:CYS715 3.9 26.5 1.0 CA A:CYS695 4.2 30.3 1.0 CA A:CYS715 4.2 26.3 1.0 NE2 A:HIS718 4.2 36.0 1.0 CG2 A:THR697 4.3 28.7 1.0 CD2 A:HIS718 4.4 35.9 1.0 CA A:CYS692 4.6 30.9 1.0 N A:HIS718 4.6 29.8 1.0 CB A:LYS694 4.6 36.6 1.0 CD A:ARG619 4.6 32.9 0.7 C A:CYS715 4.7 25.5 1.0 O A:CYS715 4.7 26.0 1.0 CA A:HIS718 4.8 31.2 1.0 C A:CYS695 4.9 30.1 1.0 CB A:HIS717 4.9 30.4 1.0 C A:LYS694 4.9 35.5 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Human Plu-1 (JARID1B) in Complex with KDOAM25A


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 KDOAM25A within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1755 b:39.9 occ:0.40 SG A:CYS708 1.9 65.7 1.0 SG A:CYS723 2.1 42.3 1.0 SG A:CYS706 2.5 38.3 1.0 SG A:CYS725 2.7 48.7 1.0 CB A:CYS708 3.0 54.6 1.0 CB A:CYS725 3.0 41.4 1.0 CB A:CYS723 3.2 39.2 1.0 CB A:CYS706 3.4 35.5 1.0 N A:CYS725 3.9 42.9 1.0 CA A:CYS708 4.1 49.1 1.0 CA A:CYS725 4.1 42.1 1.0 N A:CYS708 4.2 43.3 1.0 CE1 A:TYR730 4.2 36.2 1.0 C A:CYS708 4.5 49.1 1.0 N A:LYS709 4.5 49.1 1.0 CA A:CYS723 4.5 37.4 1.0 C A:CYS723 4.7 37.6 1.0 CG A:LYS709 4.7 54.0 1.0 CA A:CYS706 4.8 34.2 1.0 N A:SER724 4.8 40.6 1.0 CD1 A:TYR730 4.9 34.9 1.0 C A:CYS706 5.0 36.2 1.0

A.Tumber, A.Nuzzi, E.S.Hookway, S.B.Hatch, S.Velupillai, C.Johansson, A.Kawamura, P.Savitsky, C.Yapp, A.Szykowska, N.Wu, C.Bountra, C.Strain-Damerell, N.A.Burgess-Brown, G.F.Ruda, O.Fedorov, S.Munro, K.S.England, R.P.Nowak, C.J.Schofield, N.B.La Thangue, C.Pawlyn, F.Davies, G.Morgan, N.Athanasou, S.Muller, U.Oppermann, P.E.Brennan. Potent and Selective KDM5 Inhibitor Stops Cellular Demethylation of H3K4ME3 at Transcription Start Sites and Proliferation of MM1S Myeloma Cells. Cell Chem Biol V. 24 371 2017.
ISSN: ESSN 2451-9456
PubMed: 28262558
DOI: 10.1016/J.CHEMBIOL.2017.02.006