Zinc in PDB 6eiu: Crystal Structure of KDM5B in Complex with KDOPZ29A

The structure of Crystal Structure of KDM5B in Complex with KDOPZ29A, PDB code: 6eiu was solved by V.Srikannathasan, J.A.Newman, A.Szykowska, M.Wright, G.F.Ruda, S.A.Vazquez-Rodriguez, K.Kupinska, C.Strain-Damerell, N.A.Burgess-Brown, C.H.Arrowsmith, A.Edwards, C.Bountra, U.Oppermann, K.Huber, F.Vondelft, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	65.38 / 1.88
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	143.380, 143.380, 153.820, 90.00, 90.00, 120.00
R / Rfree (%)	19.6 / 22.1

The structure of Crystal Structure of KDM5B in Complex with KDOPZ29A also contains other interesting chemical elements:

Manganese

(Mn)

2 atoms

The binding sites of Zinc atom in the Crystal Structure of KDM5B in Complex with KDOPZ29A (pdb code 6eiu). 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 KDM5B in Complex with KDOPZ29A, PDB code: 6eiu:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of KDM5B in Complex with KDOPZ29A


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 KDM5B in Complex with KDOPZ29A within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn801 b:31.8 occ:1.00 ND1 A:HIS718 2.1 31.3 1.0 SG A:CYS692 2.3 30.1 1.0 SG A:CYS715 2.4 32.6 1.0 SG A:CYS695 2.4 31.5 1.0 CE1 A:HIS718 2.9 33.7 1.0 CB A:CYS692 3.2 26.5 1.0 CG A:HIS718 3.2 35.4 1.0 CB A:CYS695 3.4 30.7 1.0 CB A:CYS715 3.5 30.7 1.0 CB A:HIS718 3.7 31.6 1.0 N A:CYS695 3.9 31.9 1.0 N A:CYS715 4.0 26.8 1.0 NE2 A:HIS718 4.1 34.6 1.0 CA A:CYS695 4.2 31.6 1.0 CA A:CYS715 4.2 31.7 1.0 CD2 A:HIS718 4.3 37.1 1.0 CG2 A:THR697 4.4 30.4 1.0 CB A:LYS694 4.6 35.9 1.0 CA A:CYS692 4.7 28.1 1.0 CD A:ARG619 4.7 41.8 1.0 N A:HIS718 4.7 34.7 1.0 C A:CYS715 4.7 29.3 1.0 O A:CYS715 4.7 30.1 1.0 CA A:HIS718 4.9 34.2 1.0 CB A:HIS717 4.9 32.6 1.0 C A:CYS695 4.9 34.6 1.0 C A:LYS694 4.9 42.4 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of KDM5B in Complex with KDOPZ29A


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 KDM5B in Complex with KDOPZ29A within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn817 b:45.5 occ:0.36 SG A:CYS708 2.2 50.1 0.5 SG A:CYS723 2.3 43.6 1.0 SG A:CYS706 2.5 40.7 1.0 CB A:CYS708 2.7 51.3 0.5 SG A:CYS725 2.7 52.9 1.0 CB A:CYS708 2.8 51.5 0.5 CB A:CYS725 3.0 47.3 1.0 SG A:CYS708 3.3 54.1 0.5 CB A:CYS723 3.5 43.4 1.0 CB A:CYS706 3.6 32.8 1.0 CA A:CYS708 3.8 49.7 0.5 CA A:CYS708 3.9 49.8 0.5 N A:CYS725 4.0 45.4 1.0 N A:CYS708 4.1 45.4 1.0 CA A:CYS725 4.2 44.2 1.0 C A:CYS708 4.3 50.1 1.0 CE2 A:TYR730 4.4 41.2 1.0 N A:LYS709 4.4 44.4 1.0 CA A:CYS723 4.8 41.0 1.0 CG A:LYS709 4.8 55.9 1.0 CA A:CYS706 4.9 34.5 1.0 C A:CYS706 4.9 36.7 1.0 N A:SER724 4.9 43.9 1.0 C A:CYS723 5.0 41.9 1.0

V.Srikannathasan, V.Srikannathasan, J.A.Newman, A.Szykowska, M.Wright, G.F.Ruda, S.A.Vazquez-Rodriguez, K.Kupinska, C.Strain-Damerell, N.A.Burgess-Brown, C.H.Arrowsmith, A.Edwards, C.Bountra, U.Oppermann, K.Huber, F.Vondelft. N/A N/A.