Zinc in PDB 6ete: Crystal Structure of KDM4D with Tetrazolhydrazide Compound 5

The structure of Crystal Structure of KDM4D with Tetrazolhydrazide Compound 5, PDB code: 6ete was solved by P.H.Malecki, M.S.Weiss, U.Heinemann, A.Link, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.73 / 1.47
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	71.464, 71.464, 151.070, 90.00, 90.00, 90.00
R / Rfree (%)	12.8 / 15.3

The structure of Crystal Structure of KDM4D with Tetrazolhydrazide Compound 5 also contains other interesting chemical elements:

Nickel

(Ni)

2 atoms

The binding sites of Zinc atom in the Crystal Structure of KDM4D with Tetrazolhydrazide Compound 5 (pdb code 6ete). 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 KDM4D with Tetrazolhydrazide Compound 5, PDB code: 6ete:

Zinc binding site 1 out of 1 in the Crystal Structure of KDM4D with Tetrazolhydrazide Compound 5


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 KDM4D with Tetrazolhydrazide Compound 5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:24.4 occ:1.00 NE2 A:HIS244 2.1 22.3 1.0 SG A:CYS310 2.3 28.9 1.0 SG A:CYS238 2.3 25.3 1.0 SG A:CYS312 2.3 28.6 1.0 HB2 A:CYS238 2.9 32.0 1.0 CE1 A:HIS244 3.0 23.0 1.0 H A:CYS312 3.1 41.4 1.0 CD2 A:HIS244 3.1 21.6 1.0 CB A:CYS238 3.1 26.7 1.0 HE1 A:HIS244 3.2 27.6 1.0 HB3 A:CYS312 3.3 38.2 1.0 HB2 A:GLU314 3.3 62.4 1.0 HB2 A:CYS310 3.3 36.3 1.0 HD2 A:HIS244 3.3 25.9 1.0 CB A:CYS310 3.4 30.3 1.0 CB A:CYS312 3.4 31.8 1.0 HB3 A:CYS238 3.5 32.0 1.0 H A:GLU314 3.7 59.1 1.0 HA A:CYS310 3.8 36.5 1.0 N A:CYS312 3.9 34.5 1.0 HA A:PHE241 3.9 24.2 1.0 CA A:CYS310 4.1 30.4 1.0 H A:ALA315 4.1 63.7 1.0 ND1 A:HIS244 4.1 21.3 1.0 CA A:CYS312 4.2 34.2 1.0 HB3 A:CYS310 4.2 36.3 1.0 HB2 A:CYS312 4.2 38.2 1.0 CG A:HIS244 4.2 20.5 1.0 CB A:GLU314 4.2 52.0 1.0 O A:HOH556 4.3 42.1 1.0 N A:GLU314 4.5 49.3 1.0 H A:SER311 4.5 43.0 1.0 CA A:CYS238 4.5 28.6 1.0 HG3 A:GLU314 4.5 65.3 1.0 HA A:CYS238 4.5 34.3 1.0 HG2 A:GLU314 4.5 65.3 1.0 H A:GLY313 4.5 49.9 1.0 C A:CYS310 4.6 33.8 1.0 N A:SER311 4.6 35.8 1.0 O A:HOH785 4.6 41.5 1.0 C A:CYS312 4.7 38.0 1.0 CG A:GLU314 4.7 54.5 1.0 H A:ALA240 4.7 33.0 1.0 O A:ALA240 4.7 21.5 1.0 N A:GLY313 4.8 41.6 1.0 N A:ALA315 4.8 53.1 1.0 HB3 A:GLU314 4.8 62.4 1.0 CA A:PHE241 4.8 20.1 1.0 HB2 A:ALA315 4.9 64.1 1.0 CA A:GLU314 4.9 50.9 1.0 C A:ALA240 4.9 21.5 1.0 HD1 A:HIS244 4.9 25.6 1.0 HB3 A:ALA315 4.9 64.1 1.0 HB3 A:ALA240 4.9 31.0 1.0 N A:PHE241 5.0 20.6 1.0

P.H.Malecki, A.Link, M.S.Weiss, U.Heinemann. Crystal Structure of KDM4D with Tetrazolylhydrazide Ligand NR128 To Be Published.