Nickel in PDB 6f5r: Crystal Structure of KDM4D with GF028 Ligand

The structure of Crystal Structure of KDM4D with GF028 Ligand, PDB code: 6f5r was solved by P.H.Malecki, A.Link, M.S.Weiss, U.Heinemann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.41 / 1.61
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	72.149, 72.149, 152.392, 90.00, 90.00, 90.00
R / Rfree (%)	16.7 / 19.2

The structure of Crystal Structure of KDM4D with GF028 Ligand also contains other interesting chemical elements:

Chlorine	(Cl)	1 atom
Zinc	(Zn)	1 atom

The binding sites of Nickel atom in the Crystal Structure of KDM4D with GF028 Ligand (pdb code 6f5r). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total only one binding site of Nickel was determined in the Crystal Structure of KDM4D with GF028 Ligand, PDB code: 6f5r:

Nickel binding site 1 out of 1 in the Crystal Structure of KDM4D with GF028 Ligand


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Crystal Structure of KDM4D with GF028 Ligand within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni412 b:25.9 occ:1.00 O A:HOH618 2.1 27.4 1.0 OE2 A:GLU194 2.2 25.1 1.0 O A:HOH504 2.2 25.8 1.0 NE2 A:HIS280 2.2 23.1 1.0 NE2 A:HIS192 2.2 23.6 1.0 NAD A:CQZ415 2.3 27.4 1.0 CAF A:CQZ415 2.9 29.4 1.0 CE1 A:HIS192 3.0 26.6 1.0 CE1 A:HIS280 3.1 22.7 1.0 CD A:GLU194 3.2 35.3 1.0 CAB A:CQZ415 3.3 30.7 1.0 CD2 A:HIS280 3.3 22.8 1.0 CD2 A:HIS192 3.3 23.6 1.0 OE1 A:GLU194 3.5 31.2 1.0 NAJ A:CQZ415 3.6 33.0 1.0 O1 A:EDO409 4.1 64.2 1.0 ND1 A:HIS192 4.2 24.8 1.0 C1 A:EDO409 4.2 68.6 1.0 ND1 A:HIS280 4.3 20.9 1.0 CAE A:CQZ415 4.3 29.6 1.0 CG A:HIS192 4.4 20.4 1.0 CG A:HIS280 4.4 20.2 1.0 OG A:SER200 4.5 26.0 1.0 CAA A:CQZ415 4.5 31.9 1.0 CG A:GLU194 4.5 20.3 1.0 CAC A:CQZ415 4.9 30.3 1.0

P.H.Malecki, A.Link, M.S.Weiss, U.Heinemann. Crystal Structure of KDM4D with GF028 Ligand To Be Published.