Nickel 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:

Zinc

(Zn)

1 atom

The binding sites of Nickel 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 Nickel atom.
In total 2 binding sites of Nickel where determined in the Crystal Structure of KDM4D with Tetrazolhydrazide Compound 5, PDB code: 6ete:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in the Crystal Structure of KDM4D with Tetrazolhydrazide Compound 5


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 Tetrazolhydrazide Compound 5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni402 b:16.7 occ:0.92 H54 A:BWK413 1.3 25.1 0.9 H53 A:BWK413 1.6 25.1 0.9 N5 A:BWK413 1.8 20.9 0.9 OE2 A:GLU194 2.0 17.8 1.0 O A:BWK413 2.1 18.2 0.9 NE2 A:HIS280 2.1 13.8 1.0 O A:HOH569 2.1 22.4 1.0 NE2 A:HIS192 2.1 18.2 1.0 H52 A:BWK413 2.4 25.1 0.9 N4 A:BWK413 2.6 22.9 0.9 C3 A:BWK413 2.7 21.2 0.9 CE1 A:HIS192 3.0 20.1 1.0 CE1 A:HIS280 3.0 14.5 1.0 CD A:GLU194 3.0 17.7 1.0 HE1 A:HIS192 3.1 24.1 1.0 HE1 A:HIS280 3.1 17.4 1.0 CD2 A:HIS280 3.2 13.9 1.0 CD2 A:HIS192 3.3 20.2 1.0 HD2 A:HIS280 3.4 16.7 1.0 OE1 A:GLU194 3.4 22.1 1.0 H4 A:BWK413 3.5 27.5 0.9 HD2 A:HIS192 3.5 24.2 1.0 HO1 A:EDO410 4.0 54.3 1.0 O1 A:EDO410 4.1 45.3 1.0 ND1 A:HIS280 4.2 14.9 1.0 ND1 A:HIS192 4.2 20.9 1.0 C2 A:BWK413 4.2 24.7 0.9 CG A:HIS280 4.3 13.7 1.0 CG A:HIS192 4.3 18.3 1.0 HG21 A:THR274 4.4 19.3 1.0 CG A:GLU194 4.4 15.3 1.0 OG A:SER200 4.4 13.3 0.8 HG2 A:GLU194 4.4 18.4 1.0 HB3 A:SER200 4.5 17.3 0.2 H22 A:BWK413 4.5 29.6 0.9 H21 A:BWK413 4.6 29.6 0.9 HB3 A:SER200 4.6 16.1 0.8 HZ3 A:TRP212 4.7 18.7 1.0 HA A:GLU194 4.8 16.7 1.0 HG3 A:GLU194 4.8 18.4 1.0 HB2 A:SER200 4.9 17.3 0.2 HG A:SER200 4.9 16.0 0.8 HD1 A:HIS280 4.9 17.9 1.0 HD1 A:HIS192 4.9 25.0 1.0 HD2 A:PHE189 4.9 22.7 1.0 CB A:SER200 5.0 13.4 0.8

Nickel binding site 2 out of 2 in the Crystal Structure of KDM4D with Tetrazolhydrazide Compound 5


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Crystal Structure of KDM4D with Tetrazolhydrazide Compound 5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni403 b:44.3 occ:0.50 NE2 A:HIS156 2.2 42.9 1.0 O A:HOH721 2.3 56.7 1.0 CD2 A:HIS156 3.0 41.6 1.0 HD2 A:HIS156 3.1 49.9 1.0 O A:HOH748 3.2 39.7 1.0 O A:HOH784 3.2 48.4 1.0 CE1 A:HIS156 3.2 42.8 1.0 HE1 A:HIS156 3.4 51.3 1.0 O A:HOH837 4.0 60.5 1.0 O A:HOH600 4.0 27.3 1.0 HA A:GLU147 4.0 47.2 1.0 CG A:HIS156 4.2 37.9 1.0 ND1 A:HIS156 4.2 41.2 1.0 HD21 A:ASN153 4.5 28.1 1.0 O A:HOH790 4.5 60.9 1.0 HA3 A:GLY155 4.6 28.5 1.0 HB3 A:GLU147 4.6 55.6 1.0 HB2 A:GLU147 4.7 55.6 1.0 O A:GLY155 4.7 29.6 1.0 CA A:GLU147 4.9 39.4 1.0 CB A:GLU147 5.0 46.3 1.0

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