Nickel in PDB 3kv4: Structure of PHF8 in Complex with Histone H3

The structure of Structure of PHF8 in Complex with Histone H3, PDB code: 3kv4 was solved by J.R.Horton, A.K.Upadhyay, H.H.Qi, X.Zhang, Y.Shi, X.Cheng, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.72 / 2.19
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	73.500, 73.500, 210.800, 90.00, 90.00, 90.00
R / Rfree (%)	21.7 / 25.5

The structure of Structure of PHF8 in Complex with Histone H3 also contains other interesting chemical elements:

Iron	(Fe)	1 atom
Zinc	(Zn)	2 atoms

The binding sites of Nickel atom in the Structure of PHF8 in Complex with Histone H3 (pdb code 3kv4). 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 Structure of PHF8 in Complex with Histone H3, PDB code: 3kv4:

Nickel binding site 1 out of 1 in the Structure of PHF8 in Complex with Histone H3


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Structure of PHF8 in Complex with Histone H3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni451 b:33.9 occ:1.00 OG A:SER214 3.0 15.7 1.0 N A:LEU335 3.1 11.5 1.0 O A:HOH526 3.2 12.6 1.0 N A:VAL216 3.4 17.6 1.0 N A:TRP215 3.5 17.5 1.0 CA A:PHE334 3.7 11.2 1.0 CB A:VAL216 3.7 19.0 1.0 O A:LEU335 3.8 9.1 1.0 CG2 A:VAL216 3.9 16.0 1.0 C A:PHE334 3.9 11.7 1.0 CB A:PHE334 4.0 8.8 1.0 CB A:LEU335 4.0 8.8 1.0 CB A:SER214 4.0 15.5 1.0 CA A:LEU335 4.0 9.9 1.0 CA A:SER214 4.1 15.1 1.0 C A:SER214 4.1 16.7 1.0 CA A:VAL216 4.2 19.9 1.0 CA A:TRP215 4.2 16.4 1.0 CB A:TRP215 4.2 14.7 1.0 C A:TRP215 4.3 16.5 1.0 CZ A:PHE361 4.3 10.8 1.0 C A:LEU335 4.4 10.3 1.0 CG A:LEU335 4.5 10.1 1.0 CE1 A:PHE361 4.5 12.3 1.0 O A:ASN333 4.8 11.4 1.0 N A:GLU217 4.8 24.1 1.0 CD1 A:LEU335 4.9 8.5 1.0 N A:PHE334 4.9 11.5 1.0

J.R.Horton, A.K.Upadhyay, H.H.Qi, X.Zhang, Y.Shi, X.Cheng. Enzymatic and Structural Insights For Substrate Specificity of A Family of Jumonji Histone Lysine Demethylases. Nat.Struct.Mol.Biol. V. 17 38 2010.
ISSN: ISSN 1545-9993
PubMed: 20023638
DOI: 10.1038/NSMB.1753