Nickel in PDB 3pua: PHF2 Jumonji-Nog-Ni(II)

The structure of PHF2 Jumonji-Nog-Ni(II), PDB code: 3pua was solved by J.R.Horton, A.K.Upadhyay, H.Hashimoto, X.Zhang, X.Cheng, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	32.88 / 1.89
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	109.575, 65.767, 66.612, 90.00, 102.09, 90.00
R / Rfree (%)	16.4 / 21

The structure of PHF2 Jumonji-Nog-Ni(II) also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Nickel atom in the PHF2 Jumonji-Nog-Ni(II) (pdb code 3pua). 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 PHF2 Jumonji-Nog-Ni(II), PDB code: 3pua:

Nickel binding site 1 out of 1 in the PHF2 Jumonji-Nog-Ni(II)


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of PHF2 Jumonji-Nog-Ni(II) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni2 b:23.8 occ:1.00 OD1 A:ASP251 2.1 22.6 1.0 OH A:TYR321 2.1 21.4 1.0 O2' A:OGA454 2.1 23.7 1.0 NE2 A:HIS249 2.2 21.0 1.0 O2 A:OGA454 2.2 28.3 1.0 O A:HOH462 2.2 24.2 1.0 C2 A:OGA454 2.8 30.4 1.0 C1 A:OGA454 2.8 31.7 1.0 CG A:ASP251 3.0 22.4 1.0 CZ A:TYR321 3.1 19.5 1.0 CD2 A:HIS249 3.1 21.5 1.0 CE1 A:HIS249 3.2 23.3 1.0 OD2 A:ASP251 3.3 21.0 1.0 CE1 A:TYR321 3.8 17.9 1.0 CE2 A:TYR321 4.0 19.3 1.0 O1 A:OGA454 4.1 31.5 1.0 N1 A:OGA454 4.2 33.6 1.0 ND1 A:HIS249 4.3 20.6 1.0 CG A:HIS249 4.3 21.8 1.0 O A:HOH598 4.4 39.1 1.0 CB A:ASP251 4.4 21.9 1.0 C1 A:EDO9 4.6 51.9 1.0 CE1 A:HIS335 4.7 23.6 1.0 CA A:ASP251 4.8 18.9 1.0 C4 A:OGA454 4.9 27.9 1.0 O1 A:EDO9 4.9 63.7 1.0 CD1 A:TYR321 5.0 19.3 1.0

J.R.Horton, A.K.Upadhyay, H.Hashimoto, X.Zhang, X.Cheng. Structural Basis For Human PHF2 Jumonji Domain Interaction with Metal Ions. J.Mol.Biol. V. 406 1 2011.
ISSN: ISSN 0022-2836
PubMed: 21167174
DOI: 10.1016/J.JMB.2010.12.013