Iron in PDB 3pu8: PHF2 Jumonji-Nog-Fe(II) Complex

The structure of PHF2 Jumonji-Nog-Fe(II) Complex, PDB code: 3pu8 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)	33.87 / 1.94
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	65.748, 98.126, 66.517, 90.00, 90.13, 90.00
R / Rfree (%)	18.1 / 23.5

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

Chlorine

(Cl)

2 atoms

The binding sites of Iron atom in the PHF2 Jumonji-Nog-Fe(II) Complex (pdb code 3pu8). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 2 binding sites of Iron where determined in the PHF2 Jumonji-Nog-Fe(II) Complex, PDB code: 3pu8:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in the PHF2 Jumonji-Nog-Fe(II) Complex


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of PHF2 Jumonji-Nog-Fe(II) Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe454 b:29.0 occ:1.00 NE2 B:HIS249 2.2 27.8 1.0 OD1 B:ASP251 2.2 26.1 1.0 O2' B:OGA1 2.2 31.4 1.0 O2 B:OGA1 2.2 30.3 1.0 OH B:TYR321 2.3 23.9 1.0 O B:HOH545 2.4 31.3 1.0 C2 B:OGA1 2.9 32.6 1.0 C1 B:OGA1 2.9 37.6 1.0 CD2 B:HIS249 3.1 25.3 1.0 CG B:ASP251 3.2 26.2 1.0 CZ B:TYR321 3.2 24.1 1.0 CE1 B:HIS249 3.2 24.6 1.0 OD2 B:ASP251 3.4 25.2 1.0 CE1 B:TYR321 3.8 20.8 1.0 CE2 B:TYR321 4.1 22.7 1.0 O1 B:OGA1 4.1 33.6 1.0 N1 B:OGA1 4.2 36.5 1.0 ND1 B:HIS249 4.3 25.6 1.0 CG B:HIS249 4.3 25.2 1.0 O1 B:OXY2 4.5 47.2 1.0 CB B:ASP251 4.5 24.6 1.0 CE1 B:HIS335 4.6 32.5 1.0 O B:HOH37 4.8 35.6 1.0 CA B:ASP251 4.9 25.2 1.0 C4 B:OGA1 4.9 36.5 1.0 O2 B:OXY2 4.9 47.1 1.0 CD1 B:TYR321 5.0 21.7 1.0

Iron binding site 2 out of 2 in the PHF2 Jumonji-Nog-Fe(II) Complex


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of PHF2 Jumonji-Nog-Fe(II) Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe453 b:31.6 occ:1.00 OD1 A:ASP251 2.2 25.6 1.0 NE2 A:HIS249 2.2 29.3 1.0 O2 A:OGA2 2.3 34.3 1.0 OH A:TYR321 2.3 25.4 1.0 O2' A:OGA2 2.3 31.5 1.0 O A:HOH475 2.4 30.0 1.0 C1 A:OGA2 3.0 37.4 1.0 C2 A:OGA2 3.0 36.5 1.0 CD2 A:HIS249 3.1 26.6 1.0 CZ A:TYR321 3.2 27.0 1.0 CE1 A:HIS249 3.2 26.3 1.0 CG A:ASP251 3.2 26.5 1.0 OD2 A:ASP251 3.5 27.2 1.0 CE1 A:TYR321 3.8 22.4 1.0 CE2 A:TYR321 4.0 21.7 1.0 O1 A:OGA2 4.2 36.7 1.0 ND1 A:HIS249 4.3 27.8 1.0 CG A:HIS249 4.3 25.3 1.0 N1 A:OGA2 4.4 36.5 1.0 O2 A:OXY1 4.4 49.2 1.0 CB A:ASP251 4.6 24.6 1.0 CE1 A:HIS335 4.7 28.9 1.0 O A:HOH490 4.8 39.1 1.0 CA A:ASP251 4.9 26.1 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