Iron in PDB 2xue: Crystal Structure of JMJD3

The structure of Crystal Structure of JMJD3, PDB code: 2xue was solved by C.Chung, P.Rowland, J.Mosley, P.J.Thomas, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	71.13 / 2.00
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	61.215, 65.154, 77.462, 86.09, 67.19, 68.26
R / Rfree (%)	17.932 / 21.574

The structure of Crystal Structure of JMJD3 also contains other interesting chemical elements:

Zinc

(Zn)

2 atoms

The binding sites of Iron atom in the Crystal Structure of JMJD3 (pdb code 2xue). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 2 binding sites of Iron where determined in the Crystal Structure of JMJD3, PDB code: 2xue:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in the Crystal Structure of JMJD3


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Crystal Structure of JMJD3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe3000 b:49.1 occ:1.00 OE1 A:GLU1392 1.9 36.4 1.0 O1 A:AKG4000 2.0 47.6 1.0 NE2 A:HIS1470 2.1 36.2 1.0 NE2 A:HIS1390 2.1 36.4 1.0 O5 A:AKG4000 2.1 47.4 1.0 O A:HOH2144 2.2 36.8 1.0 C1 A:AKG4000 2.7 47.9 1.0 C2 A:AKG4000 2.8 47.2 1.0 CE1 A:HIS1470 2.9 34.9 1.0 CE1 A:HIS1390 3.0 36.2 1.0 CD A:GLU1392 3.1 35.7 1.0 CD2 A:HIS1390 3.2 33.9 1.0 CD2 A:HIS1470 3.2 33.4 1.0 OE2 A:GLU1392 3.7 37.9 1.0 O2 A:AKG4000 4.0 45.5 1.0 ND1 A:HIS1470 4.1 31.4 1.0 ND1 A:HIS1390 4.1 33.0 1.0 C3 A:AKG4000 4.3 47.7 1.0 CG A:HIS1390 4.3 32.8 1.0 CG A:HIS1470 4.3 31.6 1.0 CG A:GLU1392 4.3 32.2 1.0 O A:HOH2134 4.4 53.3 1.0 OG A:SER1398 4.5 38.6 1.0 O A:HOH2135 4.5 60.0 1.0 CB A:SER1398 4.9 34.4 1.0 O A:HOH2148 4.9 42.0 1.0 O A:HOH2045 5.0 69.1 1.0

Iron binding site 2 out of 2 in the Crystal Structure of JMJD3


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Crystal Structure of JMJD3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe3000 b:49.6 occ:1.00 OE1 B:GLU1392 1.9 34.7 1.0 O1 B:AKG4000 2.0 47.2 1.0 O5 B:AKG4000 2.1 46.0 1.0 NE2 B:HIS1390 2.1 33.3 1.0 NE2 B:HIS1470 2.1 32.2 1.0 O B:HOH2100 2.3 32.6 1.0 C1 B:AKG4000 2.7 47.3 1.0 C2 B:AKG4000 2.8 46.8 1.0 CE1 B:HIS1390 2.9 32.9 1.0 CE1 B:HIS1470 3.0 29.6 1.0 CD B:GLU1392 3.1 34.6 1.0 CD2 B:HIS1470 3.2 29.6 1.0 CD2 B:HIS1390 3.2 30.4 1.0 OE2 B:GLU1392 3.7 36.6 1.0 O2 B:AKG4000 4.0 46.3 1.0 O B:HOH2093 4.1 57.9 1.0 ND1 B:HIS1390 4.1 32.5 1.0 ND1 B:HIS1470 4.2 30.0 1.0 CG B:GLU1392 4.3 33.4 1.0 C3 B:AKG4000 4.3 47.4 1.0 CG B:HIS1390 4.3 29.3 1.0 CG B:HIS1470 4.3 29.2 1.0 OG B:SER1398 4.5 38.7 1.0 O B:HOH2105 4.8 63.5 1.0 CB B:SER1398 4.9 33.8 1.0

L.Kruidenier, C.Chung, Z.Cheng, J.Liddle, K.Che, G.Joberty, M.Bantscheff, C.Bountra, A.Bridges, H.Diallo, D.Eberhard, S.Hutchinson, E.Jones, R.Katso, M.Leveridge, P.K.Mander, J.Mosley, C.Ramirez-Molina, P.Rowland, C.J.Schofield, R.J.Sheppard, J.E.Smith, C.Swales, R.Tanner, P.Thomas, A.Tumber, G.Drewes, U.Oppermann, D.J.Patel, K.Lee, D.M.Wilson. A Selective Jumonji H3K27 Demethylase Inhibitor Modulates the Proinflammatory Macrophage Response Nature V. 488 404 2012.
ISSN: ISSN 0028-0836
PubMed: 22842901
DOI: 10.1038/NATURE11262