Nickel in PDB 4ez4: Free KDM6B Structure

The structure of Free KDM6B Structure, PDB code: 4ez4 was solved by Z.J.Cheng, D.J.Patel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.73 / 2.99
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	57.660, 123.707, 82.043, 90.00, 109.62, 90.00
R / Rfree (%)	19 / 25

The structure of Free KDM6B Structure also contains other interesting chemical elements:

Zinc

(Zn)

2 atoms

The binding sites of Nickel atom in the Free KDM6B Structure (pdb code 4ez4). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the Free KDM6B Structure, PDB code: 4ez4:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in the Free KDM6B Structure


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Free KDM6B Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni1702 b:46.5 occ:1.00 OE2 A:GLU1392 2.1 42.2 1.0 NE2 A:HIS1470 2.1 42.3 1.0 NE2 A:HIS1390 2.2 44.6 1.0 O2' A:OGA1701 2.2 67.9 1.0 O2 A:OGA1701 2.2 63.8 1.0 C2 A:OGA1701 2.9 60.8 1.0 C1 A:OGA1701 2.9 60.7 1.0 CE1 A:HIS1470 2.9 45.3 1.0 CD2 A:HIS1390 3.0 32.6 1.0 CD2 A:HIS1470 3.1 41.2 1.0 CE1 A:HIS1390 3.2 41.3 1.0 CD A:GLU1392 3.3 51.8 1.0 OE1 A:GLU1392 4.0 44.7 1.0 ND1 A:HIS1470 4.0 44.3 1.0 CG A:HIS1470 4.1 41.1 1.0 O1 A:OGA1701 4.1 50.3 1.0 CG A:HIS1390 4.2 38.4 1.0 ND1 A:HIS1390 4.2 41.1 1.0 N1 A:OGA1701 4.2 58.8 1.0 CG A:GLU1392 4.4 54.4 1.0 OG A:SER1398 4.7 57.6 1.0

Nickel binding site 2 out of 2 in the Free KDM6B Structure


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Free KDM6B Structure within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni1702 b:41.0 occ:1.00 OE2 B:GLU1392 2.0 39.0 1.0 O2' B:OGA1701 2.1 20.0 1.0 O2 B:OGA1701 2.1 20.0 1.0 NE2 B:HIS1390 2.2 44.6 1.0 NE2 B:HIS1470 2.3 39.4 1.0 C2 B:OGA1701 2.7 20.0 1.0 C1 B:OGA1701 2.8 20.0 1.0 CD2 B:HIS1390 3.1 32.0 1.0 CE1 B:HIS1470 3.1 41.6 1.0 CD B:GLU1392 3.2 51.8 1.0 CD2 B:HIS1470 3.2 40.9 1.0 CE1 B:HIS1390 3.3 39.7 1.0 OE1 B:GLU1392 3.8 43.5 1.0 O1 B:OGA1701 4.0 20.0 1.0 N1 B:OGA1701 4.1 20.0 1.0 ND1 B:HIS1470 4.2 43.2 1.0 CG B:HIS1390 4.2 37.5 1.0 ND1 B:HIS1390 4.3 41.8 1.0 CG B:HIS1470 4.3 39.8 1.0 CG B:GLU1392 4.4 56.7 1.0 OG B:SER1398 4.6 57.2 1.0 C4 B:OGA1701 4.9 20.0 1.0

L.Kruidenier, C.W.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