Zinc 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:

Nickel

(Ni)

2 atoms

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

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


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Free KDM6B Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1703 b:67.6 occ:1.00 SG A:CYS1575 2.3 83.1 1.0 SG A:CYS1605 2.3 82.2 1.0 SG A:CYS1578 2.3 48.9 1.0 SG A:CYS1602 2.3 59.6 1.0 CB A:CYS1575 2.9 45.9 1.0 CB A:CYS1605 3.0 37.7 1.0 CB A:CYS1602 3.4 56.3 1.0 CB A:CYS1578 3.5 75.4 1.0 N A:CYS1602 3.9 42.9 1.0 N A:CYS1578 3.9 55.9 1.0 N A:CYS1605 4.1 49.5 1.0 CG1 A:VAL1580 4.2 20.5 1.0 CA A:CYS1605 4.2 53.4 1.0 CA A:CYS1578 4.2 63.8 1.0 CA A:CYS1602 4.2 45.1 1.0 CA A:CYS1575 4.3 44.2 1.0 CG A:GLU1577 4.5 83.1 1.0 C A:CYS1602 4.8 59.5 1.0 O A:CYS1602 4.8 65.5 1.0 C A:CYS1578 4.9 61.9 1.0 N A:ASP1579 4.9 61.3 1.0 CB A:GLU1577 5.0 82.1 1.0

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


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Free KDM6B Structure within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1703 b:73.5 occ:1.00 SG B:CYS1575 2.1 81.8 1.0 SG B:CYS1605 2.2 80.0 1.0 SG B:CYS1578 2.4 50.9 1.0 SG B:CYS1602 2.5 56.0 1.0 CB B:CYS1575 2.8 43.8 1.0 CB B:CYS1605 2.9 40.2 1.0 CB B:CYS1602 3.6 55.4 1.0 CB B:CYS1578 3.6 77.3 1.0 N B:CYS1578 3.8 57.3 1.0 N B:CYS1602 3.9 49.9 1.0 CA B:CYS1605 4.1 51.9 1.0 N B:CYS1605 4.1 48.1 1.0 CA B:CYS1578 4.2 63.9 1.0 CA B:CYS1575 4.2 46.7 1.0 CA B:CYS1602 4.3 50.6 1.0 CG B:GLU1577 4.3 83.9 1.0 NH2 A:ARG1223 4.3 74.0 1.0 CG1 B:VAL1580 4.3 20.9 1.0 NH1 A:ARG1223 4.4 88.0 1.0 CB B:GLU1577 4.8 82.0 1.0 CZ A:ARG1223 4.8 76.4 1.0 C B:CYS1602 4.9 60.4 1.0 N B:GLU1577 4.9 72.5 1.0 C B:GLU1577 4.9 75.5 1.0 N B:ASP1579 4.9 59.5 1.0 O B:CYS1602 4.9 61.0 1.0 C B:CYS1575 4.9 62.7 1.0 C B:CYS1578 4.9 62.9 1.0 C B:HIS1601 5.0 55.1 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