Zinc 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:

Iron

(Fe)

2 atoms

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

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


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of JMJD3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2000 b:42.6 occ:1.00 SG A:CYS1602 2.3 37.7 1.0 SG A:CYS1578 2.3 42.5 1.0 SG A:CYS1575 2.3 39.0 1.0 SG A:CYS1605 2.3 46.3 1.0 CB A:CYS1575 3.2 40.6 1.0 CB A:CYS1605 3.3 45.0 1.0 CB A:CYS1578 3.4 45.5 1.0 CB A:CYS1602 3.4 38.6 1.0 N A:CYS1578 3.9 46.8 1.0 N A:CYS1602 4.0 38.0 1.0 CA A:CYS1578 4.2 45.6 1.0 CG2 A:VAL1580 4.2 37.4 0.5 N A:CYS1605 4.3 44.2 1.0 CA A:CYS1602 4.3 38.4 1.0 CA A:CYS1605 4.4 44.6 1.0 O A:HOH2102 4.5 49.5 1.0 CB A:GLU1577 4.6 51.0 1.0 CA A:CYS1575 4.7 41.6 1.0 C A:GLU1577 4.9 48.6 1.0 C A:CYS1578 4.9 44.8 1.0 C A:CYS1602 4.9 39.4 1.0

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


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of JMJD3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn2000 b:45.6 occ:1.00 SG B:CYS1575 2.3 40.7 1.0 SG B:CYS1602 2.3 43.8 1.0 SG B:CYS1605 2.3 43.7 1.0 SG B:CYS1578 2.3 46.1 1.0 CB B:CYS1575 3.2 42.8 1.0 CB B:CYS1605 3.3 45.8 1.0 CB B:CYS1578 3.4 47.5 1.0 CB B:CYS1602 3.5 42.9 1.0 N B:CYS1578 4.0 49.1 1.0 N B:CYS1602 4.1 43.4 1.0 N B:CYS1605 4.2 46.9 1.0 CA B:CYS1578 4.3 47.6 1.0 CG2 B:VAL1580 4.3 41.0 1.0 CA B:CYS1602 4.4 43.1 1.0 CA B:CYS1605 4.4 46.9 1.0 CA B:CYS1575 4.7 43.3 1.0 CB B:GLU1577 4.8 53.1 1.0 C B:CYS1578 4.9 47.0 1.0 C B:CYS1602 4.9 43.9 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