Zinc in PDB 3dxt: Crystal Structure of the Catalytic Core Domain of JMJD2D

The structure of Crystal Structure of the Catalytic Core Domain of JMJD2D, PDB code: 3dxt was solved by Z.Chen, G.Zhang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.24 / 1.80
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	71.630, 71.630, 151.295, 90.00, 90.00, 90.00
R / Rfree (%)	17.4 / 20.3

The binding sites of Zinc atom in the Crystal Structure of the Catalytic Core Domain of JMJD2D (pdb code 3dxt). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total only one binding site of Zinc was determined in the Crystal Structure of the Catalytic Core Domain of JMJD2D, PDB code: 3dxt:

Zinc binding site 1 out of 1 in the Crystal Structure of the Catalytic Core Domain of JMJD2D


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 the Catalytic Core Domain of JMJD2D within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn355 b:20.1 occ:1.00 NE2 A:HIS244 2.1 21.5 1.0 SG A:CYS310 2.2 13.1 1.0 SG A:CYS238 2.3 23.6 1.0 SG A:CYS312 2.4 11.4 1.0 CE1 A:HIS244 3.0 20.2 1.0 CB A:CYS238 3.1 24.6 1.0 CD2 A:HIS244 3.1 19.0 1.0 CB A:CYS310 3.3 14.2 1.0 CB A:CYS312 3.4 16.1 1.0 N A:CYS312 3.9 16.6 1.0 CB A:GLU314 4.0 27.9 1.0 CA A:CYS312 4.1 16.5 1.0 CA A:CYS310 4.2 14.8 1.0 ND1 A:HIS244 4.2 22.4 1.0 CG A:HIS244 4.2 21.3 1.0 N A:GLU314 4.4 26.1 1.0 O A:HOH471 4.5 28.8 1.0 CA A:CYS238 4.5 25.3 1.0 N A:SER311 4.6 16.0 1.0 C A:CYS310 4.7 15.8 1.0 O A:ALA240 4.7 20.1 1.0 C A:CYS312 4.7 17.8 1.0 N A:GLY313 4.7 19.6 1.0 CA A:GLU314 4.7 28.0 1.0 CA A:PHE241 4.8 20.3 1.0 N A:ALA315 4.9 30.6 1.0 C A:ALA240 4.9 21.1 1.0

Z.Chen, G.Zhang. Crystal Structure of the Catalytic Core Domain of JMJD2D To Be Published.