Zinc in PDB 4hoo: Crystal Structure of Human JMJD2D/KDM4D Apoenzyme

The structure of Crystal Structure of Human JMJD2D/KDM4D Apoenzyme, PDB code: 4hoo was solved by S.Krishnan, R.C.Trievel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	17.93 / 2.50
Space group	P 32
Cell size a, b, c (Å), α, β, γ (°)	73.119, 73.119, 136.028, 90.00, 90.00, 120.00
R / Rfree (%)	20.7 / 24.6

The structure of Crystal Structure of Human JMJD2D/KDM4D Apoenzyme also contains other interesting chemical elements:

Nickel

(Ni)

2 atoms

The binding sites of Zinc atom in the Crystal Structure of Human JMJD2D/KDM4D Apoenzyme (pdb code 4hoo). 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 Human JMJD2D/KDM4D Apoenzyme, PDB code: 4hoo:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of Human JMJD2D/KDM4D Apoenzyme


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 Human JMJD2D/KDM4D Apoenzyme within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:43.1 occ:1.00 SG A:CYS310 2.4 42.6 1.0 CB A:CYS238 2.4 40.4 1.0 NE2 A:HIS244 2.5 39.8 1.0 SG A:CYS312 2.6 44.3 1.0 N A:CYS238 2.9 43.7 1.0 CA A:CYS238 3.0 44.4 1.0 CD2 A:HIS244 3.4 36.1 1.0 CB A:CYS310 3.5 40.2 1.0 CE1 A:HIS244 3.5 39.0 1.0 CB A:CYS312 3.6 47.4 1.0 N A:CYS312 3.8 47.8 1.0 CA A:CYS310 4.2 41.5 1.0 CA A:CYS312 4.2 48.7 1.0 N A:GLU314 4.3 48.6 1.0 CB A:GLU314 4.3 49.9 1.0 N A:SER311 4.3 45.2 1.0 C A:CYS310 4.5 43.4 1.0 N A:ALA315 4.5 42.5 1.0 O A:ALA240 4.5 39.0 1.0 C A:CYS238 4.5 46.0 1.0 CG A:HIS244 4.5 34.8 1.0 N A:GLY313 4.5 49.0 1.0 ND1 A:HIS244 4.6 38.2 1.0 C A:CYS312 4.6 48.9 1.0 CA A:GLU314 4.7 48.4 1.0 C A:GLU314 5.0 45.1 1.0 C A:SER311 5.0 49.1 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Human JMJD2D/KDM4D Apoenzyme


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 Human JMJD2D/KDM4D Apoenzyme within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn402 b:57.8 occ:1.00 CB B:CYS238 1.9 20.0 1.0 SG B:CYS310 2.1 43.0 1.0 SG B:CYS312 2.3 45.6 1.0 NE2 B:HIS244 2.4 38.4 1.0 SG B:CYS238 2.5 20.0 1.0 CA B:CYS238 3.2 30.0 1.0 CB B:CYS310 3.2 39.1 1.0 CD2 B:HIS244 3.4 35.9 1.0 CE1 B:HIS244 3.4 39.2 1.0 CB B:CYS312 3.7 46.8 1.0 N B:CYS238 3.8 30.0 1.0 N B:CYS312 4.0 46.8 1.0 CA B:CYS310 4.1 40.3 1.0 CA B:CYS312 4.3 47.9 1.0 N B:GLY313 4.3 47.5 1.0 N B:GLU314 4.3 46.8 1.0 O B:ALA240 4.4 37.5 1.0 C B:CYS238 4.4 30.0 1.0 CB B:GLU314 4.4 45.8 1.0 N B:SER311 4.5 44.0 1.0 CG B:HIS244 4.5 35.5 1.0 C B:CYS310 4.5 42.3 1.0 ND1 B:HIS244 4.5 37.4 1.0 C B:CYS312 4.7 47.9 1.0 C B:ALA240 4.8 38.6 1.0 N B:ALA315 4.8 44.0 1.0 CA B:PHE241 4.8 38.3 1.0 CA B:GLU314 4.9 46.1 1.0 N B:PHE241 4.9 38.7 1.0

S.Krishnan, R.C.Trievel. Structural and Functional Analysis of JMJD2D Reveals Molecular Basis For Site-Specific Demethylation Among JMJD2 Demethylases. Structure V. 21 98 2013.
ISSN: ISSN 0969-2126
PubMed: 23219879
DOI: 10.1016/J.STR.2012.10.018