Zinc in PDB 4hon: Crystal Structure of Human JMJD2D/KDM4D in Complex with An H3K9ME3 Peptide and 2-Oxoglutarate

The structure of Crystal Structure of Human JMJD2D/KDM4D in Complex with An H3K9ME3 Peptide and 2-Oxoglutarate, PDB code: 4hon 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)	24.93 / 1.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	72.202, 79.675, 175.938, 90.00, 90.00, 90.00
R / Rfree (%)	18.9 / 21.4

The structure of Crystal Structure of Human JMJD2D/KDM4D in Complex with An H3K9ME3 Peptide and 2-Oxoglutarate also contains other interesting chemical elements:

Nickel

(Ni)

2 atoms

The binding sites of Zinc atom in the Crystal Structure of Human JMJD2D/KDM4D in Complex with An H3K9ME3 Peptide and 2-Oxoglutarate (pdb code 4hon). 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 in Complex with An H3K9ME3 Peptide and 2-Oxoglutarate, PDB code: 4hon:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of Human JMJD2D/KDM4D in Complex with An H3K9ME3 Peptide and 2-Oxoglutarate


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 in Complex with An H3K9ME3 Peptide and 2-Oxoglutarate within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn403 b:20.3 occ:1.00 NE2 A:HIS244 2.1 18.1 1.0 SG A:CYS238 2.2 22.1 1.0 SG A:CYS310 2.3 21.9 1.0 SG A:CYS312 2.4 25.1 1.0 CE1 A:HIS244 3.1 20.7 1.0 CD2 A:HIS244 3.1 18.6 1.0 CB A:CYS238 3.2 23.7 1.0 CB A:CYS310 3.5 23.5 1.0 CB A:CYS312 3.6 27.9 1.0 N A:CYS312 3.8 28.8 1.0 CA A:CYS310 3.9 23.6 1.0 N A:SER311 4.0 27.1 1.0 CA A:CYS312 4.2 28.1 1.0 ND1 A:HIS244 4.2 15.3 1.0 CB A:GLU314 4.2 31.5 1.0 CG A:HIS244 4.2 14.1 1.0 C A:CYS310 4.3 25.1 1.0 O A:HOH663 4.5 30.4 1.0 CA A:CYS238 4.6 23.1 1.0 N A:GLU314 4.6 30.6 1.0 C A:SER311 4.7 29.1 1.0 O A:ALA240 4.7 16.0 1.0 C A:CYS312 4.7 29.1 1.0 CG A:GLU314 4.8 36.9 1.0 N A:GLY313 4.9 29.2 1.0 CA A:SER311 4.9 28.5 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Human JMJD2D/KDM4D in Complex with An H3K9ME3 Peptide and 2-Oxoglutarate


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 in Complex with An H3K9ME3 Peptide and 2-Oxoglutarate within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn403 b:26.8 occ:1.00 SG B:CYS238 2.0 29.5 1.0 NE2 B:HIS244 2.2 24.1 1.0 SG B:CYS310 2.2 30.2 1.0 SG B:CYS312 2.4 31.6 1.0 CE1 B:HIS244 3.1 25.0 1.0 CD2 B:HIS244 3.2 23.0 1.0 CB B:CYS238 3.2 33.1 1.0 CB B:CYS310 3.4 30.3 1.0 CB B:CYS312 3.6 37.1 1.0 N B:CYS312 3.7 37.7 1.0 CA B:CYS310 4.0 30.8 1.0 N B:SER311 4.0 34.8 1.0 CA B:CYS312 4.1 37.2 1.0 CB B:GLU314 4.2 39.5 1.0 C B:CYS310 4.2 32.7 1.0 ND1 B:HIS244 4.2 20.9 1.0 CG B:HIS244 4.3 21.8 1.0 N B:GLU314 4.4 38.9 1.0 CA B:CYS238 4.5 33.7 1.0 N B:GLY313 4.6 38.2 1.0 C B:CYS312 4.6 37.8 1.0 CG B:GLU314 4.6 43.0 1.0 O B:ALA240 4.7 20.4 1.0 N B:ALA315 4.8 36.7 1.0 C B:SER311 4.8 38.0 1.0 CA B:GLU314 4.9 38.8 1.0 CA B:PHE241 4.9 20.1 0.5 CA B:SER311 5.0 37.7 1.0 C B:ALA240 5.0 21.0 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