Nickel 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:

Zinc

(Zn)

2 atoms

The binding sites of Nickel atom in the Crystal Structure of Human JMJD2D/KDM4D Apoenzyme (pdb code 4hoo). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the Crystal Structure of Human JMJD2D/KDM4D Apoenzyme, PDB code: 4hoo:
Jump to Nickel binding site number: 1; 2;

Nickel 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 Nickel with other atoms in the Ni binding site number 1 of Crystal Structure of Human JMJD2D/KDM4D Apoenzyme within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni401 b:36.1 occ:1.00 OE2 A:GLU194 1.8 22.8 1.0 NE2 A:HIS192 2.2 28.3 1.0 NE2 A:HIS280 2.2 22.6 1.0 CD A:GLU194 2.7 26.0 1.0 O A:HOH507 2.8 8.2 1.0 O A:HOH526 2.8 22.2 1.0 CE1 A:HIS192 3.0 25.2 1.0 OE1 A:GLU194 3.1 25.7 1.0 CE1 A:HIS280 3.1 22.6 1.0 CD2 A:HIS280 3.3 22.7 1.0 CD2 A:HIS192 3.3 27.8 1.0 CG A:GLU194 4.1 24.3 1.0 ND1 A:HIS192 4.1 26.5 1.0 OG A:SER200 4.2 32.5 1.0 ND1 A:HIS280 4.3 22.6 1.0 CG A:HIS192 4.3 26.3 1.0 CG A:HIS280 4.4 22.7 1.0 CB A:SER200 4.8 28.2 1.0

Nickel 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 Nickel with other atoms in the Ni binding site number 2 of Crystal Structure of Human JMJD2D/KDM4D Apoenzyme within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni401 b:38.7 occ:1.00 OE2 B:GLU194 1.9 23.8 1.0 NE2 B:HIS280 2.2 24.8 1.0 NE2 B:HIS192 2.3 27.6 1.0 O B:HOH502 2.8 16.9 1.0 CD B:GLU194 2.8 26.6 1.0 CE1 B:HIS192 3.1 25.4 1.0 OE1 B:GLU194 3.2 25.8 1.0 CD2 B:HIS280 3.2 24.7 1.0 CE1 B:HIS280 3.2 25.0 1.0 CD2 B:HIS192 3.4 26.8 1.0 CG B:GLU194 4.2 24.1 1.0 OG B:SER200 4.3 31.9 1.0 ND1 B:HIS192 4.3 25.8 1.0 ND1 B:HIS280 4.3 23.5 1.0 CG B:HIS280 4.4 23.8 1.0 CG B:HIS192 4.5 26.9 1.0 CB B:SER200 4.8 27.8 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