Nickel in PDB 5tvs: JMJD2A in Complex with Ni(II)

The structure of JMJD2A in Complex with Ni(II), PDB code: 5tvs was solved by B.Cascella, S.G.Lee, J.M.Jez, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.83 / 2.75
Space group	P 2 21 21
Cell size a, b, c (Å), α, β, γ (°)	56.689, 101.140, 148.894, 90.00, 90.00, 90.00
R / Rfree (%)	20.3 / 26.7

The structure of JMJD2A in Complex with Ni(II) also contains other interesting chemical elements:

Zinc

(Zn)

2 atoms

The binding sites of Nickel atom in the JMJD2A in Complex with Ni(II) (pdb code 5tvs). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the JMJD2A in Complex with Ni(II), PDB code: 5tvs:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in the JMJD2A in Complex with Ni(II)


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of JMJD2A in Complex with Ni(II) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni401 b:55.9 occ:1.00 OE2 A:GLU190 1.7 35.9 1.0 NE2 A:HIS276 2.1 70.1 1.0 NE2 A:HIS188 2.4 89.3 1.0 CD2 A:HIS276 2.8 53.5 1.0 CD A:GLU190 2.9 76.9 1.0 CE1 A:HIS188 3.0 94.9 1.0 CE1 A:HIS276 3.3 61.2 1.0 OE1 A:GLU190 3.5 76.2 1.0 CD2 A:HIS188 3.6 68.2 1.0 CG A:HIS276 4.1 47.5 1.0 CG A:GLU190 4.2 51.6 1.0 ND1 A:HIS188 4.2 92.8 1.0 ND1 A:HIS276 4.3 40.7 1.0 CD1 A:PHE185 4.4 53.9 1.0 CG A:HIS188 4.6 51.2 1.0 CZ3 A:TRP208 4.6 48.4 1.0 OG A:SER196 4.7 50.2 1.0 CE1 A:PHE185 4.7 42.5 1.0 CH2 A:TRP208 4.8 56.7 1.0 CG2 A:THR270 4.9 42.8 1.0

Nickel binding site 2 out of 2 in the JMJD2A in Complex with Ni(II)


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of JMJD2A in Complex with Ni(II) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni401 b:52.6 occ:1.00 OE2 B:GLU190 2.3 44.2 1.0 NE2 B:HIS188 2.4 83.5 1.0 NE2 B:HIS276 2.5 53.8 1.0 CE1 B:HIS188 2.5 64.9 1.0 CD2 B:HIS276 3.2 47.5 1.0 CD B:GLU190 3.4 62.1 1.0 CE1 B:HIS276 3.7 58.3 1.0 CD2 B:HIS188 3.8 53.1 1.0 OE1 B:GLU190 3.8 50.2 1.0 ND1 B:HIS188 3.9 61.2 1.0 OG B:SER196 4.1 53.2 1.0 CG B:HIS276 4.5 45.1 1.0 CG B:HIS188 4.5 49.4 1.0 CZ3 B:TRP208 4.6 60.5 1.0 CG B:GLU190 4.6 36.9 1.0 ND1 B:HIS276 4.7 51.2 1.0 CH2 B:TRP208 4.7 55.8 1.0 CB B:SER196 4.8 52.8 1.0 CG2 B:THR270 4.9 50.5 1.0 CD1 B:PHE185 4.9 54.5 1.0

B.Cascella, S.G.Lee, S.Singh, J.M.Jez, L.M.Mirica. The Small Molecule Jib-04 Disrupts O2 Binding in the Fe-Dependent Histone Demethylase KDM4A/JMJD2A. Chem. Commun. (Camb.) V. 53 2174 2017.
ISSN: ESSN 1364-548X
PubMed: 28144654
DOI: 10.1039/C6CC09882G