Nickel in PDB 5tvr: JMJD2A in Complex with Ni(II) and Alpha-Ketoglutarate

The structure of JMJD2A in Complex with Ni(II) and Alpha-Ketoglutarate, PDB code: 5tvr 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)	35.15 / 2.09
Space group	P 2 21 21
Cell size a, b, c (Å), α, β, γ (°)	57.143, 101.122, 149.028, 90.00, 90.00, 90.00
R / Rfree (%)	18.1 / 22.4

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

Zinc

(Zn)

2 atoms

The binding sites of Nickel atom in the JMJD2A in Complex with Ni(II) and Alpha-Ketoglutarate (pdb code 5tvr). 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) and Alpha-Ketoglutarate, PDB code: 5tvr:
Jump to Nickel binding site number: 1; 2;

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


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) and Alpha-Ketoglutarate within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni401 b:21.6 occ:1.00 OE2 A:GLU190 2.1 19.1 1.0 NE2 A:HIS188 2.1 20.4 1.0 O2 A:AKG402 2.1 27.6 1.0 NE2 A:HIS276 2.2 9.8 1.0 O5 A:AKG402 2.2 25.8 1.0 O A:HOH559 2.5 14.7 1.0 C1 A:AKG402 2.8 26.5 1.0 CE1 A:HIS188 2.9 18.4 1.0 C2 A:AKG402 2.9 27.4 1.0 CE1 A:HIS276 3.0 10.3 1.0 CD A:GLU190 3.1 18.3 1.0 CD2 A:HIS188 3.2 22.5 1.0 CD2 A:HIS276 3.2 11.2 1.0 OE1 A:GLU190 3.4 15.9 1.0 ND1 A:HIS188 4.0 18.6 1.0 O1 A:AKG402 4.1 28.5 1.0 ND1 A:HIS276 4.2 14.3 1.0 OG A:SER196 4.2 27.4 1.0 CG A:HIS188 4.2 23.7 1.0 CG A:HIS276 4.3 13.5 1.0 C3 A:AKG402 4.4 33.6 1.0 CG A:GLU190 4.5 16.5 1.0 CB A:SER196 4.8 21.0 1.0 C4 A:AKG402 5.0 38.4 1.0

Nickel binding site 2 out of 2 in the JMJD2A in Complex with Ni(II) and Alpha-Ketoglutarate


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) and Alpha-Ketoglutarate within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni401 b:17.2 occ:1.00 OE2 B:GLU190 2.1 12.4 1.0 NE2 B:HIS276 2.1 10.1 1.0 NE2 B:HIS188 2.2 18.7 1.0 O5 B:AKG402 2.3 25.8 1.0 O1 B:AKG402 2.3 27.6 1.0 O B:HOH555 2.4 13.2 1.0 C2 B:AKG402 2.9 29.3 1.0 C1 B:AKG402 3.0 27.6 1.0 CE1 B:HIS188 3.0 17.1 1.0 CE1 B:HIS276 3.0 14.7 1.0 CD B:GLU190 3.1 17.6 1.0 CD2 B:HIS276 3.2 14.3 1.0 CD2 B:HIS188 3.3 16.5 1.0 OE1 B:GLU190 3.4 19.6 1.0 ND1 B:HIS188 4.1 17.1 1.0 O2 B:AKG402 4.2 38.5 1.0 ND1 B:HIS276 4.2 15.5 1.0 OG B:SER196 4.2 21.9 1.0 CG B:HIS188 4.3 14.8 1.0 CG B:HIS276 4.3 13.8 1.0 C3 B:AKG402 4.3 34.5 1.0 CG B:GLU190 4.4 14.7 1.0 O B:HOH663 4.4 26.9 1.0 CB B:SER196 4.8 18.6 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