Zinc 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:

Nickel

(Ni)

2 atoms

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

Zinc 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 Zinc with other atoms in the Zn 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:Zn403 b:31.0 occ:1.00 SG A:CYS306 2.2 29.8 1.0 NE2 A:HIS240 2.3 27.7 1.0 SG A:CYS234 2.4 96.0 1.0 SG A:CYS308 2.5 34.7 1.0 CB A:CYS234 3.0 24.8 1.0 CD2 A:HIS240 3.2 22.0 1.0 CB A:CYS306 3.4 29.2 1.0 CE1 A:HIS240 3.4 32.4 1.0 CB A:CYS308 3.4 47.7 1.0 N A:CYS308 3.6 47.0 1.0 CA A:CYS306 3.9 30.3 1.0 N A:SER307 3.9 42.2 1.0 CA A:CYS308 4.1 46.8 1.0 C A:CYS306 4.2 35.5 1.0 CA A:CYS234 4.4 46.6 1.0 CG A:HIS240 4.4 22.9 1.0 ND1 A:HIS240 4.5 27.5 1.0 N A:ARG309 4.6 54.1 1.0 C A:CYS308 4.7 48.7 1.0 O A:ALA236 4.7 21.8 1.0 O A:HOH667 4.7 32.0 1.0 C A:SER307 4.8 49.5 1.0 CA A:PHE237 4.8 22.4 1.0 NE A:ARG309 4.8 60.5 1.0 CA A:SER307 4.9 48.1 1.0 N A:CYS234 5.0 43.4 1.0 C A:ALA236 5.0 26.9 1.0

Zinc 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 Zinc with other atoms in the Zn 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:Zn403 b:29.0 occ:1.00 NE2 B:HIS240 2.1 31.4 1.0 SG B:CYS306 2.2 25.4 1.0 SG B:CYS234 2.2 28.7 1.0 SG B:CYS308 2.4 26.2 1.0 CE1 B:HIS240 3.1 32.2 1.0 CD2 B:HIS240 3.1 27.0 1.0 CB B:CYS234 3.2 31.0 1.0 CB B:CYS306 3.4 27.7 1.0 CB B:CYS308 3.5 32.8 1.0 N B:CYS308 3.6 40.4 1.0 CA B:CYS306 3.9 31.3 1.0 N B:SER307 3.9 38.0 1.0 CA B:CYS308 4.0 38.6 1.0 C B:CYS306 4.2 35.9 1.0 O B:HOH668 4.2 33.3 1.0 ND1 B:HIS240 4.2 30.1 1.0 CG B:HIS240 4.3 26.5 1.0 C B:CYS308 4.4 38.0 1.0 CB B:LYS310 4.4 44.8 1.0 CA B:CYS234 4.5 40.6 1.0 N B:LYS310 4.5 47.9 1.0 N B:ARG309 4.6 38.6 1.0 O B:ALA236 4.6 21.4 1.0 CD B:LYS310 4.6 50.2 1.0 C B:SER307 4.7 45.5 1.0 CA B:PHE237 4.8 19.1 1.0 CG B:LYS310 4.8 48.5 1.0 CA B:SER307 4.9 44.1 1.0 C B:ALA236 4.9 27.7 1.0 O B:CYS308 5.0 38.3 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