Nickel in PDB 5fy8: Crystal Structure of Human JMJD2A in Complex with D-Threo-Isocitrate

The structure of Crystal Structure of Human JMJD2A in Complex with D-Threo-Isocitrate, PDB code: 5fy8 was solved by R.Nowak, J.Kopec, C.Johansson, A.Szykowska, F.Von Delft, C.H.Arrowsmith, C.Bountra, A.Edwards, U.Oppermann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.98 / 2.34
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	100.930, 148.910, 57.050, 90.00, 90.00, 90.00
R / Rfree (%)	18.5 / 22.9

The structure of Crystal Structure of Human JMJD2A in Complex with D-Threo-Isocitrate also contains other interesting chemical elements:

Zinc

(Zn)

2 atoms

The binding sites of Nickel atom in the Crystal Structure of Human JMJD2A in Complex with D-Threo-Isocitrate (pdb code 5fy8). 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 JMJD2A in Complex with D-Threo-Isocitrate, PDB code: 5fy8:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in the Crystal Structure of Human JMJD2A in Complex with D-Threo-Isocitrate


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 JMJD2A in Complex with D-Threo-Isocitrate within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni501 b:56.2 occ:1.00 OE2 A:GLU190 2.0 45.0 1.0 NE2 A:HIS276 2.3 36.8 1.0 O01 A:N811354 2.4 47.2 1.0 O A:HOH2050 2.4 39.2 1.0 NE2 A:HIS188 2.4 42.9 1.0 C02 A:N811354 2.5 60.1 1.0 O12 A:N811354 2.8 58.5 1.0 CD A:GLU190 3.0 38.3 1.0 C11 A:N811354 3.0 56.0 1.0 CE1 A:HIS188 3.1 42.9 1.0 CE1 A:HIS276 3.3 36.8 1.0 CD2 A:HIS276 3.3 40.7 1.0 OE1 A:GLU190 3.4 36.6 1.0 CD2 A:HIS188 3.4 38.6 1.0 C03 A:N811354 3.8 65.9 1.0 C04 A:N811354 4.1 59.9 1.0 ND1 A:HIS188 4.3 38.6 1.0 O13 A:N811354 4.3 51.1 1.0 OG A:SER196 4.3 42.9 1.0 CG A:GLU190 4.4 37.9 1.0 ND1 A:HIS276 4.4 42.2 1.0 CG A:HIS188 4.4 40.5 1.0 CG A:HIS276 4.4 38.8 1.0 C08 A:N811354 5.0 66.8 1.0

Nickel binding site 2 out of 2 in the Crystal Structure of Human JMJD2A in Complex with D-Threo-Isocitrate


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 JMJD2A in Complex with D-Threo-Isocitrate within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni501 b:57.1 occ:1.00 NE2 B:HIS188 2.2 40.0 1.0 OE2 B:GLU190 2.2 46.0 1.0 O01 B:N811354 2.3 40.1 1.0 NE2 B:HIS276 2.4 36.9 1.0 O B:HOH2048 2.4 41.4 1.0 O12 B:N811354 2.5 42.4 1.0 CE1 B:HIS188 3.1 40.5 1.0 CD B:GLU190 3.2 41.9 1.0 C11 B:N811354 3.2 50.4 1.0 CD2 B:HIS188 3.3 35.5 1.0 C02 B:N811354 3.3 48.2 1.0 CE1 B:HIS276 3.3 38.3 1.0 CD2 B:HIS276 3.5 39.2 1.0 OE1 B:GLU190 3.5 40.4 1.0 C08 B:N811354 4.2 63.6 1.0 O09 B:N811354 4.2 59.7 1.0 ND1 B:HIS188 4.2 40.1 1.0 CG B:HIS188 4.3 41.2 1.0 C03 B:N811354 4.3 48.7 1.0 O13 B:N811354 4.3 50.7 1.0 ND1 B:HIS276 4.4 40.0 1.0 OG B:SER196 4.5 50.4 1.0 CG B:GLU190 4.5 37.5 1.0 CG B:HIS276 4.6 39.1 1.0 O10 B:N811354 4.6 61.5 1.0 CE B:LYS241 4.8 64.8 1.0

R.Nowak, J.Kopec, C.Johansson, A.Szykowska, F.Von Delft, C.H.Arrowsmith, C.Bountra, A.Edwards, U.Oppermann. Crystal Structure of Human JMJD2A in Complex with D-Threo-Isocitrate To Be Published.