Zinc 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:

Nickel

(Ni)

2 atoms

The binding sites of Zinc 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 Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of Human JMJD2A in Complex with D-Threo-Isocitrate, PDB code: 5fy8:
Jump to Zinc binding site number: 1; 2;

Zinc 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 Zinc with other atoms in the Zn 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:Zn502 b:40.6 occ:1.00 NE2 A:HIS240 2.1 41.7 1.0 SG A:CYS306 2.1 43.9 1.0 SG A:CYS234 2.3 41.8 1.0 SG A:CYS308 2.4 44.9 1.0 CE1 A:HIS240 3.0 34.1 1.0 CD2 A:HIS240 3.1 39.7 1.0 CB A:CYS234 3.2 44.6 1.0 CB A:CYS306 3.4 38.5 1.0 CB A:CYS308 3.5 49.3 1.0 N A:CYS308 3.6 44.8 1.0 CA A:CYS306 3.9 45.5 1.0 N A:SER307 3.9 45.1 1.0 CA A:CYS308 4.0 48.0 1.0 ND1 A:HIS240 4.1 35.1 1.0 C A:CYS306 4.2 47.5 1.0 CG A:HIS240 4.2 38.2 1.0 CB A:LYS310 4.4 47.2 1.0 C A:CYS308 4.4 44.0 1.0 CA A:CYS234 4.5 44.6 1.0 N A:LYS310 4.5 46.9 1.0 N A:ARG309 4.5 44.0 1.0 O A:HOH2096 4.5 51.9 1.0 C A:SER307 4.7 54.1 1.0 O A:ALA236 4.8 36.9 1.0 CA A:PHE237 4.8 38.6 1.0 CG A:LYS310 4.9 50.8 1.0 N A:ASP311 4.9 56.7 1.0 CA A:SER307 4.9 43.9 1.0 CA A:LYS310 5.0 44.6 1.0 C A:ALA236 5.0 41.6 1.0

Zinc 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 Zinc with other atoms in the Zn 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:Zn502 b:45.2 occ:1.00 NE2 B:HIS240 2.1 47.9 1.0 SG B:CYS306 2.2 44.6 1.0 SG B:CYS234 2.2 47.5 1.0 SG B:CYS308 2.3 53.8 1.0 CE1 B:HIS240 3.1 39.6 1.0 CD2 B:HIS240 3.1 41.5 1.0 CB B:CYS234 3.3 53.4 1.0 CB B:CYS306 3.4 42.3 1.0 CB B:CYS308 3.5 58.1 1.0 N B:CYS308 3.6 57.9 1.0 CA B:CYS306 3.9 52.8 1.0 N B:SER307 3.9 52.5 1.0 CA B:CYS308 4.0 57.2 1.0 ND1 B:HIS240 4.2 43.4 1.0 C B:CYS306 4.2 57.1 1.0 CG B:HIS240 4.2 36.6 1.0 C B:CYS308 4.5 59.3 1.0 N B:ARG309 4.5 59.1 1.0 CA B:CYS234 4.6 55.9 1.0 CG B:ARG309 4.6 61.1 1.0 C B:SER307 4.7 67.0 1.0 CD B:ARG309 4.7 57.3 1.0 CA B:PHE237 4.8 46.5 1.0 O B:ALA236 4.8 41.1 1.0 NE B:ARG309 4.8 63.8 1.0 CA B:SER307 4.9 59.0 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.