Zinc in PDB 5fyh: Crystal Structure of Human JMJD2A in Complex with Fumarate

The structure of Crystal Structure of Human JMJD2A in Complex with Fumarate, PDB code: 5fyh 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)	29.80 / 2.35
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	100.840, 149.130, 56.940, 90.00, 90.00, 90.00
R / Rfree (%)	20.2 / 25

The structure of Crystal Structure of Human JMJD2A in Complex with Fumarate also contains other interesting chemical elements:

Manganese

(Mn)

2 atoms

The binding sites of Zinc atom in the Crystal Structure of Human JMJD2A in Complex with Fumarate (pdb code 5fyh). 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 Fumarate, PDB code: 5fyh:
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 Fumarate


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 Fumarate within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:41.1 occ:1.00 NE2 A:HIS240 2.0 42.9 1.0 SG A:CYS306 2.2 40.3 1.0 SG A:CYS234 2.2 42.6 1.0 SG A:CYS308 2.3 44.1 1.0 CE1 A:HIS240 3.0 36.2 1.0 CD2 A:HIS240 3.1 41.2 1.0 CB A:CYS234 3.2 42.6 1.0 CB A:CYS306 3.4 40.5 1.0 CB A:CYS308 3.6 48.4 1.0 N A:CYS308 3.6 49.2 1.0 N A:SER307 3.9 46.8 1.0 CA A:CYS306 3.9 46.1 1.0 CA A:CYS308 4.1 48.2 1.0 ND1 A:HIS240 4.1 37.2 1.0 CG A:HIS240 4.2 37.2 1.0 C A:CYS306 4.2 48.0 1.0 CG A:ARG309 4.3 49.0 1.0 CA A:CYS234 4.5 45.2 1.0 N A:ARG309 4.5 52.7 1.0 C A:CYS308 4.6 50.6 1.0 C A:SER307 4.6 53.7 1.0 CD A:ARG309 4.8 59.0 1.0 NE A:ARG309 4.8 58.8 1.0 CA A:SER307 4.8 51.4 1.0 O A:ALA236 4.9 33.6 1.0 CA A:PHE237 4.9 36.8 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Human JMJD2A in Complex with Fumarate


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 Fumarate within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn502 b:46.7 occ:1.00 NE2 B:HIS240 2.1 49.5 1.0 SG B:CYS306 2.2 45.2 1.0 SG B:CYS234 2.2 50.2 1.0 SG B:CYS308 2.3 56.2 1.0 CE1 B:HIS240 3.0 45.3 1.0 CD2 B:HIS240 3.2 44.7 1.0 CB B:CYS234 3.2 48.9 1.0 CB B:CYS306 3.4 50.0 1.0 CB B:CYS308 3.6 59.5 1.0 N B:CYS308 3.7 60.5 1.0 N B:SER307 3.8 53.7 1.0 CA B:CYS306 3.9 53.6 1.0 CA B:CYS308 4.1 58.8 1.0 C B:CYS306 4.1 53.8 1.0 ND1 B:HIS240 4.2 44.6 1.0 CG B:HIS240 4.3 39.8 1.0 CG B:ARG309 4.4 58.8 1.0 CA B:CYS234 4.5 56.3 1.0 N B:ARG309 4.6 57.8 1.0 C B:CYS308 4.6 56.6 1.0 C B:SER307 4.6 65.4 1.0 O B:ALA236 4.8 41.9 1.0 CD B:ARG309 4.8 55.4 1.0 CA B:SER307 4.8 59.5 1.0 CA B:PHE237 4.8 46.6 1.0 NE B:ARG309 4.8 59.6 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 Fumarate To Be Published.