Zinc in PDB 5fyi: Crystal Structure of Human JMJD2A in Complex with Pyruvate

The structure of Crystal Structure of Human JMJD2A in Complex with Pyruvate, PDB code: 5fyi 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)	29.77 / 2.10
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	100.450, 148.830, 57.060, 90.00, 90.00, 90.00
R / Rfree (%)	19.7 / 23.6

The structure of Crystal Structure of Human JMJD2A in Complex with Pyruvate 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 Pyruvate (pdb code 5fyi). 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 Pyruvate, PDB code: 5fyi:
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 Pyruvate


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 Pyruvate within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn3000 b:34.6 occ:1.00 NE2 A:HIS240 2.1 29.8 1.0 SG A:CYS306 2.1 37.1 1.0 SG A:CYS234 2.3 35.1 1.0 SG A:CYS308 2.4 36.9 1.0 CE1 A:HIS240 3.0 31.2 1.0 CD2 A:HIS240 3.1 33.1 1.0 CB A:CYS234 3.3 41.0 1.0 CB A:CYS306 3.3 31.6 1.0 CB A:CYS308 3.5 45.4 1.0 N A:CYS308 3.6 47.3 1.0 CA A:CYS306 3.9 39.5 1.0 N A:SER307 3.9 44.0 1.0 CA A:CYS308 4.0 47.0 1.0 C A:CYS306 4.1 40.6 1.0 ND1 A:HIS240 4.1 30.2 1.0 CG A:HIS240 4.2 30.7 1.0 CG A:ARG309 4.5 48.1 1.0 C A:CYS308 4.5 46.1 1.0 O A:HOH2139 4.5 42.8 1.0 N A:ARG309 4.5 48.2 1.0 CA A:CYS234 4.6 38.9 1.0 C A:SER307 4.7 48.1 1.0 O A:ALA236 4.7 29.8 1.0 CD A:ARG309 4.9 56.1 1.0 CA A:PHE237 4.9 32.7 1.0 CA A:SER307 4.9 46.8 1.0 NE A:ARG309 4.9 59.0 1.0

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


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 Pyruvate within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn502 b:40.8 occ:1.00 NE2 B:HIS240 2.1 41.6 1.0 SG B:CYS306 2.2 44.1 1.0 SG B:CYS234 2.3 39.8 1.0 SG B:CYS308 2.3 47.2 1.0 CE1 B:HIS240 3.1 41.9 1.0 CD2 B:HIS240 3.1 37.4 1.0 CB B:CYS234 3.2 39.7 1.0 CB B:CYS306 3.5 38.5 1.0 CB B:CYS308 3.5 52.1 1.0 N B:CYS308 3.6 49.1 1.0 N B:SER307 3.9 45.8 1.0 CA B:CYS306 3.9 41.2 1.0 CA B:CYS308 4.0 50.7 1.0 C B:CYS306 4.2 42.7 1.0 ND1 B:HIS240 4.2 38.8 1.0 CG B:HIS240 4.2 33.8 1.0 CG B:ARG309 4.4 58.8 1.0 N B:ARG309 4.5 53.0 1.0 C B:CYS308 4.5 51.6 1.0 CA B:CYS234 4.5 44.9 1.0 C B:SER307 4.6 59.0 1.0 O B:ALA236 4.7 35.0 1.0 CD B:ARG309 4.7 53.2 1.0 CA B:PHE237 4.8 39.6 1.0 CE B:MET312 4.8 51.1 1.0 CA B:SER307 4.8 51.6 1.0 NE B:ARG309 4.9 52.8 1.0 C B:ALA236 5.0 39.0 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 Pyruvate To Be Published.