Zinc in PDB 5fwj: Crystal Structure of Human JARID1C in Complex with KDM5-C49

The structure of Crystal Structure of Human JARID1C in Complex with KDM5-C49, PDB code: 5fwj was solved by V.Srikannathasan, A.Szykowska, C.Strain-Damerell, J.Kopec, R.Nowak, C.Gileadi, C.Johansson, K.Kupinska, N.A.Burgess-Brown, L.Shrestha, W.Dong, F.Von Delft, C.H.Arrowsmith, C.Bountra, A.Edwards, K.Huber, U.Oppermann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	51.23 / 2.10
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	60.960, 67.340, 74.730, 86.71, 76.56, 70.35
R / Rfree (%)	15.5 / 18.9

The structure of Crystal Structure of Human JARID1C in Complex with KDM5-C49 also contains other interesting chemical elements:

Magnesium	(Mg)	5 atoms
Manganese	(Mn)	2 atoms

The binding sites of Zinc atom in the Crystal Structure of Human JARID1C in Complex with KDM5-C49 (pdb code 5fwj). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of Human JARID1C in Complex with KDM5-C49, PDB code: 5fwj:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of Human JARID1C in Complex with KDM5-C49


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 JARID1C in Complex with KDM5-C49 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1770 b:30.4 occ:1.00 ND1 A:HIS733 2.1 26.4 1.0 SG A:CYS710 2.3 28.8 1.0 SG A:CYS707 2.4 27.5 1.0 SG A:CYS730 2.4 29.2 1.0 CE1 A:HIS733 2.8 32.7 1.0 CG A:HIS733 3.2 34.1 1.0 CB A:CYS707 3.3 24.9 1.0 CB A:CYS710 3.4 32.4 1.0 CB A:CYS730 3.6 29.4 1.0 CB A:HIS733 3.8 33.6 1.0 N A:CYS710 3.9 37.4 1.0 N A:CYS730 4.0 30.7 1.0 NE2 A:HIS733 4.0 32.1 1.0 NH1 A:ARG634 4.1 36.8 1.0 CA A:CYS710 4.2 32.5 1.0 CD2 A:HIS733 4.2 34.7 1.0 CG2 A:THR712 4.3 20.7 1.0 CA A:CYS730 4.3 33.2 1.0 CB A:LYS709 4.5 39.1 1.0 O A:CYS730 4.6 29.4 1.0 N A:HIS733 4.7 37.8 1.0 CA A:CYS707 4.7 30.9 1.0 C A:CYS730 4.8 30.5 1.0 CA A:HIS733 4.9 39.4 1.0 C A:CYS710 4.9 29.7 1.0 C A:LYS709 4.9 39.6 1.0 CB A:SER732 4.9 36.7 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of Human JARID1C in Complex with KDM5-C49


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 JARID1C in Complex with KDM5-C49 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1771 b:58.5 occ:1.00 SG A:CYS738 2.3 52.8 1.0 SG A:CYS721 2.3 54.7 1.0 SG A:CYS740 2.5 69.9 1.0 SG A:CYS724 2.5 60.9 1.0 CB A:CYS721 3.2 51.7 1.0 CB A:CYS740 3.2 54.1 1.0 CB A:CYS738 3.3 49.1 1.0 CB A:CYS724 3.4 66.8 1.0 N A:CYS724 3.9 65.2 1.0 CA A:CYS724 4.3 66.9 1.0 N A:CYS740 4.3 60.7 1.0 CA A:CYS740 4.4 57.1 1.0 C A:ASP723 4.5 61.9 1.0 CB A:ASP723 4.6 59.2 1.0 CA A:CYS721 4.7 49.4 1.0 CA A:CYS738 4.7 51.8 1.0 N A:ASP723 4.8 55.0 1.0 CA A:ASP723 4.9 58.2 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of Human JARID1C in Complex with KDM5-C49


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Human JARID1C in Complex with KDM5-C49 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1770 b:24.4 occ:1.00 ND1 B:HIS733 2.0 21.9 1.0 SG B:CYS710 2.3 23.6 1.0 SG B:CYS707 2.4 21.6 1.0 SG B:CYS730 2.4 21.9 1.0 CE1 B:HIS733 2.8 28.6 1.0 CB B:CYS707 3.2 14.9 1.0 CG B:HIS733 3.2 30.2 1.0 CB B:CYS710 3.4 26.6 1.0 CB B:CYS730 3.6 15.7 1.0 CB B:HIS733 3.7 27.1 1.0 N B:CYS710 3.8 28.0 1.0 N B:CYS730 4.0 19.6 1.0 NE2 B:HIS733 4.0 28.5 1.0 CA B:CYS710 4.2 24.0 1.0 CD2 B:HIS733 4.2 30.1 1.0 NH1 B:ARG634 4.3 51.9 1.0 CA B:CYS730 4.3 20.3 1.0 CG2 B:THR712 4.4 20.4 1.0 CB B:LYS709 4.5 27.9 1.0 O B:CYS730 4.6 22.2 1.0 CA B:CYS707 4.6 25.6 1.0 N B:HIS733 4.6 23.8 1.0 C B:CYS730 4.7 23.5 1.0 CA B:HIS733 4.9 27.2 1.0 C B:LYS709 4.9 30.2 1.0 C B:CYS710 4.9 21.2 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of Human JARID1C in Complex with KDM5-C49


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Human JARID1C in Complex with KDM5-C49 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1771 b:33.7 occ:1.00 SG B:CYS738 2.3 37.0 1.0 SG B:CYS721 2.4 35.7 1.0 SG B:CYS740 2.4 38.1 1.0 SG B:CYS724 2.4 38.0 1.0 CB B:CYS740 3.2 37.6 1.0 CB B:CYS721 3.3 35.6 1.0 CB B:CYS738 3.3 32.6 1.0 CB B:CYS724 3.3 37.2 1.0 N B:CYS724 3.9 44.0 1.0 N B:CYS740 4.2 41.4 1.0 CA B:CYS724 4.2 40.4 1.0 CA B:CYS740 4.3 38.1 1.0 C B:ASP723 4.5 45.8 1.0 CB B:ASP723 4.5 36.4 1.0 CA B:CYS738 4.7 36.2 1.0 CA B:CYS721 4.8 31.7 1.0 CA B:ASP723 4.8 40.9 1.0 N B:ASP723 4.9 38.5 1.0 N B:LYS739 4.9 43.8 1.0 O B:HOH2267 4.9 29.1 1.0

C.Johansson, S.Velupillai, A.Tumber, A.Szykowska, E.S.Hookway, R.P.Nowak, C.Strain-Damerell, C.Gileadi, M.Philpott, N.Burgess-Brown, N.Wu, J.Kopec, A.Nuzzi, H.Steuber, U.Egner, V.Badock, S.Munro, N.B.Lathangue, S.Westaway, J.Brown, N.Athanasou, R.Prinjha, P.E.Brennan, U.Oppermann. Structural Analysis of Human KDM5B Guides Histone Demethylase Inhibitor Development. Nat.Chem.Biol. V. 12 539 2016.
ISSN: ISSN 1552-4450
PubMed: 27214403
DOI: 10.1038/NCHEMBIO.2087