Manganese 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
Zinc	(Zn)	4 atoms

The binding sites of Manganese 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 Manganese atom.
In total 2 binding sites of Manganese where determined in the Crystal Structure of Human JARID1C in Complex with KDM5-C49, PDB code: 5fwj:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the Crystal Structure of Human JARID1C in Complex with KDM5-C49


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn 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:Mn1772 b:14.4 occ:1.00 NE2 A:HIS514 2.0 19.2 1.0 OE2 A:GLU516 2.0 19.5 1.0 O A:HOH2183 2.1 20.8 1.0 N A:MMK1775 2.1 19.0 1.0 NAR A:MMK1775 2.2 15.4 1.0 NE2 A:HIS602 2.2 18.5 1.0 CE1 A:HIS514 2.7 27.6 1.0 CAL A:MMK1775 2.9 24.9 1.0 CAM A:MMK1775 2.9 15.8 1.0 CA A:MMK1775 3.0 19.1 1.0 CE1 A:HIS602 3.1 15.9 1.0 CD A:GLU516 3.1 21.6 1.0 CAQ A:MMK1775 3.2 25.3 1.0 CD2 A:HIS514 3.2 25.3 1.0 CD2 A:HIS602 3.3 13.2 1.0 OE1 A:GLU516 3.6 23.9 1.0 ND1 A:HIS514 3.9 28.4 1.0 CG A:HIS514 4.2 24.1 1.0 ND1 A:HIS602 4.2 17.9 1.0 C A:MMK1775 4.3 23.1 1.0 CAN A:MMK1775 4.3 20.7 1.0 CG A:HIS602 4.4 18.4 1.0 CG A:GLU516 4.4 19.4 1.0 OG A:SER522 4.5 21.6 1.0 CAP A:MMK1775 4.5 25.0 1.0 O A:MMK1775 4.5 34.7 1.0 CAO A:MMK1775 4.9 21.1 1.0 CB A:SER522 5.0 15.9 1.0

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


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn 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 B:Mn1772 b:14.3 occ:1.00 O B:HOH2138 1.9 16.1 1.0 NE2 B:HIS514 2.0 16.5 1.0 OE2 B:GLU516 2.0 15.9 1.0 N B:MMK1775 2.1 16.2 1.0 NAR B:MMK1775 2.1 14.2 1.0 NE2 B:HIS602 2.3 19.1 1.0 CE1 B:HIS514 2.7 28.4 1.0 CAL B:MMK1775 2.8 24.4 1.0 CAM B:MMK1775 2.9 20.3 1.0 CA B:MMK1775 3.0 18.2 1.0 CD B:GLU516 3.1 18.5 1.0 CE1 B:HIS602 3.1 16.5 1.0 CAQ B:MMK1775 3.2 32.5 1.0 CD2 B:HIS514 3.2 24.0 1.0 CD2 B:HIS602 3.3 13.7 1.0 OE1 B:GLU516 3.6 20.2 1.0 ND1 B:HIS514 3.9 24.6 1.0 CG B:HIS514 4.2 21.6 1.0 C B:MMK1775 4.2 24.5 1.0 CAN B:MMK1775 4.3 24.6 1.0 ND1 B:HIS602 4.3 16.6 1.0 CG B:HIS602 4.4 19.2 1.0 CG B:GLU516 4.4 13.5 1.0 OG B:SER522 4.4 18.6 1.0 CAP B:MMK1775 4.4 29.3 1.0 O B:MMK1775 4.5 31.1 1.0 CAO B:MMK1775 4.9 22.4 1.0 CB B:SER522 5.0 15.0 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