Magnesium 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:

Manganese	(Mn)	2 atoms
Zinc	(Zn)	4 atoms

The binding sites of Magnesium 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 Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Crystal Structure of Human JARID1C in Complex with KDM5-C49, PDB code: 5fwj:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Crystal Structure of Human JARID1C in Complex with KDM5-C49


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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:Mg805 b:57.8 occ:1.00 O A:HOH2069 2.1 51.9 1.0 O A:HOH2067 2.2 46.9 1.0 O A:HOH2317 2.3 67.2 1.0 O A:HOH2068 2.4 37.0 1.0 O A:PRO54 3.8 26.3 1.0 O A:HOH2073 4.1 39.0 1.0 O A:HOH2188 4.1 37.1 1.0 OE1 A:GLN53 4.1 59.9 1.0 O A:HOH2190 4.3 23.6 1.0 O A:HOH2191 4.3 44.4 1.0 O A:GLN53 4.4 36.0 1.0 CB A:GLN53 4.4 36.0 1.0 C A:PRO54 4.5 32.8 1.0 C A:GLN53 4.6 34.0 1.0 CA A:PRO55 4.7 31.9 1.0 N A:PRO55 4.9 34.0 1.0 CA A:GLN53 4.9 34.7 1.0

Magnesium binding site 2 out of 5 in the Crystal Structure of Human JARID1C in Complex with KDM5-C49


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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:Mg1773 b:26.1 occ:1.00 O A:HOH2318 3.1 23.9 1.0 NH2 A:ARG627 3.2 29.1 1.0 NE2 A:GLN628 3.3 33.6 1.0 NE A:ARG627 3.7 29.3 1.0 CZ A:ARG627 3.9 28.8 1.0 CG A:GLN628 3.9 23.6 1.0 O A:HOH2247 4.1 30.4 1.0 CD A:GLN628 4.1 29.7 1.0 O A:HOH2206 4.3 28.5 1.0 CD A:ARG627 5.0 23.9 1.0

Magnesium binding site 3 out of 5 in the Crystal Structure of Human JARID1C in Complex with KDM5-C49


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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 A:Mg1774 b:16.0 occ:1.00 NH2 A:ARG627 3.0 29.1 1.0 O A:HOH2279 3.1 28.7 1.0 NZ A:LYS668 3.1 23.6 1.0 NH1 A:ARG627 3.7 20.0 1.0 CE A:LYS668 3.7 25.4 1.0 CB A:PRO624 3.7 21.4 1.0 CZ A:ARG627 3.8 28.8 1.0 CG A:PRO624 4.1 21.9 1.0 CA A:PRO624 4.9 19.7 1.0

Magnesium binding site 4 out of 5 in the Crystal Structure of Human JARID1C in Complex with KDM5-C49


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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:Mg1773 b:41.7 occ:1.00 NH1 B:ARG637 3.1 43.6 1.0 NE2 B:HIS733 3.1 28.5 1.0 CE1 B:HIS733 3.5 28.6 1.0 CD B:ARG634 3.6 37.9 1.0 CG B:ARG634 3.7 32.6 1.0 NH2 B:ARG637 3.8 53.7 1.0 CZ B:ARG637 3.9 49.3 1.0 CB B:CYS710 4.2 26.6 1.0 CD2 B:HIS733 4.4 30.1 1.0 O B:ARG634 4.5 24.8 1.0 C B:ARG634 4.8 26.5 1.0 ND1 B:HIS733 4.8 21.9 1.0 CB B:ARG634 4.9 19.9 1.0

Magnesium binding site 5 out of 5 in the Crystal Structure of Human JARID1C in Complex with KDM5-C49


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of Human JARID1C in Complex with KDM5-C49 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1774 b:91.6 occ:1.00 O B:HOH2198 1.9 12.0 1.0 NZ B:LYS668 2.1 24.1 1.0 O B:HOH2287 2.4 29.1 1.0 CG B:PRO624 3.0 19.3 1.0 CE B:LYS668 3.1 23.4 1.0 CB B:PRO624 3.1 19.8 1.0 NH2 B:ARG627 3.5 21.0 1.0 O B:HOH2230 4.0 20.2 1.0 CD B:LYS668 4.3 24.3 1.0 CA B:PRO624 4.5 15.8 1.0 CD B:PRO624 4.5 18.4 1.0 CZ B:ARG627 4.5 21.7 1.0 NH1 B:ARG627 4.7 24.0 1.0 OE2 B:GLU669 4.9 24.3 1.0 O B:HOH2225 4.9 18.5 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