Manganese in PDB 5ivf: Linked KDM5A Jmj Domain Bound to the Inhibitor N10 8-(1-Methyl-1H- Imidazol-4-Yl)-2-(4,4,4-Trifluorobutoxy)Pyrido[3,4-D]Pyrimidin-4-Ol

The structure of Linked KDM5A Jmj Domain Bound to the Inhibitor N10 8-(1-Methyl-1H- Imidazol-4-Yl)-2-(4,4,4-Trifluorobutoxy)Pyrido[3,4-D]Pyrimidin-4-Ol, PDB code: 5ivf was solved by J.R.Horton, X.Cheng, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	32.97 / 1.68
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	116.658, 62.289, 46.498, 90.00, 91.96, 90.00
R / Rfree (%)	16.9 / 20.2

The structure of Linked KDM5A Jmj Domain Bound to the Inhibitor N10 8-(1-Methyl-1H- Imidazol-4-Yl)-2-(4,4,4-Trifluorobutoxy)Pyrido[3,4-D]Pyrimidin-4-Ol also contains other interesting chemical elements:

Fluorine

(F)

3 atoms

The binding sites of Manganese atom in the Linked KDM5A Jmj Domain Bound to the Inhibitor N10 8-(1-Methyl-1H- Imidazol-4-Yl)-2-(4,4,4-Trifluorobutoxy)Pyrido[3,4-D]Pyrimidin-4-Ol (pdb code 5ivf). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total only one binding site of Manganese was determined in the Linked KDM5A Jmj Domain Bound to the Inhibitor N10 8-(1-Methyl-1H- Imidazol-4-Yl)-2-(4,4,4-Trifluorobutoxy)Pyrido[3,4-D]Pyrimidin-4-Ol, PDB code: 5ivf:

Manganese binding site 1 out of 1 in the Linked KDM5A Jmj Domain Bound to the Inhibitor N10 8-(1-Methyl-1H- Imidazol-4-Yl)-2-(4,4,4-Trifluorobutoxy)Pyrido[3,4-D]Pyrimidin-4-Ol


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Linked KDM5A Jmj Domain Bound to the Inhibitor N10 8-(1-Methyl-1H- Imidazol-4-Yl)-2-(4,4,4-Trifluorobutoxy)Pyrido[3,4-D]Pyrimidin-4-Ol within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn602 b:15.5 occ:1.00 OE2 A:GLU485 2.1 16.3 1.0 N04 A:6EB601 2.1 19.6 1.0 O A:HOH746 2.3 17.5 1.0 NE2 A:HIS483 2.3 12.2 1.0 N25 A:6EB601 2.3 15.2 1.0 NE2 A:HIS571 2.3 16.0 1.0 C05 A:6EB601 2.9 18.7 1.0 C07 A:6EB601 3.0 15.8 1.0 CE1 A:HIS571 3.1 15.4 1.0 CD A:GLU485 3.1 19.3 1.0 CE1 A:HIS483 3.2 13.6 1.0 C03 A:6EB601 3.3 20.9 1.0 CD2 A:HIS483 3.3 11.7 1.0 C24 A:6EB601 3.3 14.0 1.0 CD2 A:HIS571 3.4 14.5 1.0 OE1 A:GLU485 3.6 22.3 1.0 C06 A:6EB601 4.2 21.0 1.0 O A:HOH769 4.2 26.3 1.0 ND1 A:HIS571 4.3 10.7 1.0 ND1 A:HIS483 4.3 13.9 1.0 N02 A:6EB601 4.3 23.1 1.0 CG A:HIS483 4.4 11.7 1.0 CG A:GLU485 4.4 12.5 1.0 C08 A:6EB601 4.4 15.1 1.0 CG A:HIS571 4.5 12.1 1.0 OG A:SER491 4.6 25.2 1.0 C23 A:6EB601 4.6 15.4 1.0 O A:HOH849 4.8 42.5 1.0

J.R.Horton, X.Liu, M.Gale, L.Wu, J.R.Shanks, X.Zhang, P.J.Webber, J.S.Bell, S.C.Kales, B.T.Mott, G.Rai, D.J.Jansen, M.J.Henderson, D.J.Urban, M.D.Hall, A.Simeonov, D.J.Maloney, M.A.Johns, H.Fu, A.Jadhav, P.M.Vertino, Q.Yan, X.Cheng. Structural Basis For KDM5A Histone Lysine Demethylase Inhibition By Diverse Compounds. Cell Chem Biol V. 23 769 2016.
ISSN: ESSN 2451-9456
PubMed: 27427228
DOI: 10.1016/J.CHEMBIOL.2016.06.006