Manganese in PDB 6dq7: Linked KDM5A Jmj Domain Bound to the Potential Hydrolysis Product of Inhibitor N45 I.E. 3-((6-(4-(2-Cyano-3-Methylbut-2-Enoyl)-1,4- Diazepan-1-Yl)-2-(Pyridin-2-Yl)Pyrimidin-4-Yl)Amino)Propanoic Acid

The structure of Linked KDM5A Jmj Domain Bound to the Potential Hydrolysis Product of Inhibitor N45 I.E. 3-((6-(4-(2-Cyano-3-Methylbut-2-Enoyl)-1,4- Diazepan-1-Yl)-2-(Pyridin-2-Yl)Pyrimidin-4-Yl)Amino)Propanoic Acid, PDB code: 6dq7 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)	33.14 / 1.85
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	117.506, 62.309, 46.695, 90.00, 92.39, 90.00
R / Rfree (%)	19.2 / 20.9

The binding sites of Manganese atom in the Linked KDM5A Jmj Domain Bound to the Potential Hydrolysis Product of Inhibitor N45 I.E. 3-((6-(4-(2-Cyano-3-Methylbut-2-Enoyl)-1,4- Diazepan-1-Yl)-2-(Pyridin-2-Yl)Pyrimidin-4-Yl)Amino)Propanoic Acid (pdb code 6dq7). 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 Potential Hydrolysis Product of Inhibitor N45 I.E. 3-((6-(4-(2-Cyano-3-Methylbut-2-Enoyl)-1,4- Diazepan-1-Yl)-2-(Pyridin-2-Yl)Pyrimidin-4-Yl)Amino)Propanoic Acid, PDB code: 6dq7:

Manganese binding site 1 out of 1 in the Linked KDM5A Jmj Domain Bound to the Potential Hydrolysis Product of Inhibitor N45 I.E. 3-((6-(4-(2-Cyano-3-Methylbut-2-Enoyl)-1,4- Diazepan-1-Yl)-2-(Pyridin-2-Yl)Pyrimidin-4-Yl)Amino)Propanoic Acid


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 Potential Hydrolysis Product of Inhibitor N45 I.E. 3-((6-(4-(2-Cyano-3-Methylbut-2-Enoyl)-1,4- Diazepan-1-Yl)-2-(Pyridin-2-Yl)Pyrimidin-4-Yl)Amino)Propanoic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn602 b:19.0 occ:1.00 O A:HOH726 2.1 18.9 1.0 O A:HOH714 2.2 18.0 1.0 N29 A:H6M601 2.2 23.2 1.0 OE2 A:GLU485 2.2 23.6 1.0 NE2 A:HIS483 2.3 24.1 1.0 N28 A:H6M601 2.4 25.2 1.0 C22 A:H6M601 3.0 24.0 1.0 C23 A:H6M601 3.1 24.9 1.0 CD A:GLU485 3.1 23.5 1.0 CD2 A:HIS483 3.2 24.2 1.0 C07 A:H6M601 3.2 23.0 1.0 CE1 A:HIS483 3.3 25.7 1.0 OE1 A:GLU485 3.4 24.5 1.0 N06 A:H6M601 3.4 22.1 1.0 C27 A:H6M601 3.4 25.8 1.0 NE2 A:HIS571 3.9 16.6 1.0 O A:HOH717 4.1 43.9 1.0 O A:HOH728 4.1 43.5 1.0 CG A:HIS483 4.4 23.7 1.0 N21 A:H6M601 4.4 24.0 1.0 ND1 A:HIS483 4.4 24.7 1.0 CE1 A:HIS571 4.4 16.9 1.0 C24 A:H6M601 4.5 25.8 1.0 CG A:GLU485 4.5 22.2 1.0 C08 A:H6M601 4.6 23.6 1.0 C26 A:H6M601 4.7 26.2 1.0 C05 A:H6M601 4.9 21.4 1.0 C09 A:H6M601 5.0 24.2 1.0

J.R.Horton, X.Liu, C.B.Woodcock, J.Shanks, X.Zhang, G.Rai, B.Mott, D.J.Jansen, S.Kales, M.J.Henderson, K.Pohida, Y.Fang, X.Hu, A.Jadhav, D.Maloney, M.D.Hall, A.Simeonov, H.Fu, P.M.Vertino, X.Cheng. Structure-Based Engineering of Reversible Covalent Inhibitors Against Histone Lysine Demethylase 5A To Be Published.