Manganese in PDB 5e6h: A Linked Jumonji Domain of the KDM5A Lysine Demethylase

The structure of A Linked Jumonji Domain of the KDM5A Lysine Demethylase, PDB code: 5e6h 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)	32.60 / 2.24
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	115.365, 61.591, 46.583, 90.00, 92.55, 90.00
R / Rfree (%)	17.9 / 22

The binding sites of Manganese atom in the A Linked Jumonji Domain of the KDM5A Lysine Demethylase (pdb code 5e6h). 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 A Linked Jumonji Domain of the KDM5A Lysine Demethylase, PDB code: 5e6h:

Manganese binding site 1 out of 1 in the A Linked Jumonji Domain of the KDM5A Lysine Demethylase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of A Linked Jumonji Domain of the KDM5A Lysine Demethylase within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn601 b:23.7 occ:1.00 OE2 A:GLU485 2.1 29.7 1.0 O1 A:AKG602 2.2 24.6 1.0 O A:HOH728 2.2 30.1 1.0 NE2 A:HIS483 2.2 23.0 1.0 NE2 A:HIS571 2.2 18.3 1.0 O5 A:AKG602 2.3 29.7 1.0 C1 A:AKG602 2.9 30.3 1.0 C2 A:AKG602 2.9 31.2 1.0 CE1 A:HIS483 3.1 22.8 1.0 CE1 A:HIS571 3.1 17.9 1.0 CD A:GLU485 3.2 25.6 1.0 CD2 A:HIS483 3.3 20.6 1.0 CD2 A:HIS571 3.3 16.7 1.0 OE1 A:GLU485 3.6 26.2 1.0 O2 A:AKG602 4.2 32.5 1.0 ND1 A:HIS483 4.2 19.7 1.0 OG A:SER491 4.3 32.8 1.0 ND1 A:HIS571 4.3 19.9 1.0 CG A:HIS483 4.3 18.3 1.0 CG A:HIS571 4.4 17.7 1.0 C3 A:AKG602 4.4 28.9 1.0 CG A:GLU485 4.5 21.8 1.0 CB A:SER491 4.6 24.4 1.0 C4 A:AKG602 5.0 28.7 1.0

J.R.Horton, A.Engstrom, E.L.Zoeller, X.Liu, J.R.Shanks, X.Zhang, M.A.Johns, P.M.Vertino, H.Fu, X.Cheng. Characterization of A Linked Jumonji Domain of the KDM5/JARID1 Family of Histone H3 Lysine 4 Demethylases. J.Biol.Chem. V. 291 2631 2016.
ISSN: ESSN 1083-351X
PubMed: 26645689
DOI: 10.1074/JBC.M115.698449