Manganese in PDB 5ivb: A High Resolution Structure of A Linked KDM5A Jmj Domain with Alpha- Ketoglutarate

The structure of A High Resolution Structure of A Linked KDM5A Jmj Domain with Alpha- Ketoglutarate, PDB code: 5ivb 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)	32.88 / 1.39
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	116.340, 62.199, 46.751, 90.00, 92.63, 90.00
R / Rfree (%)	18.2 / 21.4

The binding sites of Manganese atom in the A High Resolution Structure of A Linked KDM5A Jmj Domain with Alpha- Ketoglutarate (pdb code 5ivb). 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 High Resolution Structure of A Linked KDM5A Jmj Domain with Alpha- Ketoglutarate, PDB code: 5ivb:

Manganese binding site 1 out of 1 in the A High Resolution Structure of A Linked KDM5A Jmj Domain with Alpha- Ketoglutarate


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of A High Resolution Structure of A Linked KDM5A Jmj Domain with Alpha- Ketoglutarate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn602 b:16.1 occ:1.00 OE2 A:GLU485 2.1 19.6 1.0 O1 A:AKG601 2.1 18.3 1.0 NE2 A:HIS483 2.2 16.4 1.0 O A:HOH747 2.3 18.0 1.0 NE2 A:HIS571 2.3 16.0 1.0 O5 A:AKG601 2.3 19.4 1.0 C1 A:AKG601 2.9 18.9 1.0 C2 A:AKG601 2.9 18.3 1.0 CE1 A:HIS483 3.1 16.6 1.0 CE1 A:HIS571 3.2 15.9 1.0 CD A:GLU485 3.2 19.8 1.0 CD2 A:HIS483 3.2 16.8 1.0 CD2 A:HIS571 3.3 15.8 1.0 OE1 A:GLU485 3.6 21.2 1.0 O2 A:AKG601 4.1 17.3 1.0 OG A:SER491 4.3 24.3 0.5 ND1 A:HIS483 4.3 14.9 1.0 O A:HOH732 4.3 42.3 1.0 ND1 A:HIS571 4.3 14.4 1.0 O A:HOH905 4.3 44.6 1.0 CG A:HIS483 4.3 14.8 1.0 CG A:HIS571 4.4 14.5 1.0 OG A:SER491 4.4 21.2 0.5 C3 A:AKG601 4.5 19.5 1.0 CG A:GLU485 4.5 17.4 1.0 O A:HOH886 4.6 39.3 1.0 CB A:SER491 4.7 19.8 0.5 CB A:SER491 4.7 21.6 0.5 O A:HOH777 4.8 31.8 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