Manganese in PDB 5fpl: Crystal Structure of Human JARID1B in Complex with CCT363901

The structure of Crystal Structure of Human JARID1B in Complex with CCT363901, PDB code: 5fpl was solved by V.Srikannathasan, L.B.Yann-Vai, R.Nowak, C.Johansson, C.Gileadi, F.Vondelft, C.H.Arrowsmith, C.Bountra, A.Edwards, P.Brennan, K.Huber, U.Oppermann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.17 / 2.35
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	142.910, 142.910, 152.100, 90.00, 90.00, 120.00
R / Rfree (%)	19.1 / 20.8

The structure of Crystal Structure of Human JARID1B in Complex with CCT363901 also contains other interesting chemical elements:

Zinc

(Zn)

1 atom

The binding sites of Manganese atom in the Crystal Structure of Human JARID1B in Complex with CCT363901 (pdb code 5fpl). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the Crystal Structure of Human JARID1B in Complex with CCT363901, PDB code: 5fpl:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the Crystal Structure of Human JARID1B in Complex with CCT363901


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of Human JARID1B in Complex with CCT363901 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn801 b:82.7 occ:0.59 O A:THR416 2.7 79.0 1.0 O A:LEU413 2.7 63.6 1.0 O A:LEU90 2.9 73.3 1.0 O A:GLU419 2.9 86.4 1.0 O A:HOH2058 3.1 84.5 1.0 OD1 A:ASN91 3.1 74.8 1.0 O A:HOH2096 3.7 67.9 1.0 C A:THR416 3.7 79.7 1.0 C A:LEU413 3.9 61.4 1.0 C A:LEU90 4.0 73.0 1.0 O A:VAL414 4.0 60.2 1.0 C A:GLU419 4.1 87.2 1.0 C A:VAL414 4.2 61.1 1.0 CA A:VAL414 4.2 54.7 1.0 CG A:ASN91 4.2 83.8 1.0 N A:THR416 4.4 68.4 1.0 N A:VAL414 4.5 54.8 1.0 CA A:ASN91 4.5 69.8 1.0 CA A:THR416 4.6 70.9 1.0 N A:ILE417 4.6 81.2 1.0 N A:ASN91 4.7 70.0 1.0 CA A:GLU419 4.8 84.2 1.0 CB A:GLU419 4.8 83.9 1.0 CA A:ILE417 4.8 83.8 1.0 N A:GLU419 4.8 85.0 1.0 CB A:ASN91 4.8 69.1 1.0 N A:SER415 4.9 60.6 1.0 O A:ILE417 4.9 89.3 1.0 C A:ILE417 4.9 88.8 1.0

Manganese binding site 2 out of 2 in the Crystal Structure of Human JARID1B in Complex with CCT363901


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structure of Human JARID1B in Complex with CCT363901 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn802 b:42.5 occ:1.00 N2 A:QAY901 2.0 33.2 0.8 O A:HOH2141 2.0 61.4 1.0 N5 A:QAY901 2.1 34.7 0.8 OE2 A:GLU501 2.2 58.8 1.0 NE2 A:HIS499 2.2 45.7 1.0 NE2 A:HIS587 2.2 45.7 1.0 N1 A:QAY901 2.8 37.6 0.8 C13 A:QAY901 2.9 34.0 0.8 CD A:GLU501 3.1 56.7 1.0 C12 A:QAY901 3.1 36.8 0.8 C19 A:QAY901 3.2 29.2 0.8 CD2 A:HIS587 3.2 44.5 1.0 CD2 A:HIS499 3.2 46.4 1.0 CE1 A:HIS499 3.2 44.4 1.0 CE1 A:HIS587 3.2 46.1 1.0 OE1 A:GLU501 3.5 47.4 1.0 O A:HOH2129 4.0 58.2 1.0 C11 A:QAY901 4.0 35.7 0.8 C10 A:QAY901 4.2 38.4 0.8 C14 A:QAY901 4.3 28.9 0.8 CG A:HIS587 4.3 42.6 1.0 CG A:HIS499 4.3 45.3 1.0 ND1 A:HIS499 4.3 45.8 1.0 ND1 A:HIS587 4.4 45.5 1.0 CG A:GLU501 4.4 48.5 1.0 C18 A:QAY901 4.4 28.6 0.8 OG A:SER507 4.5 53.5 1.0 C17 A:QAY901 4.9 29.3 0.8

V.Bavetsias, R.M.Lanigan, G.F.Ruda, B.Atrash, M.G.Mclaughlin, A.Tumber, N.Y.Mok, Y.Le Bihan, S.Dempster, K.J.Boxall, F.Jeganathan, S.B.Hatch, P.Savitsky, S.Velupillai, T.Krojer, K.S.England, J.Sejberg, C.Thai, A.Donovan, A.Pal, G.Scozzafava, J.M.Bennett, A.Kawamura, C.Johansson, A.Szykowska, C.Gileadi, N.A.Burgess-Brown, F.Von Delft, U.Oppermann, Z.Walters, J.Shipley, F.I.Raynaud, S.M.Westaway, R.K.Prinjha, O.Fedorov, R.Burke, C.J.Schofield, I.M.Westwood, C.Bountra, S.Muller, R.L.M.Van Montfort, P.E.Brennan, J.Blagg. 8-Substituted Pyrido[3,4-D]Pyrimidin-4(3H)-One Derivatives As Potent, Cell Permeable, KDM4 (JMJD2) and KDM5 (JARID1) Histone Lysine Demethylase Inhibitors. J.Med.Chem. V. 59 1388 2016.
ISSN: ISSN 0022-2623
PubMed: 26741168
DOI: 10.1021/ACS.JMEDCHEM.5B01635