Manganese in PDB 5a3n: Crystal Structure of Human Plu-1 (JARID1B) in Complex with KDOAM25A

The structure of Crystal Structure of Human Plu-1 (JARID1B) in Complex with KDOAM25A, PDB code: 5a3n was solved by V.Srikannathasan, C.Johansson, C.Gileadi, A.Nuzzi, G.F.Ruda, J.Kopec, F.Vondelft, C.H.Arrowsmith, C.Bountra, A.Edwards, P.Brennan, U.Oppermann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	122.87 / 2.00
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	141.874, 141.874, 151.865, 90.00, 90.00, 120.00
R / Rfree (%)	18.3 / 20.3

The structure of Crystal Structure of Human Plu-1 (JARID1B) in Complex with KDOAM25A also contains other interesting chemical elements:

Zinc

(Zn)

2 atoms

The binding sites of Manganese atom in the Crystal Structure of Human Plu-1 (JARID1B) in Complex with KDOAM25A (pdb code 5a3n). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 3 binding sites of Manganese where determined in the Crystal Structure of Human Plu-1 (JARID1B) in Complex with KDOAM25A, PDB code: 5a3n:
Jump to Manganese binding site number: 1; 2; 3;

Manganese binding site 1 out of 3 in the Crystal Structure of Human Plu-1 (JARID1B) in Complex with KDOAM25A


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 Plu-1 (JARID1B) in Complex with KDOAM25A within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn1756 b:81.8 occ:1.00 O A:LEU413 2.8 32.8 1.0 O A:GLU419 2.8 56.0 1.0 OD1 A:ASN91 2.8 39.1 1.0 O A:LEU90 2.9 34.1 1.0 O A:THR416 2.9 48.9 1.0 O A:HOH2089 3.6 40.2 1.0 O A:HOH2087 3.7 59.2 1.0 O A:HOH2090 3.7 68.5 1.0 C A:GLU419 3.8 53.6 1.0 C A:LEU413 3.9 31.5 1.0 CG A:ASN91 4.0 38.6 1.0 C A:LEU90 4.0 33.6 1.0 CB A:GLU419 4.0 55.0 1.0 C A:THR416 4.0 49.3 1.0 O A:VAL414 4.1 30.7 1.0 CA A:VAL414 4.2 31.0 1.0 C A:VAL414 4.2 31.7 1.0 CA A:ASN91 4.4 35.5 1.0 CA A:GLU419 4.4 55.7 1.0 N A:VAL414 4.5 31.6 1.0 N A:THR416 4.6 43.3 1.0 N A:ASN91 4.6 34.5 1.0 N A:ASP420 4.7 50.7 1.0 CB A:ASN91 4.7 36.7 1.0 CD2 A:LEU413 4.7 39.5 1.0 CA A:ASP420 4.8 54.8 1.0 N A:GLU419 4.8 57.7 1.0 CA A:THR416 4.8 46.9 1.0 N A:ILE417 4.9 55.6 1.0 CA A:ILE417 5.0 59.7 1.0 ND2 A:ASN91 5.0 41.4 1.0

Manganese binding site 2 out of 3 in the Crystal Structure of Human Plu-1 (JARID1B) in Complex with KDOAM25A


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 Plu-1 (JARID1B) in Complex with KDOAM25A within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn1757 b:0.7 occ:1.00 O A:HOH2399 2.0 55.8 1.0 OE2 A:GLU678 2.9 45.9 1.0 CG A:GLU678 3.6 36.2 1.0 CD A:GLU678 3.7 40.7 1.0 O A:HOH2356 3.7 33.0 1.0 O A:HOH2355 4.1 33.8 1.0 OE1 A:GLU678 4.8 47.2 1.0

Manganese binding site 3 out of 3 in the Crystal Structure of Human Plu-1 (JARID1B) in Complex with KDOAM25A


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Crystal Structure of Human Plu-1 (JARID1B) in Complex with KDOAM25A within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn1758 b:22.8 occ:1.00 OE2 A:GLU501 2.0 28.9 1.0 N09 A:LQT1759 2.1 25.5 1.0 N06 A:LQT1759 2.1 22.0 1.0 NE2 A:HIS499 2.2 26.3 1.0 O A:HOH2210 2.2 24.6 1.0 NE2 A:HIS587 2.3 25.5 1.0 C08 A:LQT1759 2.9 26.2 1.0 C07 A:LQT1759 2.9 24.6 1.0 C10 A:LQT1759 3.0 27.5 1.0 CE1 A:HIS499 3.0 26.6 1.0 C05 A:LQT1759 3.0 22.9 1.0 CD A:GLU501 3.1 26.1 1.0 CE1 A:HIS587 3.2 23.9 1.0 CD2 A:HIS499 3.3 25.4 1.0 CD2 A:HIS587 3.3 23.3 1.0 OE1 A:GLU501 3.4 30.4 1.0 ND1 A:HIS499 4.2 25.9 1.0 C11 A:LQT1759 4.2 29.4 1.0 C21 A:LQT1759 4.3 24.4 1.0 C04 A:LQT1759 4.3 22.7 1.0 ND1 A:HIS587 4.3 23.4 1.0 CG A:HIS499 4.3 25.2 1.0 CG A:GLU501 4.4 26.1 1.0 OG A:SER507 4.4 23.6 1.0 CG A:HIS587 4.4 22.6 1.0 O20 A:LQT1759 4.5 31.2 1.0 C03 A:LQT1759 4.8 24.3 1.0 CB A:SER507 5.0 24.1 1.0

A.Tumber, A.Nuzzi, E.S.Hookway, S.B.Hatch, S.Velupillai, C.Johansson, A.Kawamura, P.Savitsky, C.Yapp, A.Szykowska, N.Wu, C.Bountra, C.Strain-Damerell, N.A.Burgess-Brown, G.F.Ruda, O.Fedorov, S.Munro, K.S.England, R.P.Nowak, C.J.Schofield, N.B.La Thangue, C.Pawlyn, F.Davies, G.Morgan, N.Athanasou, S.Muller, U.Oppermann, P.E.Brennan. Potent and Selective KDM5 Inhibitor Stops Cellular Demethylation of H3K4ME3 at Transcription Start Sites and Proliferation of MM1S Myeloma Cells. Cell Chem Biol V. 24 371 2017.
ISSN: ESSN 2451-9456
PubMed: 28262558
DOI: 10.1016/J.CHEMBIOL.2017.02.006