Manganese in PDB 5a3p: Crystal Structure of the Catalytic Domain of Human PLU1 (JARID1B).

The structure of Crystal Structure of the Catalytic Domain of Human PLU1 (JARID1B)., PDB code: 5a3p was solved by R.Nowak, V.Srikannathasan, C.Johansson, C.Gileadi, C.Tallant, K.Kupinska, C.Strain-Damerell, A.Szykowska, F.Von Delft, N.A.Burgess-Brown, C.H.Arrowsmith, C.Bountra, A.M.Edwards, U.Oppermann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.56 / 2.01
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	141.788, 141.788, 152.272, 90.00, 90.00, 120.00
R / Rfree (%)	18.7 / 22.4

The structure of Crystal Structure of the Catalytic Domain of Human PLU1 (JARID1B). also contains other interesting chemical elements:

Zinc

(Zn)

2 atoms

The binding sites of Manganese atom in the Crystal Structure of the Catalytic Domain of Human PLU1 (JARID1B). (pdb code 5a3p). 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 the Catalytic Domain of Human PLU1 (JARID1B)., PDB code: 5a3p:
Jump to Manganese binding site number: 1; 2; 3;

Manganese binding site 1 out of 3 in the Crystal Structure of the Catalytic Domain of Human PLU1 (JARID1B).


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 the Catalytic Domain of Human PLU1 (JARID1B). within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn1757 b:72.9 occ:1.00 O A:HOH2129 2.0 43.7 1.0 O A:THR416 2.7 48.5 1.0 O A:LEU413 2.7 37.1 1.0 OD1 A:ASN91 2.8 38.0 1.0 O A:GLU419 2.9 58.1 1.0 O A:HOH2131 3.2 47.5 1.0 O A:LEU90 3.4 32.6 1.0 O A:HOH2132 3.5 56.0 1.0 C A:THR416 3.6 51.4 1.0 C A:LEU413 3.9 31.6 1.0 O A:VAL414 3.9 30.7 1.0 C A:GLU419 3.9 52.4 1.0 CG A:ASN91 3.9 38.4 1.0 C A:VAL414 4.0 33.2 1.0 CA A:VAL414 4.1 29.7 1.0 CB A:GLU419 4.2 49.0 1.0 N A:THR416 4.2 44.6 1.0 CA A:ASN91 4.4 35.8 1.0 C A:LEU90 4.4 31.0 1.0 CA A:GLU419 4.4 51.8 1.0 CA A:THR416 4.5 51.1 1.0 N A:ILE417 4.5 55.6 1.0 N A:VAL414 4.5 27.7 1.0 CA A:ILE417 4.6 56.4 1.0 CB A:ASN91 4.6 33.3 1.0 N A:GLU419 4.6 51.4 1.0 O A:HOH2128 4.6 47.1 1.0 N A:SER415 4.7 33.9 1.0 O A:ILE417 4.7 52.5 1.0 O A:HOH2071 4.7 58.8 1.0 C A:ILE417 4.7 56.4 1.0 N A:ASN91 4.8 34.3 1.0 N A:ASP420 4.9 50.3 1.0 C A:SER415 4.9 45.0 1.0 CB A:THR416 5.0 49.1 1.0

Manganese binding site 2 out of 3 in the Crystal Structure of the Catalytic Domain of Human PLU1 (JARID1B).


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 the Catalytic Domain of Human PLU1 (JARID1B). within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn1758 b:26.4 occ:1.00 OE2 A:GLU501 2.0 29.5 1.0 NE2 A:HIS499 2.1 29.5 1.0 O A:HOH2286 2.1 31.3 1.0 NE2 A:HIS587 2.2 26.4 1.0 O A:HOH2285 2.2 27.5 1.0 O A:HOH2291 2.3 28.7 1.0 CE1 A:HIS499 2.8 34.1 1.0 CE1 A:HIS587 3.0 24.1 1.0 CD A:GLU501 3.1 25.4 1.0 CD2 A:HIS499 3.2 27.9 1.0 CD2 A:HIS587 3.3 23.5 1.0 OE1 A:GLU501 3.5 27.1 1.0 ND1 A:HIS499 4.0 35.4 1.0 ND1 A:HIS587 4.2 24.1 1.0 O A:HOH2078 4.2 41.5 1.0 CG A:HIS499 4.2 30.3 1.0 C1 A:EDO1761 4.3 39.3 1.0 CG A:HIS587 4.3 24.7 1.0 CG A:GLU501 4.3 28.0 1.0 OG A:SER507 4.4 26.4 1.0 O1 A:EDO1761 4.4 42.2 1.0 O A:HOH2143 4.4 49.1 1.0 O A:HOH2301 4.4 31.4 1.0 O A:HOH2254 4.5 45.6 1.0 CB A:SER507 4.9 26.4 1.0

Manganese binding site 3 out of 3 in the Crystal Structure of the Catalytic Domain of Human PLU1 (JARID1B).


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 the Catalytic Domain of Human PLU1 (JARID1B). within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn1759 b:79.0 occ:1.00 O A:HOH2499 2.2 45.6 1.0 O A:HOH2397 3.5 30.7 1.0 NE2 A:HIS622 3.6 36.9 1.0 O A:HOH2402 3.6 42.6 1.0 NE2 A:HIS718 3.9 35.0 1.0 O A:HOH2366 3.9 52.2 1.0 CE A:LYS694 4.1 46.8 1.0 CE1 A:HIS622 4.3 37.8 1.0 O A:HOH2481 4.5 70.5 1.0 CD2 A:HIS718 4.5 36.6 1.0 CD2 A:HIS622 4.7 35.1 1.0 CG A:LYS694 4.8 34.0 1.0 CE1 A:HIS718 4.9 33.2 1.0

C.Johansson, S.Velupillai, A.Tumber, A.Szykowska, E.S.Hookway, R.P.Nowak, C.Strain-Damerell, C.Gileadi, M.Philpott, N.Burgess-Brown, N.Wu, J.Kopec, A.Nuzzi, H.Steuber, U.Egner, V.Badock, S.Munro, N.B.Lathangue, S.Westaway, J.Brown, N.Athanasou, R.Prinjha, P.E.Brennan, U.Oppermann. Structural Analysis of Human KDM5B Guides Histone Demethylase Inhibitor Development. Nat.Chem.Biol. V. 12 539 2016.
ISSN: ISSN 1552-4450
PubMed: 27214403
DOI: 10.1038/NCHEMBIO.2087