Manganese in PDB 5fup: Crystal Structure of Human JARID1B in Complex with 2-Oxoglutarate.

The structure of Crystal Structure of Human JARID1B in Complex with 2-Oxoglutarate., PDB code: 5fup was solved by R.Nowak, V.Srikannathasan, C.Johansson, C.Gileadi, K.Kupinska, C.Strain-Damerell, A.Szykowska, R.Talon, 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)	71.17 / 2.15
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	142.340, 142.340, 152.260, 90.00, 90.00, 120.00
R / Rfree (%)	18.3 / 22.7

The structure of Crystal Structure of Human JARID1B in Complex with 2-Oxoglutarate. also contains other interesting chemical elements:

Chlorine	(Cl)	1 atom
Zinc	(Zn)	2 atoms

The binding sites of Manganese atom in the Crystal Structure of Human JARID1B in Complex with 2-Oxoglutarate. (pdb code 5fup). 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 2-Oxoglutarate., PDB code: 5fup:
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 2-Oxoglutarate.


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 2-Oxoglutarate. within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn1757 b:32.1 occ:1.00 O A:HOH2252 2.1 32.6 1.0 OE2 A:GLU501 2.1 37.2 1.0 NE2 A:HIS499 2.2 36.5 1.0 O5 A:AKG1764 2.2 31.5 0.8 NE2 A:HIS587 2.2 32.0 1.0 O2 A:AKG1764 2.4 29.7 0.8 C2 A:AKG1764 3.0 34.7 0.8 CE1 A:HIS499 3.0 37.7 1.0 C1 A:AKG1764 3.0 35.1 0.8 CE1 A:HIS587 3.1 26.6 1.0 CD A:GLU501 3.1 32.2 1.0 CD2 A:HIS499 3.3 31.4 1.0 CD2 A:HIS587 3.3 24.3 1.0 OE1 A:GLU501 3.4 36.2 1.0 O1 A:EDO2769 4.0 51.3 1.0 ND1 A:HIS499 4.1 37.5 1.0 OG A:SER507 4.2 33.7 1.0 ND1 A:HIS587 4.2 25.6 1.0 O1 A:AKG1764 4.2 32.6 0.8 CG A:HIS499 4.3 38.7 1.0 CG A:HIS587 4.4 27.4 1.0 CG A:GLU501 4.4 31.0 1.0 C3 A:AKG1764 4.4 36.6 0.8 CB A:SER507 4.8 32.6 1.0

Manganese binding site 2 out of 2 in the Crystal Structure of Human JARID1B in Complex with 2-Oxoglutarate.


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 2-Oxoglutarate. within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn1758 b:86.9 occ:1.00 O A:HOH2456 2.0 51.1 1.0 O A:HOH2354 3.6 36.7 1.0 O A:HOH2358 3.6 53.7 1.0 NE2 A:HIS622 3.8 41.7 1.0 O A:HOH2319 3.8 57.3 1.0 NE2 A:HIS718 3.9 42.9 1.0 O A:HOH2458 4.1 72.9 1.0 O A:HOH2275 4.2 58.4 1.0 CE A:LYS694 4.3 58.5 1.0 CE1 A:HIS622 4.5 41.7 1.0 CD2 A:HIS718 4.6 40.0 1.0 CE1 A:HIS718 4.9 39.1 1.0 CD2 A:HIS622 4.9 37.2 1.0 CG A:LYS694 5.0 43.6 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