Manganese in PDB 5fys: Crystal Structure of the Catalytic Domain of Human JARID1B in Complex with D-2-Hydroxyglutarate

The structure of Crystal Structure of the Catalytic Domain of Human JARID1B in Complex with D-2-Hydroxyglutarate, PDB code: 5fys was solved by R.Nowak, J.Kopec, C.Johansson, C.Gileadi, 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)	47.88 / 1.89
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	142.080, 142.080, 152.470, 90.00, 90.00, 120.00
R / Rfree (%)	19.3 / 22.1

The structure of Crystal Structure of the Catalytic Domain of Human JARID1B in Complex with D-2-Hydroxyglutarate 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 the Catalytic Domain of Human JARID1B in Complex with D-2-Hydroxyglutarate (pdb code 5fys). 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 the Catalytic Domain of Human JARID1B in Complex with D-2-Hydroxyglutarate, PDB code: 5fys:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the Crystal Structure of the Catalytic Domain of Human JARID1B in Complex with D-2-Hydroxyglutarate


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 JARID1B in Complex with D-2-Hydroxyglutarate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn1756 b:30.7 occ:1.00 O A:HOH2089 2.1 34.3 1.0 O3 A:2HG1773 2.1 29.8 0.8 OE2 A:GLU501 2.1 31.9 1.0 NE2 A:HIS499 2.2 29.5 1.0 NE2 A:HIS587 2.2 31.0 1.0 O2 A:2HG1773 2.2 25.7 0.8 CE1 A:HIS499 3.0 34.9 1.0 C2 A:2HG1773 3.0 31.9 0.8 C1 A:2HG1773 3.0 32.2 0.8 CE1 A:HIS587 3.1 27.2 1.0 CD A:GLU501 3.2 30.2 1.0 CD2 A:HIS587 3.2 26.4 1.0 CD2 A:HIS499 3.3 28.4 1.0 OE1 A:GLU501 3.6 32.8 1.0 O5 A:2HG1773 3.9 35.0 0.8 C3 A:2HG1773 4.1 34.0 0.8 ND1 A:HIS499 4.1 31.0 1.0 OG A:SER507 4.2 28.1 0.8 NH2 A:ARG98 4.2 38.0 0.6 O1 A:2HG1773 4.2 31.5 0.8 ND1 A:HIS587 4.2 28.1 1.0 CG A:HIS499 4.3 32.4 1.0 CG A:HIS587 4.3 26.7 1.0 CG A:GLU501 4.4 28.4 1.0 OG A:SER507 4.5 27.9 0.2 O1 A:EDO1769 4.5 43.4 1.0 CB A:SER507 4.7 29.4 0.2 CB A:SER507 4.8 29.3 0.8 C1 A:EDO1769 4.8 46.3 1.0 C5 A:2HG1773 4.9 42.7 0.8 C4 A:2HG1773 5.0 35.2 0.8

Manganese binding site 2 out of 2 in the Crystal Structure of the Catalytic Domain of Human JARID1B in Complex with D-2-Hydroxyglutarate


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 JARID1B in Complex with D-2-Hydroxyglutarate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn1757 b:85.0 occ:1.00 O A:HOH2234 3.5 35.4 1.0 NE2 A:HIS718 3.7 38.1 1.0 O A:HOH2237 3.9 47.5 1.0 CE1 A:HIS622 3.9 43.9 1.0 NE2 A:HIS622 4.3 41.9 1.0 CD2 A:HIS718 4.4 36.3 1.0 CE A:LYS694 4.4 52.6 1.0 CE1 A:HIS718 4.6 39.6 1.0 CG A:LYS694 4.9 35.0 1.0

R.Nowak, J.Kopec, C.Johansson, C.Gileadi, K.Kupinska, C.Strain-Damerell, A.Szykowska, F.Von Delft, N.A.Burgess-Brown, C.H.Arrowsmith, C.Bountra, A.M.Edwards, U.Oppermann. Crystal Structure of the Catalytic Domain of Human JARID1B in Complex with D-2-Hydroxyglutarate To Be Published.