Manganese in PDB 5fym: Crystal Structure of Jmjc Domain of Human Histone Demethylase Uty in Complex with D-2-Hydroxyglutarate

The structure of Crystal Structure of Jmjc Domain of Human Histone Demethylase Uty in Complex with D-2-Hydroxyglutarate, PDB code: 5fym was solved by R.Nowak, T.Krojer, C.Johansson, C.Gileadi, K.Kupinska, F.Von Delft, C.H.Arrowsmith, C.Bountra, A.Edwards, U.Oppermann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	36.82 / 2.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	90.480, 109.340, 117.300, 90.00, 90.00, 90.00
R / Rfree (%)	19.2 / 24.5

The structure of Crystal Structure of Jmjc Domain of Human Histone Demethylase Uty in Complex with D-2-Hydroxyglutarate also contains other interesting chemical elements:

Zinc

(Zn)

2 atoms

The binding sites of Manganese atom in the Crystal Structure of Jmjc Domain of Human Histone Demethylase Uty in Complex with D-2-Hydroxyglutarate (pdb code 5fym). 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 Jmjc Domain of Human Histone Demethylase Uty in Complex with D-2-Hydroxyglutarate, PDB code: 5fym:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the Crystal Structure of Jmjc Domain of Human Histone Demethylase Uty 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 Jmjc Domain of Human Histone Demethylase Uty in Complex with D-2-Hydroxyglutarate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn2266 b:25.6 occ:1.00 OE2 A:GLU1016 2.0 27.0 1.0 O A:HOH3145 2.1 30.7 1.0 O2 A:2HG2267 2.2 29.7 1.0 NE2 A:HIS1094 2.2 25.0 1.0 O3 A:2HG2267 2.3 28.7 1.0 NE2 A:HIS1014 2.3 29.5 1.0 CE1 A:HIS1094 3.1 27.5 1.0 C1 A:2HG2267 3.1 26.0 1.0 CE1 A:HIS1014 3.1 28.9 1.0 CD A:GLU1016 3.1 21.5 1.0 C2 A:2HG2267 3.1 30.4 1.0 CD2 A:HIS1094 3.2 24.1 1.0 CD2 A:HIS1014 3.4 32.1 1.0 OE1 A:GLU1016 3.6 25.5 1.0 O A:HOH3316 3.8 38.3 1.0 ND1 A:HIS1094 4.2 24.0 1.0 O1 A:2HG2267 4.2 32.9 1.0 ND1 A:HIS1014 4.3 31.7 1.0 CG A:HIS1094 4.3 27.5 1.0 OG A:SER1022 4.3 26.1 0.2 CG A:GLU1016 4.3 22.1 1.0 O2 A:EDO2278 4.4 41.8 1.0 C3 A:2HG2267 4.4 34.4 1.0 OG A:SER1022 4.4 26.4 0.8 CG A:HIS1014 4.5 32.4 1.0 CB A:SER1022 4.7 25.2 0.8 CB A:SER1022 4.7 25.4 0.2

Manganese binding site 2 out of 2 in the Crystal Structure of Jmjc Domain of Human Histone Demethylase Uty 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 Jmjc Domain of Human Histone Demethylase Uty in Complex with D-2-Hydroxyglutarate within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn2273 b:27.1 occ:1.00 OE2 B:GLU1016 2.2 27.3 1.0 O3 B:2HG2274 2.2 29.6 1.0 O1 B:2HG2274 2.2 30.4 1.0 NE2 B:HIS1014 2.3 25.1 1.0 O B:HOH3137 2.4 32.2 1.0 NE2 B:HIS1094 2.4 28.4 1.0 C2 B:2HG2274 2.8 29.0 1.0 C1 B:2HG2274 2.8 29.2 1.0 CE1 B:HIS1014 3.2 26.8 1.0 CD B:GLU1016 3.3 25.2 1.0 CD2 B:HIS1094 3.3 25.1 1.0 CE1 B:HIS1094 3.3 22.8 1.0 CD2 B:HIS1014 3.3 24.4 1.0 OE1 B:GLU1016 3.8 26.1 1.0 O B:HOH3130 3.8 37.2 1.0 O2 B:2HG2274 4.1 30.1 1.0 C3 B:2HG2274 4.3 39.2 1.0 ND1 B:HIS1014 4.3 24.9 1.0 OG B:SER1022 4.3 29.0 1.0 O B:HOH3241 4.3 41.4 1.0 CG B:HIS1014 4.4 28.3 1.0 ND1 B:HIS1094 4.4 25.6 1.0 CG B:HIS1094 4.5 26.5 1.0 CG B:GLU1016 4.5 23.3 1.0 CB B:SER1022 4.7 25.8 1.0 O2 B:EDO2282 4.8 27.7 1.0 C4 B:2HG2274 4.9 36.7 1.0

R.Nowak, T.Krojer, C.Johansson, C.Gileadi, K.Kupinska, F.Von Delft, C.H.Arrowsmith, C.Bountra, A.Edwards, U.Oppermann. Crystal Structure of Jmjc Domain of Human Histone Demethylase Uty in Complex with D-2- Hydroxyglutarate To Be Published.