Manganese in PDB 5fy0: Crystal Structure of Jmjc Domain of Human Histone Demethylase Uty in Complex with L-Malate

The structure of Crystal Structure of Jmjc Domain of Human Histone Demethylase Uty in Complex with L-Malate, PDB code: 5fy0 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)	70.59 / 2.14
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	91.610, 110.740, 120.750, 90.00, 90.00, 90.00
R / Rfree (%)	17.9 / 22.5

The structure of Crystal Structure of Jmjc Domain of Human Histone Demethylase Uty in Complex with L-Malate 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 L-Malate (pdb code 5fy0). 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 L-Malate, PDB code: 5fy0:
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 L-Malate


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 L-Malate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn2345 b:39.6 occ:1.00 O A:HOH2142 2.0 34.8 1.0 OE2 A:GLU1095 2.1 28.7 1.0 O4B A:LMR2346 2.3 34.0 0.9 NE2 A:HIS1173 2.4 32.3 1.0 NE2 A:HIS1093 2.4 34.4 1.0 O A:HOH2150 2.6 43.1 1.0 C4 A:LMR2346 3.1 38.7 0.9 CE1 A:HIS1093 3.1 36.5 1.0 O4A A:LMR2346 3.2 36.8 0.9 CD A:GLU1095 3.2 25.7 1.0 CE1 A:HIS1173 3.2 31.7 1.0 CD2 A:HIS1173 3.4 27.3 1.0 O2 A:EDO2353 3.5 46.8 1.0 CD2 A:HIS1093 3.6 33.7 1.0 OE1 A:GLU1095 3.8 27.4 1.0 C2 A:EDO2353 4.1 42.2 1.0 OG A:SER1101 4.3 22.6 0.6 O A:HOH2148 4.3 48.0 1.0 ND1 A:HIS1093 4.4 31.1 1.0 CG A:GLU1095 4.4 24.1 1.0 ND1 A:HIS1173 4.4 31.4 1.0 CG A:HIS1173 4.5 28.2 1.0 C3 A:LMR2346 4.5 29.7 0.9 CG A:HIS1093 4.6 33.8 1.0 OG A:SER1101 4.7 24.4 0.4 CB A:SER1101 4.9 25.7 0.4 CB A:SER1101 5.0 25.8 0.6

Manganese binding site 2 out of 2 in the Crystal Structure of Jmjc Domain of Human Histone Demethylase Uty in Complex with L-Malate


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 L-Malate within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn2345 b:44.8 occ:1.00 OE2 B:GLU1095 2.1 36.7 1.0 O4B B:LMR2346 2.2 34.8 0.9 O B:HOH2130 2.3 38.0 1.0 NE2 B:HIS1173 2.4 33.4 1.0 O B:HOH2137 2.5 40.5 1.0 NE2 B:HIS1093 2.5 32.3 1.0 C4 B:LMR2346 3.2 42.3 0.9 CE1 B:HIS1093 3.2 31.7 1.0 CD B:GLU1095 3.2 25.6 1.0 CE1 B:HIS1173 3.3 29.7 1.0 O4A B:LMR2346 3.4 41.2 0.9 CD2 B:HIS1173 3.4 31.3 1.0 CD2 B:HIS1093 3.7 31.1 1.0 O2 B:EDO2354 3.8 42.8 1.0 OE1 B:GLU1095 3.8 31.6 1.0 O B:HOH2123 3.8 47.5 1.0 ND1 B:HIS1173 4.4 32.7 1.0 CG B:GLU1095 4.4 28.4 1.0 ND1 B:HIS1093 4.4 28.8 1.0 C3 B:LMR2346 4.5 33.5 0.9 CG B:HIS1173 4.5 29.8 1.0 OG B:SER1101 4.6 35.2 1.0 CG B:HIS1093 4.7 32.5 1.0 O B:HOH2124 4.7 37.6 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 L-Malate To Be Published.