Manganese in PDB 5fxx: Crystal Structure of Jmjc Domain of Human Histone Demethylase Uty in Complex with Oxaloacetate

The structure of Crystal Structure of Jmjc Domain of Human Histone Demethylase Uty in Complex with Oxaloacetate, PDB code: 5fxx 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)	42.77 / 1.99
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	91.590, 110.700, 119.740, 90.00, 90.00, 90.00
R / Rfree (%)	19.3 / 23.6

The structure of Crystal Structure of Jmjc Domain of Human Histone Demethylase Uty in Complex with Oxaloacetate 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 Oxaloacetate (pdb code 5fxx). 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 Oxaloacetate, PDB code: 5fxx:
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 Oxaloacetate


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 Oxaloacetate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn2345 b:27.4 occ:1.00 O A:HOH2129 1.6 33.0 1.0 OE2 A:GLU1095 2.2 25.6 1.0 NE2 A:HIS1173 2.2 28.7 1.0 O4 A:OAA2346 2.3 25.6 0.8 O A:HOH2136 2.3 31.3 1.0 NE2 A:HIS1093 2.4 30.4 1.0 CE1 A:HIS1173 3.1 26.9 1.0 CE1 A:HIS1093 3.2 31.8 1.0 C4 A:OAA2346 3.2 30.7 0.8 CD2 A:HIS1173 3.2 25.5 1.0 CD A:GLU1095 3.2 23.0 1.0 CD2 A:HIS1093 3.4 33.1 1.0 O5 A:OAA2346 3.5 23.2 0.8 O2 A:EDO2353 3.6 40.7 1.0 OE1 A:GLU1095 3.8 23.8 1.0 C2 A:EDO2353 4.1 34.4 1.0 ND1 A:HIS1173 4.3 28.9 1.0 OG A:SER1101 4.3 24.2 0.4 ND1 A:HIS1093 4.3 29.0 1.0 CG A:HIS1173 4.4 25.2 1.0 CG A:GLU1095 4.4 21.9 1.0 CG A:HIS1093 4.5 30.3 1.0 C3 A:OAA2346 4.6 32.4 0.8 OG A:SER1101 4.6 23.3 0.6 O A:HOH2285 4.7 45.4 1.0 CB A:SER1101 4.9 24.3 0.6 CB A:SER1101 4.9 24.3 0.4

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


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 Oxaloacetate within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn2345 b:27.6 occ:1.00 O5 B:OAA2346 2.1 30.6 0.9 O B:HOH2131 2.1 29.1 1.0 OE2 B:GLU1095 2.2 31.0 1.0 NE2 B:HIS1173 2.4 29.9 1.0 NE2 B:HIS1093 2.4 29.6 1.0 O B:HOH2139 2.5 33.4 1.0 C4 B:OAA2346 3.1 31.8 0.9 CE1 B:HIS1093 3.1 30.1 1.0 CE1 B:HIS1173 3.2 27.0 1.0 CD B:GLU1095 3.3 23.9 1.0 O4 B:OAA2346 3.4 32.3 0.9 CD2 B:HIS1173 3.4 31.1 1.0 CD2 B:HIS1093 3.5 26.7 1.0 OE1 B:GLU1095 3.8 27.7 1.0 O2 B:EDO2354 3.8 44.1 1.0 ND1 B:HIS1093 4.3 27.5 1.0 ND1 B:HIS1173 4.4 25.9 1.0 C3 B:OAA2346 4.4 33.9 0.9 O B:HOH2124 4.5 42.6 1.0 CG B:HIS1173 4.5 28.0 1.0 CG B:GLU1095 4.5 22.4 1.0 CG B:HIS1093 4.6 24.9 1.0 OG B:SER1101 4.6 31.9 1.0 O3 B:OAA2346 4.9 36.6 0.9 CB B:SER1101 4.9 24.1 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 Oxaloacetate To Be Published.