Manganese in PDB 5fy9: Crystal Structure of the Catalytic Domain of Human JARID1B in Complex with Pyruvate

The structure of Crystal Structure of the Catalytic Domain of Human JARID1B in Complex with Pyruvate, PDB code: 5fy9 was solved by R.Nowak, V.Srikannathasan, 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)	57.14 / 2.03
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	142.290, 142.290, 152.650, 90.00, 90.00, 120.00
R / Rfree (%)	19.9 / 23.4

The structure of Crystal Structure of the Catalytic Domain of Human JARID1B in Complex with Pyruvate also contains other interesting chemical elements:

Zinc

(Zn)

2 atoms

The binding sites of Manganese atom in the Crystal Structure of the Catalytic Domain of Human JARID1B in Complex with Pyruvate (pdb code 5fy9). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 3 binding sites of Manganese where determined in the Crystal Structure of the Catalytic Domain of Human JARID1B in Complex with Pyruvate, PDB code: 5fy9:
Jump to Manganese binding site number: 1; 2; 3;

Manganese binding site 1 out of 3 in the Crystal Structure of the Catalytic Domain of Human JARID1B in Complex with Pyruvate


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 Pyruvate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn1754 b:88.0 occ:1.00 O A:GLU419 2.6 76.7 1.0 O A:THR416 2.7 62.1 1.0 OD1 A:ASN91 2.7 50.2 1.0 O A:LEU413 2.8 44.8 1.0 O A:LEU90 3.3 43.7 1.0 O A:HOH2048 3.5 53.4 1.0 C A:GLU419 3.7 64.9 1.0 C A:THR416 3.9 66.0 1.0 CG A:ASN91 3.9 48.3 1.0 C A:LEU413 4.0 41.0 1.0 O A:VAL414 4.1 39.1 1.0 O A:HOH2045 4.1 52.7 1.0 C A:VAL414 4.2 41.3 1.0 CA A:VAL414 4.2 40.7 1.0 O A:HOH2047 4.2 66.7 1.0 CB A:GLU419 4.2 63.0 1.0 C A:LEU90 4.3 40.6 1.0 CA A:ASN91 4.4 45.0 1.0 CA A:GLU419 4.4 67.5 1.0 O A:ILE417 4.5 69.2 1.0 N A:THR416 4.6 56.9 1.0 CB A:ASN91 4.6 38.1 1.0 N A:GLU419 4.6 70.2 1.0 N A:VAL414 4.6 38.1 1.0 CA A:ILE417 4.7 73.7 1.0 C A:ILE417 4.7 70.4 1.0 N A:ILE417 4.7 69.1 1.0 N A:ASP420 4.8 65.1 1.0 N A:ASN91 4.8 41.8 1.0 CA A:THR416 4.8 63.5 1.0 N A:SER415 4.8 46.7 1.0 CA A:ASP420 4.9 64.8 1.0 ND2 A:ASN91 5.0 48.4 1.0

Manganese binding site 2 out of 3 in the Crystal Structure of the Catalytic Domain of Human JARID1B in Complex with Pyruvate


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 Pyruvate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn1755 b:37.6 occ:1.00 O A:HOH2106 2.1 34.5 1.0 OE2 A:GLU501 2.1 37.5 1.0 NE2 A:HIS499 2.1 39.3 1.0 O A:HOH2107 2.2 36.5 1.0 NE2 A:HIS587 2.2 35.8 1.0 O A:HOH2112 2.3 39.1 1.0 CE1 A:HIS499 2.9 38.2 1.0 CE1 A:HIS587 3.1 32.7 1.0 CD A:GLU501 3.1 36.0 1.0 CD2 A:HIS499 3.2 33.8 1.0 CD2 A:HIS587 3.3 28.3 1.0 OE1 A:GLU501 3.5 37.8 1.0 O A:HOH2119 4.0 42.2 1.0 ND1 A:HIS499 4.1 38.2 1.0 ND1 A:HIS587 4.2 31.9 1.0 OG A:SER507 4.3 34.1 1.0 CG A:HIS499 4.3 40.4 1.0 O1 A:EDO1766 4.3 49.3 1.0 CG A:HIS587 4.4 33.2 1.0 CG A:GLU501 4.4 35.4 1.0 O2 A:EDO1766 4.5 46.3 1.0 CB A:SER507 4.9 33.5 1.0

Manganese binding site 3 out of 3 in the Crystal Structure of the Catalytic Domain of Human JARID1B in Complex with Pyruvate


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Crystal Structure of the Catalytic Domain of Human JARID1B in Complex with Pyruvate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn2000 b:85.7 occ:1.00 O A:HOH2152 3.5 37.1 1.0 NE2 A:HIS718 3.6 42.8 1.0 CE1 A:HIS622 4.1 44.2 1.0 CD2 A:HIS718 4.3 41.6 1.0 CE A:LYS694 4.5 55.3 1.0 CE1 A:HIS718 4.6 40.2 1.0 NE2 A:HIS622 4.7 45.5 1.0 CG A:LYS694 4.9 41.0 1.0

R.Nowak, V.Srikannathasan, 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 Pyruvate To Be Published.