Manganese in PDB 5lw9: Crystal Structure of Human JARID1B in Complex with S40563A

The structure of Crystal Structure of Human JARID1B in Complex with S40563A, PDB code: 5lw9 was solved by V.Srikannathasan, Y.V.Le Bihan, A.Szykowska, C.Johansson, C.Gileadi, C.H.Arrowsmith, A.M.Edwards, C.Bountra, F.Von Delft, U.Oppermann, K.Huber, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	64.92 / 2.30
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	142.960, 142.960, 152.470, 90.00, 90.00, 120.00
R / Rfree (%)	18.5 / 21.8

The structure of Crystal Structure of Human JARID1B in Complex with S40563A also contains other interesting chemical elements:

Chlorine	(Cl)	2 atoms
Zinc	(Zn)	1 atom

The binding sites of Manganese atom in the Crystal Structure of Human JARID1B in Complex with S40563A (pdb code 5lw9). 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 Human JARID1B in Complex with S40563A, PDB code: 5lw9:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the Crystal Structure of Human JARID1B in Complex with S40563A


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 Human JARID1B in Complex with S40563A within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn802 b:0.7 occ:0.79 OD1 A:ASN91 2.1 90.0 1.0 O A:LEU90 2.8 90.4 1.0 O A:THR416 2.8 86.2 1.0 O A:GLU419 3.2 89.1 1.0 CG A:ASN91 3.3 90.6 1.0 O A:LEU413 3.4 61.8 1.0 C A:THR416 3.8 80.0 1.0 C A:LEU90 3.9 82.5 1.0 CA A:ILE417 4.1 94.9 1.0 ND2 A:ASN91 4.1 0.0 1.0 CA A:ASN91 4.2 82.5 1.0 CB A:ASN91 4.3 76.5 1.0 CD1 A:ILE417 4.3 84.6 1.0 O A:ILE417 4.4 0.1 1.0 C A:GLU419 4.4 90.5 1.0 N A:ILE417 4.4 86.8 1.0 C A:ILE417 4.4 95.0 1.0 O A:VAL414 4.5 58.6 1.0 C A:LEU413 4.5 57.4 1.0 N A:ASN91 4.5 82.8 1.0 C A:VAL414 4.6 54.5 1.0 CA A:VAL414 4.7 48.3 1.0 N A:THR416 4.7 75.4 1.0 CA A:THR416 4.9 77.0 1.0 N A:GLU419 5.0 93.7 1.0

Manganese binding site 2 out of 2 in the Crystal Structure of Human JARID1B in Complex with S40563A


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 Human JARID1B in Complex with S40563A within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn809 b:39.9 occ:1.00 N2 A:5UJ808 2.0 41.7 1.0 OE2 A:GLU501 2.1 50.5 1.0 NE2 A:HIS499 2.1 41.6 1.0 O A:HOH956 2.1 45.5 1.0 NE2 A:HIS587 2.2 48.6 1.0 N3 A:5UJ808 2.2 42.7 1.0 N1 A:5UJ808 2.8 43.7 1.0 C14 A:5UJ808 3.0 42.6 1.0 CE1 A:HIS587 3.1 49.9 1.0 C13 A:5UJ808 3.1 44.1 1.0 CD2 A:HIS499 3.1 46.0 1.0 CD A:GLU501 3.1 46.3 1.0 CE1 A:HIS499 3.1 48.0 1.0 CD2 A:HIS587 3.2 45.8 1.0 C15 A:5UJ808 3.3 40.0 1.0 OE1 A:GLU501 3.6 46.2 1.0 C12 A:5UJ808 4.1 39.9 1.0 O A:HOH902 4.1 64.6 1.0 ND1 A:HIS587 4.2 50.0 1.0 ND1 A:HIS499 4.2 45.2 1.0 C11 A:5UJ808 4.2 51.1 1.0 CG A:HIS499 4.2 43.8 1.0 CG A:HIS587 4.3 50.5 1.0 CG A:GLU501 4.3 40.2 1.0 C18 A:5UJ808 4.4 44.0 1.0 OG A:SER507 4.5 51.7 1.0 C16 A:5UJ808 4.6 38.5 1.0 C17 A:5UJ808 5.0 47.0 1.0

V.Srikannathasan, V.Srikannathasan, Y.V.Le Bihan, A.Szykowska, C.Johansson, C.Gileadi, C.H.Arrowsmith, A.M.Edwards, C.Bountra, F.Von Delft, U.Oppermann, K.Huber. N/A N/A.