Manganese in PDB 5fv3: Crystal Structure of Human JARID1B Construct C2 in Complex with N- Oxalylglycine.

The structure of Crystal Structure of Human JARID1B Construct C2 in Complex with N- Oxalylglycine., PDB code: 5fv3 was solved by R.Nowak, V.Srikannathasan, C.Johansson, C.Gileadi, K.Kupinska, C.Strain-Damerell, A.Szykowska, R.Talon, 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)	123.28 / 2.37
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	142.350, 142.350, 152.330, 90.00, 90.00, 120.00
R / Rfree (%)	19.4 / 23.5

The structure of Crystal Structure of Human JARID1B Construct C2 in Complex with N- Oxalylglycine. also contains other interesting chemical elements:

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

The binding sites of Manganese atom in the Crystal Structure of Human JARID1B Construct C2 in Complex with N- Oxalylglycine. (pdb code 5fv3). 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 Construct C2 in Complex with N- Oxalylglycine., PDB code: 5fv3:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the Crystal Structure of Human JARID1B Construct C2 in Complex with N- Oxalylglycine.


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 Construct C2 in Complex with N- Oxalylglycine. within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn1757 b:30.8 occ:1.00 OE2 A:GLU501 2.0 36.8 1.0 O A:HOH2054 2.1 33.5 1.0 NE2 A:HIS499 2.1 40.7 1.0 O2' A:OGA1770 2.1 39.5 1.0 NE2 A:HIS587 2.2 32.1 1.0 O1 A:OGA1770 2.3 36.4 1.0 C2 A:OGA1770 2.8 43.2 1.0 C1 A:OGA1770 2.8 50.8 1.0 CE1 A:HIS499 2.9 39.6 1.0 CE1 A:HIS587 3.1 43.6 1.0 CD A:GLU501 3.2 39.4 1.0 CD2 A:HIS499 3.2 36.6 1.0 CD2 A:HIS587 3.2 46.4 1.0 OE1 A:GLU501 3.6 47.8 1.0 O A:DMS1756 4.1 59.9 1.0 ND1 A:HIS499 4.1 44.8 1.0 N1 A:OGA1770 4.1 44.9 1.0 O2 A:OGA1770 4.1 38.6 1.0 ND1 A:HIS587 4.2 33.3 1.0 CG A:HIS499 4.3 39.8 1.0 CG A:HIS587 4.3 33.1 1.0 OG A:SER507 4.4 35.6 0.6 CG A:GLU501 4.4 36.3 1.0 OG A:SER507 4.5 41.4 0.4 CB A:SER507 4.8 35.6 0.4 CB A:SER507 4.8 35.2 0.6 C4 A:OGA1770 4.9 37.8 1.0 NH2 A:ARG98 4.9 79.4 1.0

Manganese binding site 2 out of 2 in the Crystal Structure of Human JARID1B Construct C2 in Complex with N- Oxalylglycine.


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 Construct C2 in Complex with N- Oxalylglycine. within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn1758 b:0.1 occ:1.00 O A:HOH2110 2.8 65.1 1.0 O A:HOH2073 3.5 48.6 1.0 NE2 A:HIS718 3.6 66.0 1.0 CE1 A:HIS622 3.7 68.7 1.0 NE2 A:HIS622 4.0 53.9 1.0 CD2 A:HIS718 4.4 56.8 1.0 CE A:LYS694 4.6 62.6 1.0 CE1 A:HIS718 4.6 55.9 1.0 O A:HOH2074 4.9 56.6 1.0 ND1 A:HIS622 4.9 69.2 1.0 CG A:LYS694 5.0 59.2 1.0

C.Johansson, S.Velupillai, A.Tumber, A.Szykowska, E.S.Hookway, R.P.Nowak, C.Strain-Damerell, C.Gileadi, M.Philpott, N.Burgess-Brown, N.Wu, J.Kopec, A.Nuzzi, H.Steuber, U.Egner, V.Badock, S.Munro, N.B.Lathangue, S.Westaway, J.Brown, N.Athanasou, R.Prinjha, P.E.Brennan, U.Oppermann. Structural Analysis of Human KDM5B Guides Histone Demethylase Inhibitor Development. Nat.Chem.Biol. V. 12 539 2016.
ISSN: ISSN 1552-4450
PubMed: 27214403
DOI: 10.1038/NCHEMBIO.2087