Sodium in PDB 5fyz: Crystal Structure of the Catalytic Domain of Human JARID1B in Complex with 3D Fragment 2-(2-Oxo-2,3-Dihydro-1H-Indol-3-Yl)Acetonitrile (N10063A)

The structure of Crystal Structure of the Catalytic Domain of Human JARID1B in Complex with 3D Fragment 2-(2-Oxo-2,3-Dihydro-1H-Indol-3-Yl)Acetonitrile (N10063A), PDB code: 5fyz was solved by R.Nowak, T.Krojer, C.Johansson, C.Gileadi, K.Kupinska, C.Strain-Damerell, A.Szykowska, N.A.Burgess-Brown, C.H.Arrowsmith, C.Bountra, A.M.Edwards, F.Von Delft, P.E.Brennan, U.Oppermann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	95.58 / 1.75
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	141.880, 141.880, 152.080, 90.00, 90.00, 120.00
R / Rfree (%)	20.2 / 23.1

The structure of Crystal Structure of the Catalytic Domain of Human JARID1B in Complex with 3D Fragment 2-(2-Oxo-2,3-Dihydro-1H-Indol-3-Yl)Acetonitrile (N10063A) also contains other interesting chemical elements:

Manganese	(Mn)	1 atom
Zinc	(Zn)	2 atoms

The binding sites of Sodium atom in the Crystal Structure of the Catalytic Domain of Human JARID1B in Complex with 3D Fragment 2-(2-Oxo-2,3-Dihydro-1H-Indol-3-Yl)Acetonitrile (N10063A) (pdb code 5fyz). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Crystal Structure of the Catalytic Domain of Human JARID1B in Complex with 3D Fragment 2-(2-Oxo-2,3-Dihydro-1H-Indol-3-Yl)Acetonitrile (N10063A), PDB code: 5fyz:

Sodium binding site 1 out of 1 in the Crystal Structure of the Catalytic Domain of Human JARID1B in Complex with 3D Fragment 2-(2-Oxo-2,3-Dihydro-1H-Indol-3-Yl)Acetonitrile (N10063A)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of the Catalytic Domain of Human JARID1B in Complex with 3D Fragment 2-(2-Oxo-2,3-Dihydro-1H-Indol-3-Yl)Acetonitrile (N10063A) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1773 b:49.1 occ:1.00 O A:HOH2062 2.1 35.5 1.0 O A:THR416 2.4 53.0 1.0 OD1 A:ASN91 2.6 37.9 1.0 O A:LEU413 2.7 36.8 1.0 O A:HOH2064 2.8 54.5 1.0 O A:GLU419 3.1 56.6 1.0 C A:THR416 3.4 53.3 1.0 O A:LEU90 3.6 29.9 1.0 O A:VAL414 3.7 32.7 1.0 CG A:ASN91 3.8 36.0 1.0 C A:VAL414 3.9 33.0 1.0 C A:LEU413 3.9 33.7 1.0 N A:THR416 4.0 45.2 1.0 CA A:VAL414 4.1 29.7 1.0 C A:GLU419 4.1 53.6 1.0 CA A:THR416 4.2 52.6 1.0 N A:ILE417 4.2 57.6 1.0 CB A:GLU419 4.3 47.0 1.0 CA A:ILE417 4.3 61.9 1.0 CA A:ASN91 4.4 34.0 1.0 O A:ILE417 4.4 58.8 1.0 C A:ILE417 4.5 59.0 1.0 CB A:ASN91 4.5 35.2 1.0 N A:SER415 4.5 37.3 1.0 N A:VAL414 4.5 29.4 1.0 C A:SER415 4.6 48.5 1.0 CA A:GLU419 4.6 50.3 1.0 C A:LEU90 4.6 35.3 1.0 O A:HOH2061 4.6 43.0 1.0 N A:GLU419 4.7 52.3 1.0 CB A:THR416 4.8 51.2 1.0 ND2 A:ASN91 4.9 41.2 1.0 O A:HOH2065 5.0 52.4 1.0 N A:ASN91 5.0 33.9 1.0

R.Nowak, T.Krojer, 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 N10063A To Be Published.