Sodium in PDB 6rbi: Crystal Structure of KDM5B in Complex with 5-(1H-Tetrazol-5-Yl) Quinolin-8-Ol

The structure of Crystal Structure of KDM5B in Complex with 5-(1H-Tetrazol-5-Yl) Quinolin-8-Ol, PDB code: 6rbi was solved by C.Johansson, J.A.Newman, A.Kawamura, C.J.Schofield, C.H.Arrowsmith, C.Bountra, A.Edwards, U.C.T.Oppermann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.73 / 2.21
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	142.150, 142.150, 151.540, 90.00, 90.00, 120.00
R / Rfree (%)	18.4 / 20.1

The structure of Crystal Structure of KDM5B in Complex with 5-(1H-Tetrazol-5-Yl) Quinolin-8-Ol 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 KDM5B in Complex with 5-(1H-Tetrazol-5-Yl) Quinolin-8-Ol (pdb code 6rbi). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of KDM5B in Complex with 5-(1H-Tetrazol-5-Yl) Quinolin-8-Ol, PDB code: 6rbi:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of KDM5B in Complex with 5-(1H-Tetrazol-5-Yl) Quinolin-8-Ol


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 KDM5B in Complex with 5-(1H-Tetrazol-5-Yl) Quinolin-8-Ol within 5.0Å range: probe atom residue distance (Å) B Occ A:Na810 b:62.5 occ:1.00 O A:HOH967 2.4 58.7 1.0 O A:THR416 2.4 73.1 1.0 OD1 A:ASN91 2.6 60.3 1.0 O A:LEU413 2.8 54.4 1.0 O A:GLU419 3.0 81.3 1.0 O A:HOH1012 3.2 70.2 1.0 O A:LEU90 3.5 52.2 1.0 C A:THR416 3.6 75.0 1.0 CG A:ASN91 3.8 61.0 1.0 C A:GLU419 3.9 76.7 1.0 C A:LEU413 4.0 49.6 1.0 O A:VAL414 4.0 58.3 1.0 CB A:GLU419 4.1 77.1 1.0 C A:VAL414 4.1 52.8 1.0 N A:THR416 4.2 69.0 1.0 CA A:VAL414 4.3 46.9 1.0 CA A:GLU419 4.4 77.6 1.0 CA A:THR416 4.4 76.3 1.0 N A:ILE417 4.4 78.8 1.0 CA A:ASN91 4.4 55.9 1.0 CA A:ILE417 4.5 83.3 1.0 C A:LEU90 4.5 53.4 1.0 N A:GLU419 4.6 80.2 1.0 CB A:ASN91 4.6 56.1 1.0 N A:VAL414 4.6 45.2 1.0 C A:ILE417 4.7 85.7 1.0 O A:ILE417 4.7 85.8 1.0 N A:SER415 4.8 51.9 1.0 N A:ASP420 4.8 69.3 1.0 ND2 A:ASN91 4.8 63.9 1.0 C A:SER415 4.9 64.1 1.0 CB A:THR416 4.9 78.7 1.0 N A:ASN91 5.0 48.8 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of KDM5B in Complex with 5-(1H-Tetrazol-5-Yl) Quinolin-8-Ol


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of KDM5B in Complex with 5-(1H-Tetrazol-5-Yl) Quinolin-8-Ol within 5.0Å range: probe atom residue distance (Å) B Occ A:Na811 b:60.1 occ:1.00 O A:HOH921 3.4 51.6 1.0 O A:HOH1024 3.6 72.8 1.0 O A:HOH977 3.6 43.9 1.0 CE1 A:TYR618 3.6 48.0 1.0 CD1 A:ILE500 3.8 50.0 1.0 NE1 A:TRP504 3.8 44.0 1.0 CD2 A:HIS617 3.8 61.5 1.0 NE2 A:HIS617 4.2 62.8 1.0 CD1 A:TYR618 4.2 49.9 1.0 NH2 A:ARG623 4.5 94.0 1.0 CD1 A:LEU621 4.6 73.2 1.0 CE2 A:TRP504 4.7 43.7 1.0 CD1 A:TRP504 4.7 42.7 1.0 CG1 A:ILE500 4.7 42.3 1.0 CZ A:TYR618 4.7 48.5 1.0 CD A:ARG623 4.7 86.1 1.0 OH A:TYR618 4.9 48.4 1.0 OE2 A:GLU531 4.9 59.2 1.0 CZ2 A:TRP504 4.9 44.6 1.0 CZ A:ARG623 5.0 97.0 1.0

C.Johansson, J.A.Newman, A.Kawamura, C.J.Schofield, C.H.Arrowsmith, C.Bountra, A.Edwards, U.C.T.Oppermann. Crystal Structure of KDM5B in Complex with 5-(1H-Tetrazol-5-Yl)Quinolin-8-Ol To Be Published.