Sodium in PDB 6g5w: Crystal Structure of KDM4A with Compound Yp-03-038

The structure of Crystal Structure of KDM4A with Compound Yp-03-038, PDB code: 6g5w was solved by P.H.Malecki, D.M.Carter, U.Gohlke, E.Specker, M.Nazare, M.S.Weiss, U.Heinemann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.57 / 1.83
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	99.362, 148.574, 56.390, 90.00, 90.00, 90.00
R / Rfree (%)	17.6 / 21.8

The structure of Crystal Structure of KDM4A with Compound Yp-03-038 also contains other interesting chemical elements:

Nickel	(Ni)	4 atoms
Zinc	(Zn)	2 atoms

The binding sites of Sodium atom in the Crystal Structure of KDM4A with Compound Yp-03-038 (pdb code 6g5w). 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 KDM4A with Compound Yp-03-038, PDB code: 6g5w:

Sodium binding site 1 out of 1 in the Crystal Structure of KDM4A with Compound Yp-03-038


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 KDM4A with Compound Yp-03-038 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na404 b:63.0 occ:1.00 OD1 B:ASN26 2.4 47.9 1.0 O B:HOH651 2.7 33.8 0.5 OG B:SER28 2.8 52.4 1.0 CG B:ASN26 3.3 66.5 1.0 ND2 B:ASN26 3.5 87.5 1.0 CB B:SER28 3.7 38.4 1.0 O B:HOH651 3.9 35.4 0.5 N B:SER28 4.2 34.9 1.0 O B:HOH668 4.3 38.9 0.5 CA B:SER28 4.5 40.1 1.0 N B:ARG29 4.6 40.3 1.0 CB B:ASN26 4.6 50.1 1.0 O B:HOH522 4.7 56.3 1.0 N B:PHE27 4.8 41.5 1.0 CA B:ASN26 4.9 38.5 1.0 C B:ASN26 5.0 41.9 1.0 C B:SER28 5.0 39.5 1.0

P.H.Malecki, D.M.Carter, U.Gohlke, E.Specker, M.Nazare, M.S.Weiss, U.Heinemann. Crystal Structure of KDM4A with Compound Yp-03-038 To Be Published.