Sodium in PDB 4gu1: Crystal Structure of LSD2

The structure of Crystal Structure of LSD2, PDB code: 4gu1 was solved by F.Chen, Z.Dong, J.Fang, Y.Yang, Z.Li, Y.Xu, H.Yang, P.Wang, R.Fang, Y.Shi, Y.Xu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.56 / 2.94
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	89.163, 89.216, 342.538, 90.00, 90.00, 90.00
R / Rfree (%)	18.5 / 22.8

The structure of Crystal Structure of LSD2 also contains other interesting chemical elements:

Zinc	(Zn)	6 atoms
Chlorine	(Cl)	4 atoms

The binding sites of Sodium atom in the Crystal Structure of LSD2 (pdb code 4gu1). 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 LSD2, PDB code: 4gu1:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of LSD2


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 LSD2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na904 b:88.8 occ:1.00 O A:TYR603 3.0 93.1 1.0 O A:GLY605 3.1 0.2 1.0 OE1 A:GLN787 4.0 88.5 1.0 C A:TYR603 4.1 93.7 1.0 O A:ASP606 4.2 0.4 1.0 OG1 A:THR789 4.2 84.3 1.0 O A:SER604 4.3 91.5 1.0 C A:GLY605 4.3 0.2 1.0 CG2 A:THR789 4.6 79.2 1.0 C A:SER604 4.6 96.8 1.0 C A:ASP606 4.8 1.0 1.0 CB A:TYR603 4.8 86.2 1.0 CB A:THR789 4.8 80.8 1.0 CA A:TYR603 4.9 88.9 1.0 N A:SER604 5.0 98.8 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of LSD2


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 LSD2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na904 b:86.2 occ:1.00 O B:GLY605 3.2 0.1 1.0 O B:TYR603 3.2 92.0 1.0 OE1 B:GLN787 3.8 91.0 1.0 O B:ASP606 3.9 0.6 1.0 OG1 B:THR789 4.3 85.8 1.0 C B:GLY605 4.4 0.5 1.0 C B:TYR603 4.4 92.1 1.0 O B:SER604 4.5 96.1 1.0 C B:ASP606 4.7 0.4 1.0 CG2 B:THR789 4.8 85.9 1.0 C B:SER604 4.9 0.9 1.0 CA B:ASP606 4.9 0.4 1.0 CD B:GLN787 4.9 88.1 1.0

R.Fang, F.Chen, Z.Dong, D.Hu, A.J.Barbera, E.A.Clark, J.Fang, Y.Yang, P.Mei, M.Rutenberg, Z.Li, Y.Zhang, Y.Xu, H.Yang, P.Wang, M.D.Simon, Q.Zhou, J.Li, M.P.Marynick, X.Li, H.Lu, U.B.Kaiser, R.E.Kingston, Y.Xu, Y.G.Shi. LSD2/KDM1B and Its Cofactor Npac/GLYR1 Endow A Structural and Molecular Model For Regulation of H3K4 Demethylation Mol.Cell V. 49 558 2013.
ISSN: ISSN 1097-2765
PubMed: 23260659
DOI: 10.1016/J.MOLCEL.2012.11.019