Chlorine 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
Sodium	(Na)	2 atoms

The binding sites of Chlorine atom in the Crystal Structure of LSD2 (pdb code 4gu1). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Crystal Structure of LSD2, PDB code: 4gu1:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in the Crystal Structure of LSD2


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of LSD2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl902 b:0.3 occ:1.00 OE1 A:GLU54 3.0 0.8 1.0 NZ A:LYS128 3.2 87.1 1.0 N A:HIS84 3.4 86.8 1.0 CD A:GLU54 3.7 0.4 1.0 CG A:GLU54 3.7 0.3 1.0 O A:TRP82 3.7 99.5 1.0 CA A:TYR83 3.8 89.8 1.0 CD1 A:TYR83 4.0 96.5 1.0 CB A:HIS84 4.1 84.1 1.0 C A:TYR83 4.1 90.1 1.0 CE A:LYS128 4.2 85.1 1.0 NH2 A:ARG81 4.2 0.0 1.0 CA A:HIS84 4.3 85.0 1.0 NE A:ARG81 4.5 0.2 1.0 CB A:TYR83 4.5 88.9 1.0 C A:TRP82 4.6 94.1 1.0 CG A:TYR83 4.6 91.8 1.0 CE1 A:TYR83 4.7 0.6 1.0 N A:TYR83 4.7 90.8 1.0 OE2 A:GLU54 4.8 0.9 1.0 O A:HIS84 4.8 83.2 1.0 CZ A:ARG81 4.9 0.5 1.0 CB A:LYS55 4.9 93.2 1.0 N A:LYS55 4.9 0.7 1.0

Chlorine binding site 2 out of 4 in the Crystal Structure of LSD2


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of LSD2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl903 b:0.5 occ:1.00 NZ A:LYS330 2.8 89.7 1.0 NZ A:LYS165 3.2 87.3 1.0 NE2 A:HIS334 3.9 89.5 1.0 CE A:LYS330 4.2 80.2 1.0 CE A:LYS165 4.3 96.3 1.0 CE1 A:HIS334 4.5 92.5 1.0

Chlorine binding site 3 out of 4 in the Crystal Structure of LSD2


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of LSD2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl902 b:0.2 occ:1.00 OE1 B:GLU54 2.8 0.8 1.0 NZ B:LYS128 3.1 85.8 1.0 N B:HIS84 3.3 90.6 1.0 CG B:GLU54 3.5 0.5 1.0 CD B:GLU54 3.6 0.4 1.0 O B:TRP82 3.8 98.2 1.0 CA B:TYR83 3.9 95.0 1.0 CB B:HIS84 4.0 84.9 1.0 C B:TYR83 4.1 93.7 1.0 CE B:LYS128 4.1 79.9 1.0 CD1 B:TYR83 4.1 98.5 1.0 CA B:HIS84 4.2 86.7 1.0 NH2 B:ARG81 4.5 0.1 1.0 CB B:TYR83 4.6 92.0 1.0 O B:HIS84 4.6 84.2 1.0 C B:TRP82 4.7 94.4 1.0 CG B:TYR83 4.7 94.2 1.0 OE2 B:GLU54 4.7 0.4 1.0 N B:TYR83 4.8 94.5 1.0 N B:LYS55 4.9 0.4 1.0 CE1 B:TYR83 4.9 0.9 1.0 C B:HIS84 4.9 88.4 1.0 CB B:LYS55 4.9 92.6 1.0 NE B:ARG81 5.0 0.4 1.0

Chlorine binding site 4 out of 4 in the Crystal Structure of LSD2


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Crystal Structure of LSD2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl903 b:98.0 occ:1.00 NZ B:LYS330 2.8 0.5 1.0 NZ B:LYS165 3.1 89.4 1.0 CE B:LYS330 3.8 89.9 1.0 NE2 B:HIS334 3.9 91.6 1.0 CE B:LYS165 4.3 96.5 1.0 CE1 B:HIS334 4.4 93.4 1.0 CD B:LYS330 4.7 85.2 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