Zinc 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:

Chlorine	(Cl)	4 atoms
Sodium	(Na)	2 atoms

The binding sites of Zinc atom in the Crystal Structure of LSD2 (pdb code 4gu1). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Crystal Structure of LSD2, PDB code: 4gu1:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in the Crystal Structure of LSD2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of LSD2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn905 b:72.8 occ:1.00 ND1 A:HIS84 2.2 80.5 1.0 SG A:CYS58 2.2 78.2 1.0 NE2 A:HIS90 2.2 73.7 1.0 SG A:CYS53 2.4 86.8 1.0 CD2 A:HIS90 2.9 72.1 1.0 CB A:CYS58 2.9 78.1 1.0 CE1 A:HIS84 3.0 81.3 1.0 CB A:CYS53 3.2 92.8 1.0 CG A:HIS84 3.2 80.4 1.0 CE1 A:HIS90 3.3 76.0 1.0 CB A:HIS84 3.6 84.1 1.0 NE2 A:HIS84 4.1 82.0 1.0 CG A:HIS90 4.2 74.4 1.0 CD2 A:HIS84 4.3 80.4 1.0 CA A:CYS58 4.3 82.2 1.0 CA A:HIS84 4.3 85.0 1.0 ND1 A:HIS90 4.3 72.7 1.0 O A:SER86 4.4 85.1 1.0 CA A:CYS53 4.7 88.1 1.0 CB A:LYS55 4.7 93.2 1.0 CG A:LYS55 5.0 89.8 1.0

Zinc binding site 2 out of 6 in the Crystal Structure of LSD2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of LSD2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn906 b:96.4 occ:1.00 SG A:CYS92 2.3 92.0 1.0 SG A:CYS95 2.3 99.9 1.0 SG A:CYS73 2.6 99.3 1.0 SG A:CYS65 2.6 90.8 1.0 CB A:CYS92 3.4 97.4 1.0 O A:ALA67 3.5 0.1 1.0 CB A:CYS73 3.5 0.9 1.0 CB A:CYS95 3.6 97.1 1.0 CB A:CYS65 3.6 87.0 1.0 CA A:CYS73 3.7 0.2 1.0 N A:CYS92 3.8 94.4 1.0 N A:ALA74 4.0 0.4 1.0 CA A:CYS92 4.2 96.9 1.0 C A:CYS73 4.3 0.5 1.0 N A:CYS95 4.4 0.2 1.0 C A:ALA67 4.5 0.3 1.0 CA A:CYS95 4.6 0.9 1.0 C A:CYS92 4.7 98.3 1.0 O A:CYS92 4.7 98.3 1.0 N A:CYS73 4.9 0.0 1.0 C A:PHE91 5.0 91.3 1.0

Zinc binding site 3 out of 6 in the Crystal Structure of LSD2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of LSD2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn907 b:0.5 occ:1.00 SG A:CYS147 2.3 96.9 1.0 SG A:CYS142 2.4 0.1 1.0 SG A:CYS185 2.4 0.5 1.0 SG A:CYS169 2.4 89.8 1.0 CB A:CYS147 3.0 1.0 1.0 CB A:CYS142 3.2 98.0 1.0 CB A:CYS169 3.5 0.6 1.0 CB A:CYS185 3.7 0.2 1.0 CA A:CYS185 3.9 0.7 1.0 N A:CYS169 4.1 0.1 1.0 NH1 A:ARG151 4.3 1.0 1.0 CA A:CYS169 4.4 0.1 1.0 CA A:CYS147 4.5 0.6 1.0 CA A:CYS142 4.6 95.5 1.0 CG A:LYS144 4.6 0.8 1.0 N A:CYS185 4.8 0.3 1.0 CE A:LYS144 4.8 0.6 1.0 C A:CYS185 5.0 0.2 1.0

Zinc binding site 4 out of 6 in the Crystal Structure of LSD2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of LSD2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn905 b:73.6 occ:1.00 NE2 B:HIS90 2.1 73.7 1.0 ND1 B:HIS84 2.1 83.4 1.0 SG B:CYS58 2.3 73.1 1.0 SG B:CYS53 2.3 85.0 1.0 CB B:CYS58 3.0 79.9 1.0 CE1 B:HIS84 3.0 83.4 1.0 CD2 B:HIS90 3.0 73.5 1.0 CB B:CYS53 3.2 90.5 1.0 CE1 B:HIS90 3.2 75.3 1.0 CG B:HIS84 3.2 83.9 1.0 CB B:HIS84 3.6 84.9 1.0 NE2 B:HIS84 4.1 85.9 1.0 CG B:HIS90 4.2 77.6 1.0 ND1 B:HIS90 4.2 73.8 1.0 CD2 B:HIS84 4.2 83.2 1.0 CA B:HIS84 4.3 86.7 1.0 CA B:CYS58 4.3 85.6 1.0 O B:SER86 4.5 83.1 1.0 CB B:LYS55 4.5 92.6 1.0 CA B:CYS53 4.6 87.2 1.0 CG B:LYS55 4.9 88.2 1.0

Zinc binding site 5 out of 6 in the Crystal Structure of LSD2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of LSD2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn906 b:98.1 occ:1.00 SG B:CYS92 2.2 90.1 1.0 SG B:CYS95 2.3 97.0 1.0 SG B:CYS65 2.4 0.9 1.0 SG B:CYS73 2.5 0.5 1.0 CB B:CYS65 3.4 90.1 1.0 CB B:CYS92 3.4 98.1 1.0 CB B:CYS73 3.5 1.0 1.0 CB B:CYS95 3.5 0.1 1.0 O B:ALA67 3.6 0.1 1.0 CA B:CYS73 3.7 0.9 1.0 N B:ALA74 3.9 0.7 1.0 N B:CYS92 3.9 97.4 1.0 CA B:CYS92 4.2 99.9 1.0 C B:CYS73 4.3 0.9 1.0 N B:CYS95 4.3 0.7 1.0 CA B:CYS95 4.5 0.9 1.0 O B:CYS92 4.5 0.1 1.0 C B:ALA67 4.6 0.6 1.0 C B:CYS92 4.7 99.0 1.0 CA B:CYS65 4.9 85.1 1.0 CA B:ALA74 5.0 0.4 1.0

Zinc binding site 6 out of 6 in the Crystal Structure of LSD2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of LSD2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn907 b:0.9 occ:1.00 SG B:CYS142 2.4 0.5 1.0 SG B:CYS169 2.4 96.7 1.0 SG B:CYS147 2.5 96.6 1.0 SG B:CYS185 2.6 0.9 1.0 CB B:CYS169 3.0 0.6 1.0 CB B:CYS142 3.1 99.7 1.0 CB B:CYS147 3.4 0.8 1.0 CB B:CYS185 3.7 0.4 1.0 CA B:CYS185 3.7 0.1 1.0 N B:CYS169 3.8 0.0 1.0 CA B:CYS169 4.0 0.8 1.0 C B:CYS185 4.5 0.3 1.0 CA B:CYS142 4.5 94.5 1.0 O B:CYS185 4.5 0.5 1.0 NH1 B:ARG151 4.6 0.2 1.0 N B:CYS185 4.8 0.6 1.0 CA B:CYS147 4.8 0.8 1.0 CG B:LYS144 4.9 1.0 1.0 C B:ARG168 5.0 0.2 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