Zinc in PDB 4hsu: Crystal Structure of LSD2-Npac with H3(1-26)in Space Group P21

The structure of Crystal Structure of LSD2-Npac with H3(1-26)in Space Group P21, PDB code: 4hsu was solved by F.Chen, Z.Dong, J.Fang, Y.Xu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.44 / 1.99
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	62.754, 89.481, 88.349, 90.00, 102.89, 90.00
R / Rfree (%)	19.9 / 23.2

The binding sites of Zinc atom in the Crystal Structure of LSD2-Npac with H3(1-26)in Space Group P21 (pdb code 4hsu). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Crystal Structure of LSD2-Npac with H3(1-26)in Space Group P21, PDB code: 4hsu:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Crystal Structure of LSD2-Npac with H3(1-26)in Space Group P21


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-Npac with H3(1-26)in Space Group P21 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn902 b:42.8 occ:1.00 NE2 A:HIS90 2.2 37.9 1.0 SG A:CYS58 2.4 47.3 1.0 ND1 A:HIS84 2.4 43.1 1.0 SG A:CYS53 2.5 48.0 1.0 CD2 A:HIS90 3.0 39.5 1.0 CB A:CYS58 3.1 57.3 1.0 CE1 A:HIS90 3.2 38.0 1.0 CB A:CYS53 3.3 58.2 1.0 CG A:HIS84 3.3 44.1 1.0 CE1 A:HIS84 3.4 45.2 1.0 CB A:HIS84 3.5 43.2 1.0 O A:SER86 4.1 41.1 1.0 CG A:HIS90 4.2 39.1 1.0 CB A:LYS55 4.3 58.2 1.0 ND1 A:HIS90 4.3 41.4 1.0 CB A:ALA60 4.4 52.3 1.0 NE2 A:HIS84 4.5 43.9 1.0 CD2 A:HIS84 4.5 41.5 1.0 CA A:HIS84 4.5 44.0 1.0 CA A:CYS58 4.6 61.0 1.0 CA A:CYS53 4.8 55.4 1.0 CA A:CYS87 4.9 42.1 1.0 C A:SER86 4.9 40.6 1.0

Zinc binding site 2 out of 3 in the Crystal Structure of LSD2-Npac with H3(1-26)in Space Group P21


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-Npac with H3(1-26)in Space Group P21 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn903 b:40.5 occ:1.00 SG A:CYS95 2.3 36.8 1.0 SG A:CYS65 2.5 37.1 1.0 SG A:CYS73 2.5 40.5 1.0 SG A:CYS92 2.5 37.4 1.0 CB A:CYS65 3.2 37.8 1.0 CB A:CYS73 3.2 42.6 1.0 CB A:CYS95 3.2 42.3 1.0 CA A:CYS73 3.6 42.4 1.0 CB A:CYS92 3.7 35.2 1.0 N A:SER68 4.0 42.6 1.0 N A:CYS92 4.0 39.1 1.0 N A:ALA74 4.0 43.4 1.0 N A:CYS95 4.1 37.6 1.0 CA A:SER68 4.3 42.8 1.0 C A:CYS73 4.3 39.9 1.0 CA A:CYS95 4.3 43.4 1.0 CA A:CYS92 4.4 40.1 1.0 O A:CYS92 4.7 36.7 1.0 CA A:CYS65 4.7 41.5 1.0 CB A:ALA67 4.8 36.8 1.0 N A:LYS75 4.8 46.4 1.0 N A:ALA69 4.8 40.9 1.0 N A:CYS73 4.9 39.4 1.0 C A:CYS92 4.9 39.6 1.0

Zinc binding site 3 out of 3 in the Crystal Structure of LSD2-Npac with H3(1-26)in Space Group P21


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-Npac with H3(1-26)in Space Group P21 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn904 b:39.2 occ:1.00 SG A:CYS147 2.3 37.4 1.0 SG A:CYS142 2.3 35.5 1.0 SG A:CYS185 2.4 38.6 1.0 SG A:CYS169 2.5 35.0 1.0 CB A:CYS142 3.1 31.1 1.0 CB A:CYS147 3.1 39.2 1.0 CB A:CYS185 3.2 43.7 1.0 CB A:CYS169 3.3 37.2 1.0 CA A:CYS185 3.6 43.6 1.0 N A:CYS169 3.8 32.7 1.0 CA A:CYS169 4.2 33.1 1.0 N A:CYS185 4.5 46.5 1.0 CB A:LYS144 4.5 42.3 1.0 O A:HOH1171 4.6 39.3 1.0 CA A:CYS147 4.6 42.0 1.0 CA A:CYS142 4.6 33.0 1.0 C A:CYS185 4.7 46.9 1.0 O A:CYS185 4.7 48.7 1.0 N A:ARG148 4.8 37.5 1.0 N A:LYS149 4.8 35.0 1.0 CB A:LYS149 4.9 33.8 1.0 CD A:LYS144 4.9 42.7 1.0 C A:ARG168 4.9 32.4 1.0 NH1 A:ARG151 5.0 38.5 1.0

F.Chen, H.Yang, Z.Dong, J.Fang, P.Wang, T.Zhu, W.Gong, R.Fang, Y.G.Shi, Z.Li, Y.Xu. Structural Insight Into Substrate Recognition By Histone Demethylase LSD2/KDM1B. Cell Res. V. 23 306 2013.
ISSN: ISSN 1001-0602
PubMed: 23357850
DOI: 10.1038/CR.2013.17