Zinc in PDB 4gus: Crystal Structure of LSD2-Npac with H3 in Space Group P3221

The structure of Crystal Structure of LSD2-Npac with H3 in Space Group P3221, PDB code: 4gus 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)	29.04 / 2.23
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	101.083, 101.083, 177.372, 90.00, 90.00, 120.00
R / Rfree (%)	20.7 / 23.7

The structure of Crystal Structure of LSD2-Npac with H3 in Space Group P3221 also contains other interesting chemical elements:

Iodine

(I)

6 atoms

The binding sites of Zinc atom in the Crystal Structure of LSD2-Npac with H3 in Space Group P3221 (pdb code 4gus). 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 in Space Group P3221, PDB code: 4gus:
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 in Space Group P3221


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 in Space Group P3221 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn910 b:42.6 occ:1.00 NE2 A:HIS90 2.1 40.9 1.0 ND1 A:HIS84 2.1 44.9 1.0 SG A:CYS53 2.2 48.1 1.0 SG A:CYS58 2.3 44.8 1.0 CD2 A:HIS90 2.8 42.0 1.0 CE1 A:HIS84 3.0 45.1 1.0 CB A:CYS53 3.1 50.1 1.0 CB A:CYS58 3.2 47.7 1.0 CG A:HIS84 3.2 45.0 1.0 CE1 A:HIS90 3.3 42.3 1.0 CB A:HIS84 3.6 45.8 1.0 O A:SER86 3.9 41.5 1.0 CG A:HIS90 4.1 41.3 1.0 NE2 A:HIS84 4.2 46.0 1.0 ND1 A:HIS90 4.3 39.3 1.0 CD2 A:HIS84 4.3 46.6 1.0 CA A:HIS84 4.4 45.6 1.0 CB A:LYS55 4.4 52.6 1.0 CA A:CYS53 4.5 52.4 1.0 CA A:CYS58 4.6 48.2 1.0 CB A:ALA60 4.7 49.0 1.0 CA A:CYS87 4.8 43.6 1.0 C A:SER86 4.8 43.5 1.0 CG A:LYS55 4.9 54.0 1.0

Zinc binding site 2 out of 3 in the Crystal Structure of LSD2-Npac with H3 in Space Group P3221


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 in Space Group P3221 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn911 b:47.1 occ:1.00 SG A:CYS92 2.1 48.7 1.0 SG A:CYS95 2.3 53.1 1.0 SG A:CYS73 2.4 52.0 1.0 SG A:CYS65 2.4 49.3 1.0 CB A:CYS73 3.2 53.2 1.0 CB A:CYS65 3.2 48.0 1.0 CB A:CYS95 3.4 53.3 1.0 CB A:CYS92 3.5 50.5 1.0 CA A:CYS73 3.5 55.0 1.0 N A:ALA74 3.9 53.7 1.0 N A:CYS92 4.0 49.4 1.0 N A:SER68 4.0 52.1 1.0 C A:CYS73 4.1 54.3 1.0 N A:CYS95 4.2 56.8 1.0 CA A:CYS92 4.3 51.7 1.0 CA A:SER68 4.3 51.9 1.0 CA A:CYS95 4.4 55.3 1.0 CB A:ALA67 4.6 50.1 1.0 O A:CYS92 4.6 51.6 1.0 N A:LYS75 4.7 52.2 1.0 CA A:CYS65 4.7 49.1 1.0 N A:ALA69 4.8 52.1 1.0 C A:CYS92 4.8 53.1 1.0 N A:CYS73 4.8 57.8 1.0

Zinc binding site 3 out of 3 in the Crystal Structure of LSD2-Npac with H3 in Space Group P3221


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 in Space Group P3221 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn912 b:57.2 occ:1.00 SG A:CYS169 2.2 55.5 1.0 SG A:CYS147 2.4 56.0 1.0 SG A:CYS142 2.4 53.2 1.0 SG A:CYS185 2.5 60.1 1.0 CB A:CYS169 3.1 60.4 1.0 CB A:CYS142 3.1 54.1 1.0 CB A:CYS185 3.2 63.2 1.0 CB A:CYS147 3.3 58.6 1.0 CA A:CYS185 3.6 64.0 1.0 N A:CYS169 3.8 60.1 1.0 CA A:CYS169 4.0 60.8 1.0 N A:CYS185 4.5 65.3 1.0 CA A:CYS142 4.6 52.4 1.0 O A:CYS185 4.6 62.0 1.0 C A:CYS185 4.6 63.7 1.0 CA A:CYS147 4.7 59.3 1.0 CB A:LYS144 4.7 63.7 1.0 N A:ARG148 4.8 56.4 1.0 N A:LYS149 4.9 50.1 1.0 C A:ARG168 5.0 61.5 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