Zinc in PDB 4gut: Crystal Structure of LSD2-Npac

The structure of Crystal Structure of LSD2-Npac, PDB code: 4gut 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)	35.92 / 2.00
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	62.000, 89.762, 86.694, 90.00, 104.96, 90.00
R / Rfree (%)	19.6 / 20.7

The binding sites of Zinc atom in the Crystal Structure of LSD2-Npac (pdb code 4gut). 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, PDB code: 4gut:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Crystal Structure of LSD2-Npac


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn904 b:47.4 occ:1.00 NE2 A:HIS90 2.1 45.8 1.0 SG A:CYS58 2.1 59.1 1.0 ND1 A:HIS84 2.2 51.9 1.0 SG A:CYS53 2.4 62.3 1.0 CB A:CYS58 3.0 66.9 1.0 CD2 A:HIS90 3.1 45.2 1.0 CE1 A:HIS84 3.1 50.8 1.0 CE1 A:HIS90 3.2 44.7 1.0 CB A:CYS53 3.2 56.0 1.0 CG A:HIS84 3.3 46.2 1.0 CB A:HIS84 3.7 46.5 1.0 O A:SER86 4.0 47.7 1.0 CG A:HIS90 4.3 44.6 1.0 ND1 A:HIS90 4.3 45.0 1.0 NE2 A:HIS84 4.3 50.1 1.0 CD2 A:HIS84 4.4 46.2 1.0 CB A:LYS55 4.4 58.0 1.0 CA A:CYS58 4.4 67.8 1.0 CB A:ALA60 4.5 61.5 1.0 CA A:HIS84 4.5 47.5 1.0 CA A:CYS87 4.6 51.8 1.0 CA A:CYS53 4.7 59.0 1.0 C A:SER86 4.8 45.6 1.0 O A:CYS87 5.0 52.5 1.0

Zinc binding site 2 out of 3 in the Crystal Structure of LSD2-Npac


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn905 b:37.8 occ:1.00 SG A:CYS95 2.0 30.5 1.0 SG A:CYS65 2.3 40.5 1.0 SG A:CYS92 2.4 39.8 1.0 SG A:CYS73 2.4 36.8 1.0 CB A:CYS95 3.2 42.1 1.0 CB A:CYS73 3.2 37.1 1.0 CB A:CYS65 3.2 38.8 1.0 CB A:CYS92 3.6 44.4 1.0 CA A:CYS73 3.6 42.8 1.0 N A:CYS92 3.9 45.8 1.0 N A:SER68 4.0 38.6 1.0 N A:ALA74 4.1 45.1 1.0 CA A:SER68 4.2 34.7 1.0 CA A:CYS92 4.3 47.1 1.0 N A:CYS95 4.3 40.9 1.0 C A:CYS73 4.3 43.7 1.0 CA A:CYS95 4.3 46.8 1.0 O A:CYS92 4.6 38.8 1.0 CA A:CYS65 4.6 40.9 1.0 N A:LYS75 4.7 46.6 1.0 C A:CYS92 4.8 44.3 1.0 CB A:ALA67 4.8 37.2 1.0 N A:CYS73 4.9 40.5 1.0 N A:ALA69 5.0 33.0 1.0

Zinc binding site 3 out of 3 in the Crystal Structure of LSD2-Npac


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn906 b:44.4 occ:1.00 SG A:CYS147 2.1 40.8 1.0 SG A:CYS185 2.3 49.3 1.0 SG A:CYS142 2.4 37.3 1.0 SG A:CYS169 2.4 43.5 1.0 CB A:CYS147 3.0 45.3 1.0 CB A:CYS142 3.1 35.4 1.0 CB A:CYS185 3.2 48.0 1.0 CB A:CYS169 3.4 36.2 1.0 CA A:CYS185 3.6 50.1 1.0 N A:CYS169 3.9 34.9 1.0 CA A:CYS169 4.3 40.3 1.0 CA A:CYS147 4.4 47.7 1.0 N A:CYS185 4.6 49.0 1.0 CA A:CYS142 4.6 34.6 1.0 O A:HOH1240 4.6 48.1 1.0 CB A:LYS144 4.6 49.7 1.0 O A:CYS185 4.7 50.1 1.0 C A:CYS185 4.7 52.3 1.0 N A:ARG148 4.7 43.4 1.0 C A:CYS147 4.9 45.7 1.0 N A:LYS149 4.9 41.8 1.0 C A:ARG168 4.9 35.1 1.0 CB A:ARG168 5.0 41.0 1.0 CD A:LYS144 5.0 53.9 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