Zinc in PDB 4guu: Crystal Structure of LSD2-Npac with Tranylcypromine

The structure of Crystal Structure of LSD2-Npac with Tranylcypromine, PDB code: 4guu was solved by F.Chen, Z.Dong, J.Fang, Y.Yang, Z.Li, Y.Xu, H.Yang, P.Wang, Y.Xu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	36.23 / 2.30
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	62.820, 90.157, 87.824, 90.00, 104.20, 90.00
R / Rfree (%)	19.9 / 23.1

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

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


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 Tranylcypromine within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn902 b:42.0 occ:1.00 ND1 A:HIS84 2.1 40.2 1.0 NE2 A:HIS90 2.2 33.6 1.0 SG A:CYS58 2.3 47.8 1.0 SG A:CYS53 2.4 49.5 1.0 CB A:CYS58 3.0 50.1 1.0 CD2 A:HIS90 3.1 31.5 1.0 CG A:HIS84 3.1 38.6 1.0 CE1 A:HIS84 3.2 40.5 1.0 CE1 A:HIS90 3.2 38.9 1.0 CB A:CYS53 3.2 43.3 1.0 CB A:HIS84 3.3 37.5 1.0 O A:SER86 3.9 39.9 1.0 CB A:LYS55 4.1 50.8 1.0 CD2 A:HIS84 4.2 35.6 1.0 NE2 A:HIS84 4.3 38.4 1.0 CG A:HIS90 4.3 32.8 1.0 ND1 A:HIS90 4.3 33.8 1.0 CA A:HIS84 4.4 35.1 1.0 CA A:CYS58 4.4 53.9 1.0 CB A:ALA60 4.6 51.6 1.0 CA A:CYS53 4.6 55.9 1.0 CA A:CYS87 4.7 43.9 1.0 CG A:LYS55 4.7 53.7 1.0 C A:SER86 4.7 35.6 1.0

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


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 Tranylcypromine within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn903 b:38.4 occ:1.00 SG A:CYS95 2.2 30.6 1.0 SG A:CYS65 2.4 38.4 1.0 SG A:CYS92 2.5 36.9 1.0 SG A:CYS73 2.6 36.9 1.0 CB A:CYS95 3.2 43.9 1.0 CB A:CYS65 3.3 35.5 1.0 CB A:CYS73 3.4 38.5 1.0 CB A:CYS92 3.7 37.0 1.0 CA A:CYS73 3.8 31.0 1.0 N A:SER68 3.9 32.9 1.0 N A:CYS92 3.9 42.4 1.0 N A:ALA74 4.1 37.1 1.0 CA A:SER68 4.2 35.9 1.0 N A:CYS95 4.2 40.0 1.0 CA A:CYS95 4.3 47.8 1.0 CA A:CYS92 4.4 44.9 1.0 C A:CYS73 4.4 38.3 1.0 O A:CYS92 4.6 35.5 1.0 CB A:ALA67 4.6 36.1 1.0 N A:LYS75 4.7 41.0 1.0 N A:ALA69 4.7 42.2 1.0 CA A:CYS65 4.8 40.5 1.0 C A:CYS92 4.8 40.0 1.0 C A:ALA67 4.9 40.8 1.0

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


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 Tranylcypromine within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn904 b:40.8 occ:1.00 SG A:CYS147 2.4 35.6 1.0 SG A:CYS142 2.5 37.4 1.0 SG A:CYS169 2.5 40.8 1.0 SG A:CYS185 2.5 41.9 1.0 CB A:CYS147 3.1 42.3 1.0 CB A:CYS142 3.2 36.5 1.0 CB A:CYS185 3.3 50.3 1.0 CB A:CYS169 3.4 34.1 1.0 CA A:CYS185 3.7 43.3 1.0 N A:CYS169 3.8 38.5 1.0 CA A:CYS169 4.2 38.4 1.0 CA A:CYS147 4.6 42.4 1.0 O A:HOH1127 4.6 34.7 1.0 CB A:LYS144 4.6 39.0 1.0 O A:CYS185 4.6 49.7 1.0 CA A:CYS142 4.7 33.5 1.0 N A:CYS185 4.7 47.1 1.0 C A:CYS185 4.7 49.6 1.0 N A:ARG148 4.8 39.2 1.0 C A:ARG168 4.9 40.1 1.0 N A:LYS149 4.9 37.7 1.0 C A:CYS147 5.0 41.9 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