Zinc in PDB 4fwe: Native Structure of LSD2 /AOF1/KDM1B in Spacegroup of C2221 at 2.13A

The structure of Native Structure of LSD2 /AOF1/KDM1B in Spacegroup of C2221 at 2.13A, PDB code: 4fwe was solved by Q.Zhang, Z.Chen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.13
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	93.691, 96.273, 182.797, 90.00, 90.00, 90.00
R / Rfree (%)	20.3 / 24.6

The binding sites of Zinc atom in the Native Structure of LSD2 /AOF1/KDM1B in Spacegroup of C2221 at 2.13A (pdb code 4fwe). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Native Structure of LSD2 /AOF1/KDM1B in Spacegroup of C2221 at 2.13A, PDB code: 4fwe:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Native Structure of LSD2 /AOF1/KDM1B in Spacegroup of C2221 at 2.13A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Native Structure of LSD2 /AOF1/KDM1B in Spacegroup of C2221 at 2.13A within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn901 b:55.3 occ:1.00 NE2 A:HIS90 2.0 43.8 1.0 ND1 A:HIS84 2.1 52.7 1.0 SG A:CYS58 2.2 58.0 1.0 SG A:CYS53 2.3 55.6 1.0 CD2 A:HIS90 2.9 43.7 1.0 CE1 A:HIS84 2.9 54.8 1.0 CE1 A:HIS90 3.0 45.7 1.0 CB A:CYS53 3.1 55.6 1.0 CG A:HIS84 3.2 53.9 1.0 CB A:CYS58 3.4 66.7 1.0 CB A:HIS84 3.6 54.7 1.0 O A:SER86 3.8 56.2 1.0 CG A:HIS90 4.1 42.9 1.0 ND1 A:HIS90 4.1 45.2 1.0 NE2 A:HIS84 4.1 53.0 1.0 CD2 A:HIS84 4.2 53.4 1.0 CA A:HIS84 4.3 52.2 1.0 CA A:CYS53 4.5 59.0 1.0 CA A:CYS58 4.7 68.8 1.0 C A:SER86 4.7 51.8 1.0 CA A:CYS87 4.7 54.8 1.0 CB A:LYS55 4.7 72.3 1.0 CB A:ALA60 4.8 54.3 1.0

Zinc binding site 2 out of 3 in the Native Structure of LSD2 /AOF1/KDM1B in Spacegroup of C2221 at 2.13A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Native Structure of LSD2 /AOF1/KDM1B in Spacegroup of C2221 at 2.13A within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn902 b:49.3 occ:1.00 SG A:CYS92 2.2 47.4 1.0 SG A:CYS95 2.3 48.1 1.0 SG A:CYS65 2.3 49.7 1.0 SG A:CYS73 2.4 48.4 1.0 CB A:CYS95 3.1 47.1 1.0 CB A:CYS65 3.1 50.2 1.0 CB A:CYS73 3.3 51.9 1.0 CB A:CYS92 3.5 44.7 1.0 CA A:CYS73 3.8 54.9 1.0 N A:CYS92 3.9 46.6 1.0 N A:SER68 4.0 55.5 1.0 N A:ALA74 4.0 53.8 1.0 N A:CYS95 4.1 48.3 0.5 CA A:CYS95 4.2 46.5 0.5 CA A:CYS92 4.2 48.2 1.0 C A:CYS73 4.3 54.7 1.0 CA A:SER68 4.3 54.1 1.0 CA A:CYS65 4.6 51.3 1.0 N A:LYS75 4.6 54.2 1.0 CB A:ALA67 4.7 52.6 1.0 O A:CYS92 4.7 49.3 1.0 N A:ALA69 4.8 50.8 1.0 C A:CYS92 4.8 51.5 1.0 C A:ALA67 4.9 53.3 1.0

Zinc binding site 3 out of 3 in the Native Structure of LSD2 /AOF1/KDM1B in Spacegroup of C2221 at 2.13A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Native Structure of LSD2 /AOF1/KDM1B in Spacegroup of C2221 at 2.13A within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn903 b:48.1 occ:1.00 SG A:CYS147 2.1 44.2 1.0 SG A:CYS169 2.3 49.7 1.0 SG A:CYS185 2.4 57.4 1.0 SG A:CYS142 2.4 44.9 1.0 CB A:CYS147 3.1 48.0 1.0 CB A:CYS142 3.1 40.8 1.0 CB A:CYS185 3.2 56.2 1.0 CB A:CYS169 3.3 51.7 1.0 CA A:CYS185 3.5 55.8 1.0 N A:CYS169 3.7 54.0 1.0 CA A:CYS169 4.1 54.6 1.0 N A:CYS185 4.4 57.2 1.0 CA A:CYS147 4.5 53.4 1.0 CA A:CYS142 4.5 44.9 1.0 O A:CYS185 4.6 55.0 1.0 C A:CYS185 4.6 55.1 1.0 CB A:LYS144 4.7 59.1 1.0 N A:LYS149 4.8 48.4 1.0 N A:ARG148 4.8 51.5 1.0 C A:ARG168 4.9 55.6 1.0 CB A:LYS149 4.9 45.5 1.0 C A:CYS147 4.9 50.7 1.0

Q.Zhang, S.Qi, M.Xu, L.Yu, Y.Tao, Z.Deng, W.Wu, J.Li, Z.Chen, J.Wong. Structure-Function Analysis Reveals A Novel Mechanism For Regulation of Histone Demethylase LSD2/AOF1/KDM1B Cell Res. V. 23 225 2013.
ISSN: ISSN 1001-0602
PubMed: 23266887
DOI: 10.1038/CR.2012.177