Zinc in PDB 4fwj: Native Structure of LSD2/AOF1/KDM1B in Spacegroup of I222 at 2.9A

The structure of Native Structure of LSD2/AOF1/KDM1B in Spacegroup of I222 at 2.9A, PDB code: 4fwj 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 / 2.90
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	144.322, 170.933, 202.566, 90.00, 90.00, 90.00
R / Rfree (%)	18.6 / 22.2

The structure of Native Structure of LSD2/AOF1/KDM1B in Spacegroup of I222 at 2.9A also contains other interesting chemical elements:

Potassium

(K)

1 atom

The binding sites of Zinc atom in the Native Structure of LSD2/AOF1/KDM1B in Spacegroup of I222 at 2.9A (pdb code 4fwj). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Native Structure of LSD2/AOF1/KDM1B in Spacegroup of I222 at 2.9A, PDB code: 4fwj:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in the Native Structure of LSD2/AOF1/KDM1B in Spacegroup of I222 at 2.9A


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 I222 at 2.9A within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn901 b:60.0 occ:1.00 SG A:CYS169 2.2 42.7 1.0 SG A:CYS185 2.2 47.8 1.0 SG A:CYS147 2.2 44.0 1.0 SG A:CYS142 2.4 45.6 1.0 CB A:CYS142 3.0 42.7 1.0 CB A:CYS185 3.2 49.1 1.0 CB A:CYS169 3.2 48.6 1.0 CB A:CYS147 3.3 45.8 1.0 CA A:CYS185 3.5 48.2 1.0 N A:CYS169 3.8 51.1 1.0 CA A:CYS169 4.1 50.6 1.0 N A:CYS185 4.4 52.2 1.0 CA A:CYS142 4.5 41.4 1.0 C A:CYS185 4.6 46.6 1.0 O A:CYS185 4.6 45.7 1.0 CB A:LYS149 4.7 37.8 1.0 CA A:CYS147 4.7 45.4 1.0 N A:LYS149 4.8 40.2 1.0 N A:ARG148 4.9 44.1 1.0 NE A:ARG151 4.9 36.4 1.0 CB A:LYS144 5.0 57.2 1.0

Zinc binding site 2 out of 6 in the Native Structure of LSD2/AOF1/KDM1B in Spacegroup of I222 at 2.9A


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 I222 at 2.9A within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn902 b:53.0 occ:1.00 NE2 A:HIS90 2.1 37.3 1.0 ND1 A:HIS84 2.2 38.9 1.0 SG A:CYS53 2.2 46.8 1.0 SG A:CYS58 2.3 43.5 1.0 CD2 A:HIS90 3.0 38.8 1.0 CE1 A:HIS84 3.0 37.5 1.0 CE1 A:HIS90 3.1 36.9 1.0 CG A:HIS84 3.2 38.7 1.0 CB A:CYS58 3.2 47.8 1.0 CB A:CYS53 3.2 49.2 1.0 CB A:HIS84 3.6 40.7 1.0 O A:SER86 3.9 41.0 1.0 CG A:HIS90 4.2 38.1 1.0 NE2 A:HIS84 4.2 36.7 1.0 ND1 A:HIS90 4.2 36.8 1.0 CD2 A:HIS84 4.3 37.7 1.0 CA A:HIS84 4.4 41.5 1.0 CA A:CYS58 4.6 49.2 1.0 CA A:CYS53 4.6 52.9 1.0 C A:SER86 4.8 39.6 1.0 CB A:LYS55 4.8 48.7 1.0 O A:CYS87 4.9 41.7 1.0 CA A:CYS87 4.9 41.1 1.0

Zinc binding site 3 out of 6 in the Native Structure of LSD2/AOF1/KDM1B in Spacegroup of I222 at 2.9A


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 I222 at 2.9A within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn903 b:62.2 occ:1.00 SG A:CYS73 2.2 64.2 1.0 SG A:CYS65 2.4 50.7 1.0 SG A:CYS92 2.4 51.4 1.0 SG A:CYS95 2.5 53.2 1.0 CB A:CYS65 3.2 50.1 1.0 CB A:CYS73 3.2 66.5 1.0 CB A:CYS95 3.5 52.5 1.0 CB A:CYS92 3.6 50.8 1.0 O A:ALA67 3.8 56.6 1.0 CA A:CYS73 3.9 68.7 1.0 N A:CYS92 4.0 48.3 1.0 N A:ALA74 4.3 68.7 1.0 N A:CYS95 4.4 56.4 0.5 CA A:CYS92 4.4 49.9 1.0 C A:CYS73 4.4 68.5 1.0 C A:ALA67 4.5 54.3 1.0 O A:ALA74 4.5 71.8 1.0 CA A:CYS95 4.5 55.3 0.5 CA A:CYS65 4.6 47.9 1.0 CA A:SER68 4.8 60.3 1.0 O A:CYS92 4.9 52.7 1.0 C A:CYS92 5.0 52.5 1.0 C A:ALA74 5.0 69.5 1.0 N A:SER68 5.0 56.7 1.0

Zinc binding site 4 out of 6 in the Native Structure of LSD2/AOF1/KDM1B in Spacegroup of I222 at 2.9A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Native Structure of LSD2/AOF1/KDM1B in Spacegroup of I222 at 2.9A within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn901 b:51.8 occ:1.00 SG B:CYS142 2.2 53.1 1.0 SG B:CYS169 2.3 40.2 1.0 SG B:CYS147 2.3 45.2 1.0 SG B:CYS185 2.4 45.8 1.0 CB B:CYS147 2.9 48.1 1.0 CB B:CYS142 3.1 49.5 1.0 CB B:CYS169 3.3 43.2 1.0 CB B:CYS185 3.4 44.6 1.0 CA B:CYS185 3.8 42.8 1.0 N B:CYS169 3.8 45.9 1.0 CA B:CYS169 4.1 44.0 1.0 CA B:CYS147 4.4 48.6 1.0 CA B:CYS142 4.5 48.4 1.0 CB B:LYS144 4.7 56.3 1.0 N B:CYS185 4.7 43.9 1.0 O B:CYS185 4.7 41.5 1.0 C B:CYS185 4.7 42.1 1.0 NZ B:LYS144 4.8 63.3 1.0 N B:ARG148 4.8 46.9 1.0 CE B:LYS144 4.8 63.7 1.0 C B:ARG168 4.9 48.0 1.0 C B:CYS147 4.9 47.6 1.0

Zinc binding site 5 out of 6 in the Native Structure of LSD2/AOF1/KDM1B in Spacegroup of I222 at 2.9A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Native Structure of LSD2/AOF1/KDM1B in Spacegroup of I222 at 2.9A within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn902 b:88.1 occ:1.00 ND1 B:HIS84 2.0 89.8 1.0 NE2 B:HIS90 2.2 58.7 1.0 SG B:CYS58 2.2 89.6 1.0 SG B:CYS53 2.6 99.5 1.0 CE1 B:HIS84 2.8 89.1 1.0 CE1 B:HIS90 3.0 57.3 1.0 CG B:HIS84 3.1 89.1 1.0 CD2 B:HIS90 3.3 60.2 1.0 CB B:CYS58 3.5 94.7 1.0 CB B:HIS84 3.6 89.1 1.0 CB B:CYS53 3.7 99.8 1.0 NE2 B:HIS84 4.0 88.1 1.0 CD2 B:HIS84 4.2 88.0 1.0 ND1 B:HIS90 4.2 56.8 1.0 O B:SER86 4.3 79.5 1.0 CG B:HIS90 4.4 58.5 1.0 CB B:LYS55 4.6 96.4 1.0 CA B:HIS84 4.7 87.0 1.0 CA B:CYS58 4.8 96.7 1.0 CB B:ALA60 4.9 97.1 1.0

Zinc binding site 6 out of 6 in the Native Structure of LSD2/AOF1/KDM1B in Spacegroup of I222 at 2.9A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Native Structure of LSD2/AOF1/KDM1B in Spacegroup of I222 at 2.9A within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn903 b:0.4 occ:1.00 SG B:CYS92 2.4 82.6 1.0 SG B:CYS95 2.5 94.0 1.0 SG B:CYS65 2.5 95.5 1.0 SG B:CYS73 2.6 0.5 1.0 O B:ALA74 3.4 0.7 1.0 O B:ALA67 3.4 96.2 1.0 CB B:CYS65 3.5 93.0 1.0 CB B:CYS73 3.8 0.6 1.0 N B:ALA74 4.0 0.4 1.0 CB B:CYS95 4.1 94.1 1.0 CB B:CYS92 4.1 84.6 1.0 CA B:CYS73 4.2 0.1 1.0 C B:ALA74 4.3 0.5 1.0 C B:CYS73 4.3 0.4 1.0 C B:ALA67 4.4 93.8 1.0 N B:CYS92 4.4 79.3 1.0 CA B:SER68 4.7 97.9 1.0 N B:ALA69 4.7 0.0 1.0 N B:CYS95 4.7 98.7 0.5 CA B:ALA74 4.7 0.9 1.0 CA B:CYS95 4.8 97.5 0.5 CA B:CYS92 4.8 83.6 1.0 CA B:CYS65 4.9 90.2 1.0 N B:SER68 5.0 95.4 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