Zinc in PDB 4gu0: Crystal Structure of LSD2 with H3

The structure of Crystal Structure of LSD2 with H3, PDB code: 4gu0 was solved by F.Chen, H.Yang, Z.Dong, J.Fang, T.Zhu, W.Gong, Y.Xu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.06 / 3.10
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	101.843, 108.926, 120.825, 94.47, 112.34, 117.95
R / Rfree (%)	20.4 / 22.1

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Zinc atom in the Crystal Structure of LSD2 with H3 (pdb code 4gu0). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 12 binding sites of Zinc where determined in the Crystal Structure of LSD2 with H3, PDB code: 4gu0:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 12 in the Crystal Structure of LSD2 with H3


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 with H3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn902 b:77.5 occ:1.00 NE2 A:HIS90 2.3 64.2 1.0 ND1 A:HIS84 2.3 60.1 1.0 SG A:CYS53 2.4 71.7 1.0 SG A:CYS58 2.4 87.8 1.0 CD2 A:HIS90 2.8 61.2 1.0 CB A:CYS58 3.2 81.0 1.0 CE1 A:HIS84 3.2 70.0 1.0 CB A:CYS53 3.2 79.7 1.0 CG A:HIS84 3.3 58.4 1.0 CE1 A:HIS90 3.5 71.8 1.0 CB A:HIS84 3.7 55.5 1.0 O A:SER86 3.9 70.8 1.0 CG A:HIS90 4.1 65.5 1.0 NE2 A:HIS84 4.4 69.7 1.0 ND1 A:HIS90 4.4 72.4 1.0 CD2 A:HIS84 4.4 68.4 1.0 CA A:HIS84 4.4 61.7 1.0 CA A:CYS58 4.6 93.2 1.0 CA A:CYS53 4.6 86.3 1.0 CG A:LYS55 4.7 74.3 1.0

Zinc binding site 2 out of 12 in the Crystal Structure of LSD2 with H3


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 with H3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn903 b:53.5 occ:1.00 SG A:CYS92 2.4 65.3 1.0 SG A:CYS95 2.5 62.7 1.0 SG A:CYS65 2.5 70.7 1.0 SG A:CYS73 2.5 68.2 1.0 CB A:CYS65 3.0 67.2 1.0 CB A:CYS92 3.6 65.9 1.0 CB A:CYS73 3.6 89.8 1.0 CB A:CYS95 3.7 63.5 1.0 CA A:CYS73 4.0 80.1 1.0 N A:ALA74 4.0 75.8 1.0 N A:CYS92 4.0 61.9 1.0 CA A:CYS92 4.4 62.9 1.0 C A:CYS73 4.4 75.8 1.0 CA A:CYS65 4.5 75.0 1.0 N A:SER68 4.5 71.9 1.0 N A:LYS75 4.5 72.8 1.0 CB A:ALA67 4.6 71.0 1.0 N A:CYS95 4.6 73.4 1.0 CA A:CYS95 4.7 67.5 1.0

Zinc binding site 3 out of 12 in the Crystal Structure of LSD2 with H3


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 with H3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn904 b:65.5 occ:1.00 SG A:CYS169 2.5 63.5 1.0 SG A:CYS142 2.6 88.4 1.0 SG A:CYS147 2.6 73.2 1.0 SG A:CYS185 2.6 73.6 1.0 CB A:CYS169 3.1 63.5 1.0 CB A:CYS185 3.2 75.0 1.0 CB A:CYS147 3.2 75.6 1.0 CB A:CYS142 3.2 67.2 1.0 N A:CYS169 3.7 73.2 1.0 CA A:CYS185 3.8 79.7 1.0 CA A:CYS169 4.0 65.6 1.0 CB A:LYS144 4.4 92.4 1.0 CG A:LYS144 4.5 99.1 1.0 N A:CYS185 4.7 76.2 1.0 CA A:CYS147 4.7 86.7 1.0 CA A:CYS142 4.7 67.4 1.0 C A:ARG168 4.8 75.7 1.0 C A:CYS185 4.9 85.7 1.0 O A:CYS185 4.9 98.2 1.0 NH1 A:ARG151 4.9 67.9 1.0 N A:ARG148 4.9 86.8 1.0

Zinc binding site 4 out of 12 in the Crystal Structure of LSD2 with H3


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of LSD2 with H3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn902 b:57.8 occ:1.00 NE2 B:HIS90 2.3 63.0 1.0 ND1 B:HIS84 2.3 63.9 1.0 SG B:CYS58 2.4 86.0 1.0 SG B:CYS53 2.5 84.1 1.0 CD2 B:HIS90 2.8 65.0 1.0 CB B:CYS58 3.2 89.8 1.0 CE1 B:HIS84 3.2 69.5 1.0 CG B:HIS84 3.4 63.1 1.0 CB B:CYS53 3.4 80.9 1.0 CE1 B:HIS90 3.5 68.2 1.0 CB B:HIS84 3.7 65.4 1.0 CG B:HIS90 4.1 61.7 1.0 CB B:LYS55 4.2 90.6 1.0 NE2 B:HIS84 4.4 65.2 1.0 ND1 B:HIS90 4.4 67.0 1.0 O B:SER86 4.5 69.7 1.0 CD2 B:HIS84 4.5 62.9 1.0 CA B:HIS84 4.5 60.5 1.0 CA B:CYS58 4.6 93.0 1.0 CA B:CYS53 4.9 88.8 1.0 CG B:LYS55 4.9 87.1 1.0 O B:LYS52 5.0 99.7 1.0

Zinc binding site 5 out of 12 in the Crystal Structure of LSD2 with H3


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of LSD2 with H3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn903 b:53.8 occ:1.00 SG B:CYS65 2.4 72.7 1.0 SG B:CYS92 2.4 68.0 1.0 SG B:CYS73 2.5 76.0 1.0 SG B:CYS95 2.5 63.1 1.0 CB B:CYS65 3.0 69.5 1.0 CB B:CYS73 3.6 96.4 1.0 CB B:CYS92 3.7 74.4 1.0 CB B:CYS95 3.7 67.1 1.0 CA B:CYS73 3.9 86.8 1.0 N B:ALA74 4.0 78.9 1.0 N B:CYS92 4.1 67.5 1.0 N B:SER68 4.1 75.8 1.0 C B:CYS73 4.3 78.7 1.0 N B:LYS75 4.4 86.0 1.0 CA B:SER68 4.5 84.5 1.0 CA B:CYS65 4.5 78.2 1.0 CA B:CYS92 4.5 74.0 1.0 N B:CYS95 4.5 77.6 1.0 CA B:CYS95 4.7 69.7 1.0 CB B:ALA67 4.8 72.6 1.0

Zinc binding site 6 out of 12 in the Crystal Structure of LSD2 with H3


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of LSD2 with H3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn904 b:67.7 occ:1.00 SG B:CYS147 2.4 78.4 1.0 SG B:CYS169 2.5 63.9 1.0 SG B:CYS185 2.5 74.6 1.0 SG B:CYS142 2.6 76.6 1.0 CB B:CYS147 3.1 73.4 1.0 CB B:CYS169 3.2 64.7 1.0 CB B:CYS185 3.2 75.8 1.0 CB B:CYS142 3.4 69.5 1.0 CA B:CYS185 3.6 79.0 1.0 N B:CYS169 4.0 71.4 1.0 CA B:CYS169 4.2 70.1 1.0 NH1 B:ARG151 4.4 73.6 1.0 N B:CYS185 4.4 71.3 1.0 CA B:CYS147 4.6 87.2 1.0 C B:CYS185 4.7 82.4 1.0 O B:CYS185 4.8 86.9 1.0 CA B:CYS142 4.9 69.1 1.0 N B:ARG148 4.9 92.6 1.0 CB B:LYS144 4.9 89.7 1.0

Zinc binding site 7 out of 12 in the Crystal Structure of LSD2 with H3


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of LSD2 with H3 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn902 b:71.6 occ:1.00 NE2 C:HIS90 2.3 59.7 1.0 ND1 C:HIS84 2.4 68.8 1.0 SG C:CYS58 2.4 80.9 1.0 SG C:CYS53 2.6 90.2 1.0 CD2 C:HIS90 2.9 59.3 1.0 CB C:CYS53 3.1 89.2 1.0 CE1 C:HIS84 3.3 74.9 1.0 CG C:HIS84 3.4 70.0 1.0 CE1 C:HIS90 3.5 67.0 1.0 CB C:CYS58 3.5 91.7 1.0 CB C:HIS84 3.6 68.5 1.0 CB C:LYS55 4.0 88.5 1.0 CG C:HIS90 4.2 58.8 1.0 CB C:ALA60 4.3 97.0 1.0 ND1 C:HIS90 4.4 64.0 1.0 NE2 C:HIS84 4.4 82.1 1.0 O C:SER86 4.5 70.3 1.0 CD2 C:HIS84 4.5 76.4 1.0 CG C:LYS55 4.5 88.7 1.0 CA C:HIS84 4.6 66.0 1.0 CA C:CYS53 4.6 0.1 1.0 CA C:CYS58 4.9 92.0 1.0

Zinc binding site 8 out of 12 in the Crystal Structure of LSD2 with H3


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of LSD2 with H3 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn903 b:0.7 occ:1.00 SG C:CYS65 2.4 63.8 1.0 SG C:CYS92 2.4 60.8 1.0 SG C:CYS95 2.6 53.1 1.0 SG C:CYS73 2.6 68.0 1.0 CB C:CYS65 3.1 65.4 1.0 CB C:CYS92 3.5 67.2 1.0 CB C:CYS73 3.6 81.7 1.0 CB C:CYS95 3.8 66.0 1.0 CA C:CYS73 3.9 78.3 1.0 N C:SER68 3.9 70.8 1.0 N C:CYS92 4.1 62.8 1.0 CA C:SER68 4.1 72.0 1.0 N C:ALA74 4.1 69.0 1.0 C C:CYS73 4.4 73.6 1.0 CA C:CYS92 4.4 65.9 1.0 N C:LYS75 4.6 71.6 1.0 CA C:CYS65 4.6 63.1 1.0 N C:CYS95 4.7 70.0 1.0 CA C:CYS95 4.8 63.0 1.0 N C:ALA69 4.9 63.5 1.0 CB C:ALA67 5.0 65.3 1.0

Zinc binding site 9 out of 12 in the Crystal Structure of LSD2 with H3


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Crystal Structure of LSD2 with H3 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn904 b:96.6 occ:1.00 SG C:CYS142 2.6 1.0 1.0 SG C:CYS147 2.6 84.9 1.0 SG C:CYS169 2.7 83.3 1.0 SG C:CYS185 2.7 0.1 1.0 CB C:CYS147 3.0 0.5 1.0 CB C:CYS169 3.3 95.6 1.0 CB C:CYS142 3.3 94.3 1.0 CB C:CYS185 3.4 0.2 1.0 CA C:CYS185 3.8 0.3 1.0 N C:CYS169 3.8 94.4 1.0 CA C:CYS169 4.1 90.6 1.0 CA C:CYS147 4.5 0.6 1.0 CB C:LYS144 4.5 0.2 1.0 N C:CYS185 4.6 0.6 1.0 N C:ARG148 4.7 99.9 1.0 CA C:CYS142 4.8 90.4 1.0 CD C:LYS144 4.8 0.9 1.0 C C:CYS185 4.9 0.9 1.0 O C:CYS185 4.9 0.8 1.0 C C:ARG168 4.9 97.1 1.0 N C:LYS149 5.0 0.4 1.0

Zinc binding site 10 out of 12 in the Crystal Structure of LSD2 with H3


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Crystal Structure of LSD2 with H3 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn902 b:69.8 occ:1.00 NE2 D:HIS90 2.1 70.2 1.0 ND1 D:HIS84 2.3 65.4 1.0 SG D:CYS58 2.4 80.1 1.0 SG D:CYS53 2.4 80.4 1.0 CD2 D:HIS90 2.8 67.6 1.0 CB D:CYS53 3.0 80.7 1.0 CE1 D:HIS84 3.2 78.1 1.0 CE1 D:HIS90 3.3 74.8 1.0 CG D:HIS84 3.4 74.9 1.0 CB D:CYS58 3.5 90.1 1.0 CB D:HIS84 3.8 75.9 1.0 CG D:HIS90 4.0 72.9 1.0 O D:SER86 4.1 77.8 1.0 ND1 D:HIS90 4.2 72.8 1.0 CB D:LYS55 4.3 86.3 1.0 CB D:ALA60 4.3 0.3 1.0 NE2 D:HIS84 4.3 87.3 1.0 CD2 D:HIS84 4.5 83.1 1.0 CA D:CYS53 4.5 92.4 1.0 CA D:HIS84 4.5 73.2 1.0 CA D:CYS58 4.9 92.8 1.0 CG D:LYS55 5.0 90.1 1.0

F.Chen, H.Yang, Z.Dong, J.Fang, P.Wang, T.Zhu, W.Gong, R.Fang, Y.G.Shi, Z.Li, Y.Xu. Structural Insight Into Substrate Recognition By Histone Demethylase LSD2/KDM1B Cell Res. V. 23 306 2013.
ISSN: ISSN 1001-0602
PubMed: 23357850
DOI: 10.1038/CR.2013.17