Zinc in PDB 6r25: Structure of LSD2/Npac-Linker/Nucleosome Core Particle Complex: Class 3

The binding sites of Zinc atom in the Structure of LSD2/Npac-Linker/Nucleosome Core Particle Complex: Class 3 (pdb code 6r25). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Structure of LSD2/Npac-Linker/Nucleosome Core Particle Complex: Class 3, PDB code: 6r25:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Structure of LSD2/Npac-Linker/Nucleosome Core Particle Complex: Class 3


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of LSD2/Npac-Linker/Nucleosome Core Particle Complex: Class 3 within 5.0Å range: probe atom residue distance (Å) B Occ K:Zn902 b:42.8 occ:1.00 NE2 K:HIS90 2.2 37.9 1.0 SG K:CYS58 2.4 47.3 1.0 ND1 K:HIS84 2.4 43.1 1.0 SG K:CYS53 2.5 48.0 1.0 CD2 K:HIS90 3.0 39.5 1.0 CB K:CYS58 3.1 57.3 1.0 CE1 K:HIS90 3.2 38.0 1.0 CB K:CYS53 3.3 58.2 1.0 CG K:HIS84 3.3 44.1 1.0 CE1 K:HIS84 3.4 45.2 1.0 CB K:HIS84 3.5 43.2 1.0 O K:SER86 4.1 41.1 1.0 CG K:HIS90 4.2 39.1 1.0 CB K:LYS55 4.3 58.2 1.0 ND1 K:HIS90 4.3 41.4 1.0 CB K:ALA60 4.4 52.3 1.0 NE2 K:HIS84 4.5 43.9 1.0 CD2 K:HIS84 4.5 41.5 1.0 CA K:HIS84 4.5 44.0 1.0 CA K:CYS58 4.6 61.0 1.0 CA K:CYS53 4.8 55.4 1.0 CA K:CYS87 4.9 42.1 1.0 C K:SER86 4.9 40.6 1.0

Zinc binding site 2 out of 3 in the Structure of LSD2/Npac-Linker/Nucleosome Core Particle Complex: Class 3


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of LSD2/Npac-Linker/Nucleosome Core Particle Complex: Class 3 within 5.0Å range: probe atom residue distance (Å) B Occ K:Zn903 b:40.5 occ:1.00 SG K:CYS95 2.3 36.8 1.0 SG K:CYS65 2.5 37.1 1.0 SG K:CYS73 2.5 40.5 1.0 SG K:CYS92 2.5 37.4 1.0 CB K:CYS65 3.2 37.8 1.0 CB K:CYS73 3.2 42.6 1.0 CB K:CYS95 3.2 42.3 1.0 CA K:CYS73 3.6 42.4 1.0 CB K:CYS92 3.7 35.2 1.0 N K:SER68 4.0 42.6 1.0 N K:CYS92 4.0 39.1 1.0 N K:ALA74 4.0 43.4 1.0 N K:CYS95 4.1 37.6 1.0 CA K:SER68 4.3 42.8 1.0 C K:CYS73 4.3 39.9 1.0 CA K:CYS95 4.3 43.4 1.0 CA K:CYS92 4.4 40.1 1.0 O K:CYS92 4.7 36.7 1.0 CA K:CYS65 4.7 41.5 1.0 CB K:ALA67 4.8 36.8 1.0 N K:LYS75 4.8 46.4 1.0 N K:ALA69 4.8 40.9 1.0 N K:CYS73 4.9 39.4 1.0 C K:CYS92 4.9 39.6 1.0

Zinc binding site 3 out of 3 in the Structure of LSD2/Npac-Linker/Nucleosome Core Particle Complex: Class 3


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of LSD2/Npac-Linker/Nucleosome Core Particle Complex: Class 3 within 5.0Å range: probe atom residue distance (Å) B Occ K:Zn904 b:39.2 occ:1.00 SG K:CYS147 2.3 37.4 1.0 SG K:CYS142 2.3 35.5 1.0 SG K:CYS185 2.4 38.6 1.0 SG K:CYS169 2.5 35.0 1.0 CB K:CYS142 3.1 31.1 1.0 CB K:CYS147 3.1 39.2 1.0 CB K:CYS185 3.2 43.7 1.0 CB K:CYS169 3.3 37.2 1.0 CA K:CYS185 3.6 43.6 1.0 N K:CYS169 3.8 32.7 1.0 CA K:CYS169 4.2 33.1 1.0 N K:CYS185 4.5 46.5 1.0 CB K:LYS144 4.5 42.3 1.0 O K:HOH1063 4.6 39.3 1.0 CA K:CYS147 4.6 42.0 1.0 CA K:CYS142 4.6 33.0 1.0 C K:CYS185 4.7 46.9 1.0 O K:CYS185 4.7 48.7 1.0 N K:ARG148 4.8 37.5 1.0 N K:LYS149 4.8 35.0 1.0 CB K:LYS149 4.9 33.8 1.0 CD K:LYS144 4.9 42.7 1.0 C K:ARG168 4.9 32.4 1.0 NH1 K:ARG151 5.0 38.5 1.0

C.Marabelli, B.Marrocco, S.Pilotto, S.Chittori, S.Picaud, S.Marchese, G.Ciossani, F.Forneris, P.Filippakopoulos, G.Schoehn, D.Rhodes, S.Subramaniam, A.Mattevi. A Tail-Based Mechanism Drives Nucleosome Demethylation By the LSD2/Npac Multimeric Complex. Cell Rep V. 27 387 2019.
ISSN: ESSN 2211-1247
PubMed: 30970244
DOI: 10.1016/J.CELREP.2019.03.061