Fluorine in PDB 8kcc: Complex of DDM1-Nucleosome(H2A.W) Complex with DDM1 Bound to SHL2

All present enzymatic activity of Complex of DDM1-Nucleosome(H2A.W) Complex with DDM1 Bound to SHL2:
3.6.4.12;

The binding sites of Fluorine atom in the Complex of DDM1-Nucleosome(H2A.W) Complex with DDM1 Bound to SHL2 (pdb code 8kcc). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Complex of DDM1-Nucleosome(H2A.W) Complex with DDM1 Bound to SHL2, PDB code: 8kcc:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Complex of DDM1-Nucleosome(H2A.W) Complex with DDM1 Bound to SHL2


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Complex of DDM1-Nucleosome(H2A.W) Complex with DDM1 Bound to SHL2 within 5.0Å range: probe atom residue distance (Å) B Occ K:F802 b:174.1 occ:1.00 F1 K:BEF802 0.0 174.1 1.0 BE K:BEF802 1.4 174.1 1.0 F3 K:BEF802 2.2 174.1 1.0 F2 K:BEF802 2.2 174.1 1.0 O2B K:ADP801 2.3 180.5 1.0 OD2 K:ASP333 2.8 154.0 1.0 OD1 K:ASP333 3.2 154.0 1.0 CG K:ASP333 3.4 154.0 1.0 PB K:ADP801 3.4 180.5 1.0 O1B K:ADP801 3.4 180.5 1.0 OE1 K:GLU334 3.5 161.3 1.0 OE2 K:GLU334 3.8 161.3 1.0 CD K:GLU334 4.0 161.3 1.0 O3B K:ADP801 4.1 180.5 1.0 CG2 K:THR234 4.4 168.9 1.0 CD K:LYS233 4.5 168.8 1.0 CA K:GLY606 4.5 172.8 1.0 CE K:LYS233 4.6 168.8 1.0 O3A K:ADP801 4.7 180.5 1.0 CB K:LYS233 4.8 168.8 1.0 OG1 K:THR261 4.8 153.7 1.0 CB K:ASP333 4.8 154.0 1.0

Fluorine binding site 2 out of 3 in the Complex of DDM1-Nucleosome(H2A.W) Complex with DDM1 Bound to SHL2


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Complex of DDM1-Nucleosome(H2A.W) Complex with DDM1 Bound to SHL2 within 5.0Å range: probe atom residue distance (Å) B Occ K:F802 b:174.1 occ:1.00 F2 K:BEF802 0.0 174.1 1.0 BE K:BEF802 1.4 174.1 1.0 F3 K:BEF802 2.2 174.1 1.0 F1 K:BEF802 2.2 174.1 1.0 O1B K:ADP801 2.6 180.5 1.0 O2B K:ADP801 3.1 180.5 1.0 OE1 K:GLU334 3.1 161.3 1.0 PB K:ADP801 3.2 180.5 1.0 NH1 K:ARG636 3.5 187.6 1.0 CA K:GLY606 3.5 172.8 1.0 O3B K:ADP801 3.6 180.5 1.0 NH2 K:ARG633 3.6 183.5 1.0 N K:GLY606 4.1 172.8 1.0 CD K:GLU334 4.2 161.3 1.0 C K:GLY606 4.4 172.8 1.0 CZ K:ARG636 4.4 187.6 1.0 OE2 K:GLU334 4.5 161.3 1.0 CZ K:ARG633 4.6 183.5 1.0 O K:GLY606 4.6 172.8 1.0 NH2 K:ARG636 4.6 187.6 1.0 CD K:LYS233 4.8 168.8 1.0 O3A K:ADP801 4.8 180.5 1.0 OD2 K:ASP333 4.8 154.0 1.0

Fluorine binding site 3 out of 3 in the Complex of DDM1-Nucleosome(H2A.W) Complex with DDM1 Bound to SHL2


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Complex of DDM1-Nucleosome(H2A.W) Complex with DDM1 Bound to SHL2 within 5.0Å range: probe atom residue distance (Å) B Occ K:F802 b:174.1 occ:1.00 F3 K:BEF802 0.0 174.1 1.0 BE K:BEF802 1.4 174.1 1.0 F1 K:BEF802 2.2 174.1 1.0 F2 K:BEF802 2.2 174.1 1.0 O1B K:ADP801 2.3 180.5 1.0 O2B K:ADP801 3.0 180.5 1.0 O K:GLY606 3.2 172.8 1.0 PB K:ADP801 3.2 180.5 1.0 CA K:GLY606 3.3 172.8 1.0 C K:GLY606 3.6 172.8 1.0 OG1 K:THR261 4.0 153.7 1.0 NH1 K:ARG636 4.1 187.6 1.0 OD2 K:ASP333 4.1 154.0 1.0 O3A K:ADP801 4.2 180.5 1.0 O1A K:ADP801 4.3 180.5 1.0 O3B K:ADP801 4.3 180.5 1.0 OE1 K:GLU334 4.3 161.3 1.0 OD1 K:ASN608 4.4 175.4 1.0 N K:GLY606 4.5 172.8 1.0 CG2 K:THR234 4.6 168.9 1.0 NH2 K:ARG636 4.6 187.6 1.0 N K:ILE607 4.8 175.6 1.0 CZ K:ARG636 4.8 187.6 1.0 OE2 K:GLU334 4.9 161.3 1.0 ND2 K:ASN264 4.9 154.4 1.0 PA K:ADP801 4.9 180.5 1.0

H.Zhang, Z.Gu, Y.Zeng, Y.Zhang. Mechanism of Heterochromatin Remodeling Revealed By the DDM1 Bound Nucleosome Structures. Structure 2024.
ISSN: ISSN 0969-2126
PubMed: 38870940
DOI: 10.1016/J.STR.2024.05.013