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

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

The binding sites of Fluorine atom in the Complex of DDM1-Nucleosome(H2A) Complex with DDM1 Bound to SHL2 (pdb code 8kcb). 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) Complex with DDM1 Bound to SHL2, PDB code: 8kcb:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Complex of DDM1-Nucleosome(H2A) 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) Complex with DDM1 Bound to SHL2 within 5.0Å range: probe atom residue distance (Å) B Occ K:F901 b:179.6 occ:1.00 F1 K:BEF901 0.0 179.6 1.0 BE K:BEF901 1.7 181.6 1.0 F3 K:BEF901 2.6 183.1 1.0 F2 K:BEF901 2.8 182.0 1.0 CA K:GLY606 3.0 170.2 1.0 NH2 K:ARG633 3.0 189.0 1.0 N K:GLY606 3.1 169.6 1.0 O1B K:ADP902 3.3 189.9 1.0 NH1 K:ARG636 3.4 196.9 1.0 OE2 K:GLU334 3.5 182.6 1.0 CZ K:ARG633 3.5 188.8 1.0 C K:GLY606 3.8 168.8 1.0 NE K:ARG633 4.0 186.1 1.0 NH1 K:ARG633 4.1 191.8 1.0 O K:GLY606 4.2 169.9 1.0 C K:LEU605 4.3 167.5 1.0 O3B K:ADP902 4.3 190.1 1.0 PB K:ADP902 4.4 191.8 1.0 CZ K:ARG636 4.5 195.9 1.0 N K:ILE607 4.6 164.2 1.0 CD K:GLU334 4.6 181.1 1.0 OE1 K:GLN629 4.8 189.9 1.0 CA K:LEU605 4.9 166.3 1.0 NH2 K:ARG636 5.0 196.0 1.0

Fluorine binding site 2 out of 3 in the Complex of DDM1-Nucleosome(H2A) 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) Complex with DDM1 Bound to SHL2 within 5.0Å range: probe atom residue distance (Å) B Occ K:F901 b:182.0 occ:1.00 F2 K:BEF901 0.0 182.0 1.0 BE K:BEF901 1.7 181.6 1.0 F3 K:BEF901 2.7 183.1 1.0 OE2 K:GLU334 2.8 182.6 1.0 O1B K:ADP902 2.8 189.9 1.0 F1 K:BEF901 2.8 179.6 1.0 OD2 K:ASP333 3.4 158.5 1.0 OD1 K:ASP333 3.4 160.0 1.0 CG K:ASP333 3.8 157.0 1.0 PB K:ADP902 3.9 191.8 1.0 CD K:GLU334 4.0 181.1 1.0 O2B K:ADP902 4.1 187.2 1.0 O3B K:ADP902 4.7 190.1 1.0 OE1 K:GLU334 4.8 182.1 1.0 CG K:GLU334 4.8 179.1 1.0

Fluorine binding site 3 out of 3 in the Complex of DDM1-Nucleosome(H2A) 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) Complex with DDM1 Bound to SHL2 within 5.0Å range: probe atom residue distance (Å) B Occ K:F901 b:183.1 occ:1.00 F3 K:BEF901 0.0 183.1 1.0 BE K:BEF901 1.7 181.6 1.0 F1 K:BEF901 2.6 179.6 1.0 F2 K:BEF901 2.7 182.0 1.0 O1B K:ADP902 3.0 189.9 1.0 CA K:GLY606 3.3 170.2 1.0 O K:GLY606 3.4 169.9 1.0 OD2 K:ASP333 3.6 158.5 1.0 C K:GLY606 3.8 168.8 1.0 OE2 K:GLU334 4.0 182.6 1.0 N K:GLY606 4.3 169.6 1.0 PB K:ADP902 4.5 191.8 1.0 CG2 K:THR261 4.5 160.2 1.0 CG K:ASP333 4.7 157.0 1.0 NH1 K:ARG636 4.8 196.9 1.0 CB K:THR261 4.9 158.4 1.0 OD1 K:ASP333 5.0 160.0 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