Fluorine in PDB 8wha: Structure of DDM1-Nucleosome Complex in the Adp-Befx State with DDM1 Bound to SHL2 and Shl-2

Enzymatic activity of Structure of DDM1-Nucleosome Complex in the Adp-Befx State with DDM1 Bound to SHL2 and Shl-2

All present enzymatic activity of Structure of DDM1-Nucleosome Complex in the Adp-Befx State with DDM1 Bound to SHL2 and Shl-2:
3.6.4.12;

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Structure of DDM1-Nucleosome Complex in the Adp-Befx State with DDM1 Bound to SHL2 and Shl-2 (pdb code 8wha). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Structure of DDM1-Nucleosome Complex in the Adp-Befx State with DDM1 Bound to SHL2 and Shl-2, PDB code: 8wha:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 8wha

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Fluorine binding site 1 out of 6 in the Structure of DDM1-Nucleosome Complex in the Adp-Befx State with DDM1 Bound to SHL2 and Shl-2


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Structure of DDM1-Nucleosome Complex in the Adp-Befx State with DDM1 Bound to SHL2 and Shl-2 within 5.0Å range:
probe atom residue distance (Å) B Occ
K:F801

b:303.6
occ:1.00
 F1 K:BEF801 0.0 303.6 1.0
BE K:BEF801 1.6 303.6 1.0
F3 K:BEF801 2.5 303.6 1.0
F2 K:BEF801 2.6 303.6 1.0
O3B K:ADP802 3.1 309.2 1.0
O1B K:ADP802 3.8 309.2 1.0
PB K:ADP802 3.9 309.2 1.0
CD K:LYS233 3.9 302.1 1.0
NH2 K:ARG633 4.2 307.4 1.0
O2B K:ADP802 4.4 309.2 1.0
NZ K:LYS233 4.4 302.1 1.0
NH1 K:ARG636 4.6 314.4 1.0
CE K:LYS233 4.7 302.1 1.0

Fluorine binding site 2 out of 6 in 8wha

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Fluorine binding site 2 out of 6 in the Structure of DDM1-Nucleosome Complex in the Adp-Befx State with DDM1 Bound to SHL2 and Shl-2


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Structure of DDM1-Nucleosome Complex in the Adp-Befx State with DDM1 Bound to SHL2 and Shl-2 within 5.0Å range:
probe atom residue distance (Å) B Occ
K:F801

b:303.6
occ:1.00
 F2 K:BEF801 0.0 303.6 1.0
BE K:BEF801 1.5 303.6 1.0
NH1 K:ARG636 2.5 314.4 1.0
F3 K:BEF801 2.5 303.6 1.0
F1 K:BEF801 2.6 303.6 1.0
CZ K:ARG636 2.8 314.4 1.0
O3B K:ADP802 3.0 309.2 1.0
NH2 K:ARG636 3.1 314.4 1.0
NH2 K:ARG633 3.4 307.4 1.0
O1B K:ADP802 3.7 309.2 1.0
NE K:ARG636 3.7 314.4 1.0
CA K:GLY606 3.8 298.4 1.0
PB K:ADP802 3.9 309.2 1.0
C K:GLY606 4.1 298.4 1.0
CZ K:ARG633 4.2 307.4 1.0
N K:GLY606 4.3 298.4 1.0
CD K:ARG636 4.4 314.4 1.0
O K:GLY606 4.5 298.4 1.0
NE K:ARG633 4.6 307.4 1.0
N K:ILE607 4.6 307.4 1.0
O3A K:ADP802 4.8 309.2 1.0

Fluorine binding site 3 out of 6 in 8wha

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Fluorine binding site 3 out of 6 in the Structure of DDM1-Nucleosome Complex in the Adp-Befx State with DDM1 Bound to SHL2 and Shl-2


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Structure of DDM1-Nucleosome Complex in the Adp-Befx State with DDM1 Bound to SHL2 and Shl-2 within 5.0Å range:
probe atom residue distance (Å) B Occ
K:F801

b:303.6
occ:1.00
 F3 K:BEF801 0.0 303.6 1.0
BE K:BEF801 1.5 303.6 1.0
F1 K:BEF801 2.5 303.6 1.0
F2 K:BEF801 2.5 303.6 1.0
O1B K:ADP802 2.6 309.2 1.0
CG2 K:THR234 3.3 302.5 1.0
O3B K:ADP802 3.7 309.2 1.0
PB K:ADP802 3.7 309.2 1.0
NH1 K:ARG636 3.9 314.4 1.0
OG1 K:THR234 4.3 302.5 1.0
CB K:THR234 4.5 302.5 1.0
O2B K:ADP802 4.6 309.2 1.0
CA K:GLY606 4.8 298.4 1.0
NE1 K:TRP265 4.8 282.9 1.0
CZ K:ARG636 4.9 314.4 1.0
O3A K:ADP802 4.9 309.2 1.0

Fluorine binding site 4 out of 6 in 8wha

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Fluorine binding site 4 out of 6 in the Structure of DDM1-Nucleosome Complex in the Adp-Befx State with DDM1 Bound to SHL2 and Shl-2


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Structure of DDM1-Nucleosome Complex in the Adp-Befx State with DDM1 Bound to SHL2 and Shl-2 within 5.0Å range:
probe atom residue distance (Å) B Occ
L:F801

b:178.2
occ:1.00
 F1 L:BEF801 0.0 178.2 1.0
BE L:BEF801 1.6 178.2 1.0
F3 L:BEF801 2.5 178.2 1.0
F2 L:BEF801 2.6 178.2 1.0
CE L:LYS233 2.8 179.9 1.0
O3B L:ADP802 3.1 187.2 1.0
NZ L:LYS233 3.3 179.9 1.0
O1B L:ADP802 3.8 187.2 1.0
PB L:ADP802 3.9 187.2 1.0
CD L:LYS233 3.9 179.9 1.0
NH2 L:ARG633 4.2 169.8 1.0
CG L:LYS233 4.3 179.9 1.0
O2B L:ADP802 4.4 187.2 1.0
NH1 L:ARG636 4.6 180.4 1.0

Fluorine binding site 5 out of 6 in 8wha

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Fluorine binding site 5 out of 6 in the Structure of DDM1-Nucleosome Complex in the Adp-Befx State with DDM1 Bound to SHL2 and Shl-2


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Structure of DDM1-Nucleosome Complex in the Adp-Befx State with DDM1 Bound to SHL2 and Shl-2 within 5.0Å range:
probe atom residue distance (Å) B Occ
L:F801

b:178.2
occ:1.00
 F2 L:BEF801 0.0 178.2 1.0
BE L:BEF801 1.5 178.2 1.0
NH1 L:ARG636 2.5 180.4 1.0
F3 L:BEF801 2.5 178.2 1.0
F1 L:BEF801 2.6 178.2 1.0
CZ L:ARG636 2.8 180.4 1.0
O3B L:ADP802 3.0 187.2 1.0
NH2 L:ARG636 3.1 180.4 1.0
NH2 L:ARG633 3.4 169.8 1.0
O1B L:ADP802 3.7 187.2 1.0
NE L:ARG636 3.7 180.4 1.0
CA L:GLY606 3.8 164.0 1.0
PB L:ADP802 3.9 187.2 1.0
C L:GLY606 4.1 164.0 1.0
CZ L:ARG633 4.2 169.8 1.0
N L:GLY606 4.3 164.0 1.0
CD L:ARG636 4.4 180.4 1.0
O L:GLY606 4.5 164.0 1.0
NE L:ARG633 4.6 169.8 1.0
N L:ILE607 4.6 162.6 1.0
O3A L:ADP802 4.8 187.2 1.0

Fluorine binding site 6 out of 6 in 8wha

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Fluorine binding site 6 out of 6 in the Structure of DDM1-Nucleosome Complex in the Adp-Befx State with DDM1 Bound to SHL2 and Shl-2


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Structure of DDM1-Nucleosome Complex in the Adp-Befx State with DDM1 Bound to SHL2 and Shl-2 within 5.0Å range:
probe atom residue distance (Å) B Occ
L:F801

b:178.2
occ:1.00
 F3 L:BEF801 0.0 178.2 1.0
BE L:BEF801 1.5 178.2 1.0
F1 L:BEF801 2.5 178.2 1.0
F2 L:BEF801 2.5 178.2 1.0
O1B L:ADP802 2.6 187.2 1.0
O3B L:ADP802 3.7 187.2 1.0
PB L:ADP802 3.7 187.2 1.0
CE L:LYS233 3.8 179.9 1.0
NH1 L:ARG636 3.9 180.4 1.0
CB L:THR234 4.4 181.1 1.0
O2B L:ADP802 4.6 187.2 1.0
CG L:LYS233 4.6 179.9 1.0
NZ L:LYS233 4.7 179.9 1.0
CG2 L:THR234 4.8 181.1 1.0
CA L:GLY606 4.8 164.0 1.0
NE1 L:TRP265 4.8 160.1 1.0
CD L:LYS233 4.8 179.9 1.0
CZ L:ARG636 4.9 180.4 1.0
O3A L:ADP802 4.9 187.2 1.0

Reference:

Y.Liu, Z.Zhang, H.Hu, W.Chen, F.Zhang, Q.Wang, C.Wang, K.Yan, J.Du. Molecular Basis of Chromatin Remodelling By DDM1 Involved in Plant Dna Methylation. Nat.Plants V. 10 374 2024.
ISSN: ESSN 2055-0278
PubMed: 38413824
DOI: 10.1038/S41477-024-01640-Z
Page generated: Sat Aug 3 01:38:07 2024

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