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Fluorine in PDB 5w77: Complex of Dna and Compounds

Other elements in 5w77:

The structure of Complex of Dna and Compounds also contains other interesting chemical elements:

Potassium (K) 30 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Complex of Dna and Compounds (pdb code 5w77). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Complex of Dna and Compounds, PDB code: 5w77:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 5w77

Go back to Fluorine Binding Sites List in 5w77
Fluorine binding site 1 out of 6 in the Complex of Dna and Compounds


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Complex of Dna and Compounds within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F103

b:0.0
occ:1.00
F1 A:9WP103 0.0 0.0 1.0
C17 A:9WP103 1.4 0.0 1.0
F3 A:9WP103 2.1 0.0 1.0
F2 A:9WP103 2.1 0.0 1.0
C11 A:9WP103 2.5 0.0 1.0
H16 A:9WP103 2.7 0.0 1.0
C16 A:9WP103 2.9 0.0 1.0
C12 A:9WP103 3.7 0.0 1.0
H12 A:9WP103 4.1 0.0 1.0
H5' A:DG8 4.2 0.0 1.0
C15 A:9WP103 4.3 0.0 1.0
H1' A:DG7 4.5 0.0 1.0
H22 A:DG7 4.5 0.0 1.0
H4' A:DG8 4.7 0.0 1.0
N3 A:DG7 4.9 0.0 1.0
C13 A:9WP103 4.9 0.0 1.0
H15 A:9WP103 5.0 0.0 1.0
C5' A:DG8 5.0 0.0 1.0

Fluorine binding site 2 out of 6 in 5w77

Go back to Fluorine Binding Sites List in 5w77
Fluorine binding site 2 out of 6 in the Complex of Dna and Compounds


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Complex of Dna and Compounds within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F103

b:0.0
occ:1.00
F2 A:9WP103 0.0 0.0 1.0
C17 A:9WP103 1.4 0.0 1.0
F1 A:9WP103 2.1 0.0 1.0
F3 A:9WP103 2.2 0.0 1.0
C11 A:9WP103 2.4 0.0 1.0
H12 A:9WP103 2.9 0.0 1.0
C12 A:9WP103 3.0 0.0 1.0
C16 A:9WP103 3.4 0.0 1.0
H16 A:9WP103 3.7 0.0 1.0
C13 A:9WP103 4.3 0.0 1.0
C15 A:9WP103 4.6 0.0 1.0
H13 A:9WP103 5.0 0.0 1.0
C14 A:9WP103 5.0 0.0 1.0

Fluorine binding site 3 out of 6 in 5w77

Go back to Fluorine Binding Sites List in 5w77
Fluorine binding site 3 out of 6 in the Complex of Dna and Compounds


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Complex of Dna and Compounds within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F103

b:0.0
occ:1.00
F3 A:9WP103 0.0 0.0 1.0
C17 A:9WP103 1.4 0.0 1.0
F1 A:9WP103 2.1 0.0 1.0
F2 A:9WP103 2.2 0.0 1.0
C11 A:9WP103 2.4 0.0 1.0
H12 A:9WP103 2.8 0.0 1.0
C12 A:9WP103 3.0 0.0 1.0
H22 A:DG7 3.3 0.0 1.0
C16 A:9WP103 3.5 0.0 1.0
H16 A:9WP103 3.8 0.0 1.0
N2 A:DG7 4.2 0.0 1.0
C13 A:9WP103 4.3 0.0 1.0
H4' A:DG8 4.4 0.0 1.0
C15 A:9WP103 4.7 0.0 1.0
H21 A:DG7 4.7 0.0 1.0
O4' A:DG8 4.7 0.0 1.0
N3 A:DG7 4.8 0.0 1.0
H5' A:DG8 4.9 0.0 1.0
C2 A:DG7 4.9 0.0 1.0
H13 A:9WP103 4.9 0.0 1.0
C14 A:9WP103 5.0 0.0 1.0

Fluorine binding site 4 out of 6 in 5w77

Go back to Fluorine Binding Sites List in 5w77
Fluorine binding site 4 out of 6 in the Complex of Dna and Compounds


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Complex of Dna and Compounds within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F104

b:0.0
occ:1.00
F1 A:9WP104 0.0 0.0 1.0
C17 A:9WP104 1.4 0.0 1.0
F3 A:9WP104 2.1 0.0 1.0
F2 A:9WP104 2.2 0.0 1.0
C11 A:9WP104 2.5 0.0 1.0
H16 A:9WP104 2.7 0.0 1.0
C16 A:9WP104 2.9 0.0 1.0
H22 A:DG18 3.0 0.0 1.0
N2 A:DG18 3.3 0.0 1.0
H21 A:DG18 3.4 0.0 1.0
C12 A:9WP104 3.7 0.0 1.0
N7 A:DG22 3.9 0.0 1.0
H8 A:DG22 3.9 0.0 1.0
H12 A:9WP104 4.1 0.0 1.0
C2 A:DG18 4.1 0.0 1.0
C8 A:DG22 4.2 0.0 1.0
H2'' A:DG21 4.3 0.0 1.0
C15 A:9WP104 4.3 0.0 1.0
H2' A:DG21 4.4 0.0 1.0
N3 A:DG18 4.5 0.0 1.0
C2' A:DG21 4.9 0.0 1.0
C13 A:9WP104 4.9 0.0 1.0
N1 A:DG18 4.9 0.0 1.0
H1 A:DG18 4.9 0.0 1.0
H15 A:9WP104 4.9 0.0 1.0

Fluorine binding site 5 out of 6 in 5w77

Go back to Fluorine Binding Sites List in 5w77
Fluorine binding site 5 out of 6 in the Complex of Dna and Compounds


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Complex of Dna and Compounds within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F104

b:0.0
occ:1.00
F2 A:9WP104 0.0 0.0 1.0
C17 A:9WP104 1.3 0.0 1.0
F1 A:9WP104 2.2 0.0 1.0
F3 A:9WP104 2.2 0.0 1.0
C11 A:9WP104 2.3 0.0 1.0
C12 A:9WP104 3.1 0.0 1.0
H12 A:9WP104 3.1 0.0 1.0
C16 A:9WP104 3.3 0.0 1.0
H16 A:9WP104 3.5 0.0 1.0
C13 A:9WP104 4.3 0.0 1.0
C15 A:9WP104 4.5 0.0 1.0
H22 A:DG18 4.6 0.0 1.0
N2 A:DG18 4.8 0.0 1.0
C14 A:9WP104 4.9 0.0 1.0

Fluorine binding site 6 out of 6 in 5w77

Go back to Fluorine Binding Sites List in 5w77
Fluorine binding site 6 out of 6 in the Complex of Dna and Compounds


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Complex of Dna and Compounds within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F104

b:0.0
occ:1.00
F3 A:9WP104 0.0 0.0 1.0
C17 A:9WP104 1.4 0.0 1.0
F1 A:9WP104 2.1 0.0 1.0
F2 A:9WP104 2.2 0.0 1.0
C11 A:9WP104 2.4 0.0 1.0
H12 A:9WP104 2.8 0.0 1.0
H22 A:DG18 2.8 0.0 1.0
C12 A:9WP104 2.9 0.0 1.0
N3 A:DG18 3.2 0.0 1.0
N2 A:DG18 3.2 0.0 1.0
C2 A:DG18 3.4 0.0 1.0
C16 A:9WP104 3.6 0.0 1.0
H21 A:DG18 3.8 0.0 1.0
H16 A:9WP104 4.0 0.0 1.0
H1' A:DG18 4.1 0.0 1.0
C4 A:DG18 4.1 0.0 1.0
C13 A:9WP104 4.3 0.0 1.0
N1 A:DG18 4.4 0.0 1.0
H2'' A:DG18 4.5 0.0 1.0
C15 A:9WP104 4.8 0.0 1.0
N9 A:DG18 4.8 0.0 1.0
C1' A:DG18 4.8 0.0 1.0
H1 A:DG18 4.8 0.0 1.0
H13 A:9WP104 4.9 0.0 1.0
H2' A:DG21 4.9 0.0 1.0

Reference:

D.R.Calabrese, X.Chen, E.C.Leon, S.M.Gaikwad, Z.Phyo, W.M.Hewitt, S.Alden, T.A.Hilimire, F.He, A.M.Michalowski, J.K.Simmons, L.B.Saunders, S.Zhang, D.Connors, K.J.Walters, B.A.Mock, J.S.Schneekloth Jr.. Chemical and Structural Studies Provide A Mechanistic Basis For Recognition of the Myc G-Quadruplex. Nat Commun V. 9 4229 2018.
ISSN: ESSN 2041-1723
PubMed: 30315240
DOI: 10.1038/S41467-018-06315-W
Page generated: Tue Jul 15 08:48:45 2025

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