Fluorine in PDB 8y1i: Structure of Guanosine-2''-Fluorinated [D(Aaccggtt)]2

The binding sites of Fluorine atom in the Structure of Guanosine-2''-Fluorinated [D(Aaccggtt)]2 (pdb code 8y1i). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Structure of Guanosine-2''-Fluorinated [D(Aaccggtt)]2, PDB code: 8y1i:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in the Structure of Guanosine-2''-Fluorinated [D(Aaccggtt)]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 Guanosine-2''-Fluorinated [D(Aaccggtt)]2 within 5.0Å range: probe atom residue distance (Å) B Occ A:F5 b:0.0 occ:1.00 F A:GF25 0.0 0.0 1.0 C2' A:GF25 1.4 0.0 1.0 H2' A:GF25 2.1 0.0 1.0 H5' A:GF26 2.3 0.0 1.0 C3' A:GF25 2.4 0.0 1.0 C1' A:GF25 2.4 0.0 1.0 H1' A:GF25 2.5 0.0 1.0 O3' A:GF25 2.6 0.0 1.0 H4' A:GF25 2.9 0.0 1.0 C4' A:GF25 3.0 0.0 1.0 O4' A:GF25 3.0 0.0 1.0 C5' A:GF26 3.2 0.0 1.0 H3' A:GF25 3.3 0.0 1.0 O4' A:GF26 3.3 0.0 1.0 O5' A:GF26 3.4 0.0 1.0 N9 A:GF25 3.7 0.0 1.0 C4' A:GF26 3.7 0.0 1.0 P A:GF26 3.8 0.0 1.0 H4' A:GF26 3.9 0.0 1.0 H8 A:GF26 4.0 0.0 1.0 H5'A A:GF26 4.1 0.0 1.0 C5' A:GF25 4.5 0.0 1.0 C8 A:GF26 4.5 0.0 1.0 C4 A:GF25 4.5 0.0 1.0 C8 A:GF25 4.6 0.0 1.0 C1' A:GF26 4.6 0.0 1.0 H8 A:GF25 4.6 0.0 1.0 OP1 A:GF26 4.6 0.0 1.0 OP2 A:GF26 4.7 0.0 1.0 N3 A:GF25 4.7 0.0 1.0 N9 A:GF26 4.7 0.0 1.0 H5'A A:GF25 4.9 0.0 1.0

Fluorine binding site 2 out of 4 in the Structure of Guanosine-2''-Fluorinated [D(Aaccggtt)]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 Guanosine-2''-Fluorinated [D(Aaccggtt)]2 within 5.0Å range: probe atom residue distance (Å) B Occ A:F6 b:0.0 occ:1.00 F A:GF26 0.0 0.0 1.0 C2' A:GF26 1.4 0.0 1.0 H2' A:GF26 2.1 0.0 1.0 O5' A:DT7 2.3 0.0 1.0 H6 A:DT7 2.4 0.0 1.0 C1' A:GF26 2.4 0.0 1.0 C3' A:GF26 2.4 0.0 1.0 H1' A:GF26 2.4 0.0 1.0 O3' A:GF26 2.5 0.0 1.0 H5' A:DT7 2.6 0.0 1.0 O4' A:DT7 2.6 0.0 1.0 C5' A:DT7 2.8 0.0 1.0 P A:DT7 2.9 0.0 1.0 C6 A:DT7 3.0 0.0 1.0 H3' A:GF26 3.0 0.0 1.0 H72 A:DT7 3.2 0.0 1.0 C4' A:DT7 3.3 0.0 1.0 N9 A:GF26 3.3 0.0 1.0 OP2 A:DT7 3.4 0.0 1.0 O4' A:GF26 3.5 0.0 1.0 C4' A:GF26 3.5 0.0 1.0 N1 A:DT7 3.6 0.0 1.0 C1' A:DT7 3.7 0.0 1.0 C5 A:DT7 3.8 0.0 1.0 H5'' A:DT7 3.9 0.0 1.0 C4 A:GF26 3.9 0.0 1.0 N3 A:GF26 4.0 0.0 1.0 C7 A:DT7 4.0 0.0 1.0 H3' A:DT7 4.0 0.0 1.0 H4' A:GF26 4.1 0.0 1.0 H4' A:DT7 4.1 0.0 1.0 C3' A:DT7 4.1 0.0 1.0 OP1 A:DT7 4.2 0.0 1.0 C8 A:GF26 4.3 0.0 1.0 H1' A:DT7 4.5 0.0 1.0 C2' A:DT7 4.5 0.0 1.0 H8 A:GF26 4.6 0.0 1.0 H71 A:DT7 4.7 0.0 1.0 H2' A:DT7 4.7 0.0 1.0 C5' A:GF26 4.7 0.0 1.0 H73 A:DT7 4.7 0.0 1.0 C2 A:DT7 4.8 0.0 1.0 O5' A:GF26 4.8 0.0 1.0 C4 A:DT7 5.0 0.0 1.0

Fluorine binding site 3 out of 4 in the Structure of Guanosine-2''-Fluorinated [D(Aaccggtt)]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 Guanosine-2''-Fluorinated [D(Aaccggtt)]2 within 5.0Å range: probe atom residue distance (Å) B Occ B:F13 b:0.0 occ:1.00 F B:GF213 0.0 0.0 1.0 C2' B:GF213 1.4 0.0 1.0 H2' B:GF213 2.1 0.0 1.0 H5' B:GF214 2.3 0.0 1.0 C1' B:GF213 2.4 0.0 1.0 C3' B:GF213 2.4 0.0 1.0 H1' B:GF213 2.5 0.0 1.0 O3' B:GF213 2.6 0.0 1.0 H4' B:GF213 2.9 0.0 1.0 C4' B:GF213 3.0 0.0 1.0 O4' B:GF213 3.0 0.0 1.0 C5' B:GF214 3.3 0.0 1.0 H3' B:GF213 3.3 0.0 1.0 O4' B:GF214 3.5 0.0 1.0 O5' B:GF214 3.5 0.0 1.0 N9 B:GF213 3.7 0.0 1.0 P B:GF214 3.8 0.0 1.0 C4' B:GF214 3.9 0.0 1.0 H8 B:GF214 4.0 0.0 1.0 H4' B:GF214 4.1 0.0 1.0 H5'A B:GF214 4.1 0.0 1.0 C5' B:GF213 4.5 0.0 1.0 C8 B:GF214 4.5 0.0 1.0 C4 B:GF213 4.5 0.0 1.0 C8 B:GF213 4.6 0.0 1.0 N3 B:GF213 4.6 0.0 1.0 OP1 B:GF214 4.7 0.0 1.0 H8 B:GF213 4.7 0.0 1.0 OP2 B:GF214 4.7 0.0 1.0 C1' B:GF214 4.7 0.0 1.0 N9 B:GF214 4.8 0.0 1.0 H5'A B:GF213 4.8 0.0 1.0

Fluorine binding site 4 out of 4 in the Structure of Guanosine-2''-Fluorinated [D(Aaccggtt)]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 Guanosine-2''-Fluorinated [D(Aaccggtt)]2 within 5.0Å range: probe atom residue distance (Å) B Occ B:F14 b:0.0 occ:1.00 F B:GF214 0.0 0.0 1.0 C2' B:GF214 1.4 0.0 1.0 H2' B:GF214 2.1 0.0 1.0 O5' B:DT15 2.4 0.0 1.0 H6 B:DT15 2.4 0.0 1.0 C1' B:GF214 2.4 0.0 1.0 C3' B:GF214 2.4 0.0 1.0 H1' B:GF214 2.4 0.0 1.0 O3' B:GF214 2.5 0.0 1.0 H5' B:DT15 2.8 0.0 1.0 O4' B:DT15 2.8 0.0 1.0 P B:DT15 2.9 0.0 1.0 C6 B:DT15 2.9 0.0 1.0 C5' B:DT15 3.0 0.0 1.0 H3' B:GF214 3.0 0.0 1.0 H72 B:DT15 3.0 0.0 1.0 OP2 B:DT15 3.3 0.0 1.0 N9 B:GF214 3.3 0.0 1.0 C4' B:DT15 3.4 0.0 1.0 O4' B:GF214 3.5 0.0 1.0 C4' B:GF214 3.5 0.0 1.0 N1 B:DT15 3.6 0.0 1.0 C5 B:DT15 3.6 0.0 1.0 C1' B:DT15 3.8 0.0 1.0 C7 B:DT15 3.8 0.0 1.0 C4 B:GF214 3.9 0.0 1.0 N3 B:GF214 3.9 0.0 1.0 H5'' B:DT15 4.0 0.0 1.0 H3' B:DT15 4.1 0.0 1.0 H4' B:GF214 4.1 0.0 1.0 OP1 B:DT15 4.3 0.0 1.0 C3' B:DT15 4.3 0.0 1.0 C8 B:GF214 4.3 0.0 1.0 H4' B:DT15 4.3 0.0 1.0 H71 B:DT15 4.5 0.0 1.0 H8 B:GF214 4.5 0.0 1.0 H73 B:DT15 4.6 0.0 1.0 C2' B:DT15 4.6 0.0 1.0 H1' B:DT15 4.6 0.0 1.0 C5' B:GF214 4.7 0.0 1.0 C2 B:DT15 4.7 0.0 1.0 H2' B:DT15 4.8 0.0 1.0 O5' B:GF214 4.8 0.0 1.0 C4 B:DT15 4.8 0.0 1.0

R.Q.Gao, X.D.Hu, Q.Zhou, X.F.Hou, C.Cao, G.L.Tang. Different Dna Binding and Damage Mode Between Anticancer Antibiotics Trioxacarcin A and Ll-D49194 Alpha 1 Jacs Au V. 4 3641 2024.
ISSN: ESSN 2691-3704
DOI: 10.1021/JACSAU.4C00611