Fluorine in PDB 9d6d: Gag Ca-SP1 Immature Lattice Bound with Lenacapavir From Enveloped Virus Like Particles

The structure of Gag Ca-SP1 Immature Lattice Bound with Lenacapavir From Enveloped Virus Like Particles also contains other interesting chemical elements:

Chlorine

(Cl)

18 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 40; Page 5, Binding sites: 41 - 50; Page 6, Binding sites: 51 - 60; Page 7, Binding sites: 61 - 70; Page 8, Binding sites: 71 - 80; Page 9, Binding sites: 81 - 90; Page 10, Binding sites: 91 - 100; Page 11, Binding sites: 101 - 110; Page 12, Binding sites: 111 - 120; Page 13, Binding sites: 121 - 130; Page 14, Binding sites: 131 - 140; Page 15, Binding sites: 141 - 150; Page 16, Binding sites: 151 - 160; Page 17, Binding sites: 161 - 170; Page 18, Binding sites: 171 - 180;

Binding sites:

The binding sites of Fluorine atom in the Gag Ca-SP1 Immature Lattice Bound with Lenacapavir From Enveloped Virus Like Particles (pdb code 9d6d). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 180 binding sites of Fluorine where determined in the Gag Ca-SP1 Immature Lattice Bound with Lenacapavir From Enveloped Virus Like Particles, PDB code: 9d6d:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 180 in the Gag Ca-SP1 Immature Lattice Bound with Lenacapavir From Enveloped Virus Like Particles


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Gag Ca-SP1 Immature Lattice Bound with Lenacapavir From Enveloped Virus Like Particles within 5.0Å range: probe atom residue distance (Å) B Occ A:F301 b:35.7 occ:1.00 F26 A:QNG301 0.0 35.7 1.0 C24 A:QNG301 1.4 21.8 1.0 C25 A:QNG301 2.4 19.7 1.0 C23 A:QNG301 2.4 23.9 1.0 CA A:LYS70 3.2 28.1 1.0 CD1 A:ILE73 3.2 18.4 1.0 N A:LYS70 3.3 25.9 1.0 CB A:LYS70 3.4 29.7 1.0 C20 A:QNG301 3.6 23.6 1.0 C22 A:QNG301 3.6 23.6 1.0 CG A:LEU69 3.7 23.1 1.0 C A:LEU69 3.7 24.9 1.0 O A:LEU69 4.0 27.7 1.0 CD2 A:LEU69 4.1 28.0 1.0 O A:MET66 4.1 30.6 0.9 O A:MET66 4.1 30.2 0.1 CG A:LYS70 4.1 35.2 1.0 C21 A:QNG301 4.1 22.6 1.0 CG1 A:ILE73 4.3 25.2 1.0 CB A:LEU69 4.3 23.7 1.0 CE A:LYS70 4.3 32.2 1.0 CD1 A:LEU56 4.3 18.0 1.0 C A:LYS70 4.6 30.4 1.0 CA A:LEU69 4.6 25.5 1.0 CB A:ILE73 4.7 23.8 1.0 F27 A:QNG301 4.8 31.4 1.0 CD1 A:LEU69 4.8 21.4 1.0 C11 A:QNG301 4.8 27.9 1.0 CD A:LYS70 4.8 38.6 1.0 C19 A:QNG301 4.9 21.9 1.0 F53 A:QNG301 4.9 39.2 1.0 O A:LYS70 5.0 33.2 1.0

Fluorine binding site 2 out of 180 in the Gag Ca-SP1 Immature Lattice Bound with Lenacapavir From Enveloped Virus Like Particles


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Gag Ca-SP1 Immature Lattice Bound with Lenacapavir From Enveloped Virus Like Particles within 5.0Å range: probe atom residue distance (Å) B Occ A:F301 b:31.4 occ:1.00 F27 A:QNG301 0.0 31.4 1.0 C22 A:QNG301 1.4 23.6 1.0 C21 A:QNG301 2.4 22.6 1.0 C23 A:QNG301 2.4 23.9 1.0 CB A:MET66 3.2 25.4 0.9 CB A:MET66 3.2 27.1 0.1 SD A:MET66 3.2 26.2 0.1 CE A:MET66 3.2 20.3 0.9 C31 A:QNG301 3.3 30.1 1.0 CG A:MET66 3.4 26.9 0.1 C36 A:QNG301 3.4 34.2 1.0 F53 A:QNG301 3.5 39.2 1.0 CG A:MET66 3.5 26.7 0.9 C35 A:QNG301 3.6 32.7 1.0 C20 A:QNG301 3.6 23.6 1.0 C24 A:QNG301 3.6 21.8 1.0 C32 A:QNG301 3.7 31.9 1.0 O A:LEU56 3.8 24.4 1.0 C37 A:QNG301 3.8 39.0 1.0 C40 A:QNG301 4.1 37.5 1.0 F41 A:QNG301 4.1 38.3 1.0 N34 A:QNG301 4.1 37.5 1.0 C25 A:QNG301 4.1 19.7 1.0 C38 A:QNG301 4.1 37.0 1.0 N33 A:QNG301 4.2 30.8 1.0 SD A:MET66 4.2 33.2 0.9 CA A:MET66 4.3 28.2 0.1 CA A:MET66 4.3 28.4 0.9 O A:MET66 4.5 30.6 0.9 O A:MET66 4.5 30.2 0.1 F52 A:QNG301 4.5 44.3 1.0 C A:LEU56 4.6 21.7 1.0 C A:MET66 4.6 28.6 0.9 C A:MET66 4.6 28.0 0.1 C39 A:QNG301 4.7 42.3 1.0 F26 A:QNG301 4.8 35.7 1.0 CE A:MET66 4.8 27.4 0.1 CB A:LEU56 4.8 21.7 1.0 C19 A:QNG301 4.9 21.9 1.0

Fluorine binding site 3 out of 180 in the Gag Ca-SP1 Immature Lattice Bound with Lenacapavir From Enveloped Virus Like Particles


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Gag Ca-SP1 Immature Lattice Bound with Lenacapavir From Enveloped Virus Like Particles within 5.0Å range: probe atom residue distance (Å) B Occ A:F301 b:38.3 occ:1.00 F41 A:QNG301 0.0 38.3 1.0 C38 A:QNG301 1.4 37.0 1.0 F42 A:QNG301 2.2 40.8 1.0 C37 A:QNG301 2.3 39.0 1.0 C32 A:QNG301 2.4 31.9 1.0 OD1 A:ASN57 3.0 26.9 1.0 N33 A:QNG301 3.3 30.8 1.0 C31 A:QNG301 3.4 30.1 1.0 C36 A:QNG301 3.4 34.2 1.0 CA A:ASN57 3.5 22.9 1.0 C30 A:QNG301 3.6 27.7 1.0 CB B:ASN21 3.6 18.2 1.0 CG B:ASN21 3.7 20.4 1.0 ND2 B:ASN21 3.7 23.5 1.0 O A:ASN57 3.7 30.6 1.0 C39 A:QNG301 3.8 42.3 1.0 CG A:ASN57 3.8 20.1 1.0 CB A:ASN57 3.8 20.4 1.0 C A:ASN57 4.1 23.7 1.0 O B:PRO17 4.1 32.4 1.0 F27 A:QNG301 4.1 31.4 1.0 C21 A:QNG301 4.2 22.6 1.0 N43 A:QNG301 4.2 24.9 1.0 OD1 B:ASN21 4.3 27.9 1.0 C28 A:QNG301 4.4 26.4 1.0 N34 A:QNG301 4.4 37.5 1.0 O A:LEU56 4.5 24.4 1.0 C35 A:QNG301 4.5 32.7 1.0 N A:ASN57 4.6 22.6 1.0 C B:PRO17 4.6 24.7 1.0 C22 A:QNG301 4.7 23.6 1.0 CB B:PRO17 4.9 25.3 1.0 CA B:ASN21 4.9 21.1 1.0 C A:LEU56 4.9 21.7 1.0

Fluorine binding site 4 out of 180 in the Gag Ca-SP1 Immature Lattice Bound with Lenacapavir From Enveloped Virus Like Particles


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Gag Ca-SP1 Immature Lattice Bound with Lenacapavir From Enveloped Virus Like Particles within 5.0Å range: probe atom residue distance (Å) B Occ A:F301 b:40.8 occ:1.00 F42 A:QNG301 0.0 40.8 1.0 C38 A:QNG301 1.4 37.0 1.0 F41 A:QNG301 2.2 38.3 1.0 C37 A:QNG301 2.3 39.0 1.0 C32 A:QNG301 2.4 31.9 1.0 C39 A:QNG301 3.0 42.3 1.0 CB B:ASN21 3.2 18.2 1.0 C36 A:QNG301 3.2 34.2 1.0 C31 A:QNG301 3.3 30.1 1.0 N33 A:QNG301 3.3 30.8 1.0 CG B:ASN21 3.4 20.4 1.0 OD1 B:ASN21 3.5 27.9 1.0 NE B:ARG18 3.7 44.7 1.0 C30 A:QNG301 3.8 27.7 1.0 CD B:ARG18 4.1 34.1 1.0 ND2 B:ASN21 4.1 23.5 1.0 O B:PRO17 4.2 32.4 1.0 CA B:ARG18 4.2 24.7 1.0 CG B:ARG18 4.2 31.2 1.0 CZ B:ARG18 4.4 44.6 1.0 C35 A:QNG301 4.4 32.7 1.0 N34 A:QNG301 4.4 37.5 1.0 C B:PRO17 4.5 24.7 1.0 N B:ARG18 4.6 28.2 1.0 NH2 B:ARG18 4.6 39.1 1.0 CA B:ASN21 4.7 21.1 1.0 CB B:ARG18 4.8 26.9 1.0 OD1 A:ASN57 4.8 26.9 1.0

Fluorine binding site 5 out of 180 in the Gag Ca-SP1 Immature Lattice Bound with Lenacapavir From Enveloped Virus Like Particles


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Gag Ca-SP1 Immature Lattice Bound with Lenacapavir From Enveloped Virus Like Particles within 5.0Å range: probe atom residue distance (Å) B Occ A:F301 b:44.3 occ:1.00 F52 A:QNG301 0.0 44.3 1.0 C40 A:QNG301 1.4 37.5 1.0 F53 A:QNG301 2.2 39.2 1.0 F64 A:QNG301 2.2 50.0 1.0 C35 A:QNG301 2.4 32.7 1.0 C31 A:QNG301 2.9 30.1 1.0 C36 A:QNG301 3.2 34.2 1.0 NE2 A:GLN63 3.4 52.6 1.0 CD A:GLN63 3.6 53.6 1.0 N34 A:QNG301 3.6 37.5 1.0 OE1 A:GLN67 3.7 54.5 1.0 O A:GLN63 3.8 34.3 1.0 N A:GLN67 4.0 28.5 1.0 CG A:GLN63 4.0 43.9 1.0 CB A:MET66 4.0 27.1 0.1 CB A:MET66 4.1 25.4 0.9 OE1 A:GLN63 4.1 53.0 1.0 C32 A:QNG301 4.2 31.9 1.0 C39 A:QNG301 4.2 42.3 1.0 CA A:GLN67 4.3 30.0 1.0 C A:MET66 4.3 28.6 0.9 C A:MET66 4.3 28.0 0.1 CB A:GLN67 4.4 33.4 1.0 NH2 B:ARG18 4.5 39.1 1.0 F27 A:QNG301 4.5 31.4 1.0 N33 A:QNG301 4.6 30.8 1.0 CD A:GLN67 4.6 52.1 1.0 C A:GLN63 4.6 32.1 1.0 O A:MET66 4.7 30.6 0.9 O A:MET66 4.7 30.2 0.1 C37 A:QNG301 4.7 39.0 1.0 CA A:GLN63 4.7 32.6 1.0 CA A:MET66 4.8 28.2 0.1 CA A:MET66 4.8 28.4 0.9 CB A:GLN63 4.8 37.9 1.0

Fluorine binding site 6 out of 180 in the Gag Ca-SP1 Immature Lattice Bound with Lenacapavir From Enveloped Virus Like Particles


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Gag Ca-SP1 Immature Lattice Bound with Lenacapavir From Enveloped Virus Like Particles within 5.0Å range: probe atom residue distance (Å) B Occ A:F301 b:39.2 occ:1.00 F53 A:QNG301 0.0 39.2 1.0 C40 A:QNG301 1.4 37.5 1.0 F52 A:QNG301 2.2 44.3 1.0 F64 A:QNG301 2.2 50.0 1.0 C35 A:QNG301 2.4 32.7 1.0 O A:MET66 3.1 30.6 0.9 O A:MET66 3.1 30.2 0.1 C A:MET66 3.2 28.6 0.9 C A:MET66 3.2 28.0 0.1 N34 A:QNG301 3.2 37.5 1.0 C31 A:QNG301 3.3 30.1 1.0 N A:GLN67 3.4 28.5 1.0 F27 A:QNG301 3.5 31.4 1.0 C23 A:QNG301 3.5 23.9 1.0 CB A:MET66 3.6 27.1 0.1 CB A:MET66 3.6 25.4 0.9 CA A:GLN67 3.7 30.0 1.0 C22 A:QNG301 3.7 23.6 1.0 CE A:LYS70 3.8 32.2 1.0 OE1 A:GLN67 3.9 54.5 1.0 CA A:MET66 4.0 28.2 0.1 CA A:MET66 4.0 28.4 0.9 CB A:LYS70 4.1 29.7 1.0 C36 A:QNG301 4.1 34.2 1.0 CD A:LYS70 4.3 38.6 1.0 NZ A:LYS70 4.3 32.3 1.0 N33 A:QNG301 4.4 30.8 1.0 C32 A:QNG301 4.4 31.9 1.0 CD A:GLN67 4.5 52.1 1.0 C24 A:QNG301 4.5 21.8 1.0 CB A:GLN67 4.5 33.4 1.0 O A:GLN63 4.7 34.3 1.0 C21 A:QNG301 4.8 22.6 1.0 CG A:LYS70 4.8 35.2 1.0 C A:GLN67 4.8 32.4 1.0 F26 A:QNG301 4.9 35.7 1.0 CG A:MET66 4.9 26.9 0.1 NE2 A:GLN67 5.0 50.9 1.0

Fluorine binding site 7 out of 180 in the Gag Ca-SP1 Immature Lattice Bound with Lenacapavir From Enveloped Virus Like Particles


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Gag Ca-SP1 Immature Lattice Bound with Lenacapavir From Enveloped Virus Like Particles within 5.0Å range: probe atom residue distance (Å) B Occ A:F301 b:38.3 occ:1.00 F61 A:QNG301 0.0 38.3 1.0 C60 A:QNG301 1.4 37.9 1.0 F62 A:QNG301 2.2 46.8 1.0 F63 A:QNG301 2.2 51.8 1.0 C18 A:QNG301 2.4 30.0 1.0 N14 A:QNG301 2.6 32.8 1.0 C04 A:QNG301 3.0 26.8 1.0 C08 A:QNG301 3.1 33.1 1.0 NE D:ARG82 3.3 49.6 1.0 CD D:ARG82 3.3 51.0 1.0 N15 A:QNG301 3.4 40.3 1.0 C07 A:QNG301 3.4 27.2 1.0 CB A:THR107 3.5 37.1 1.0 C13 A:QNG301 3.5 22.6 1.0 CZ D:ARG82 3.5 48.5 1.0 CG2 A:THR107 3.6 33.5 1.0 CA A:THR107 3.7 36.4 1.0 C03 A:QNG301 3.7 25.8 1.0 NH1 D:ARG82 3.8 46.4 1.0 C09 A:QNG301 4.0 34.9 1.0 C16 A:QNG301 4.2 37.2 1.0 NH2 D:ARG82 4.2 48.6 1.0 C05 A:QNG301 4.5 19.7 1.0 O A:THR107 4.5 47.7 1.0 C12 A:QNG301 4.6 26.7 1.0 C A:THR107 4.6 38.9 1.0 C02 A:QNG301 4.7 25.5 1.0 N A:THR107 4.8 37.0 1.0 CG D:ARG82 4.8 46.7 1.0 OG1 A:THR107 4.8 45.9 1.0 OE1 D:GLU79 4.8 48.9 1.0

Fluorine binding site 8 out of 180 in the Gag Ca-SP1 Immature Lattice Bound with Lenacapavir From Enveloped Virus Like Particles


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Gag Ca-SP1 Immature Lattice Bound with Lenacapavir From Enveloped Virus Like Particles within 5.0Å range: probe atom residue distance (Å) B Occ A:F301 b:46.8 occ:1.00 F62 A:QNG301 0.0 46.8 1.0 C60 A:QNG301 1.4 37.9 1.0 F61 A:QNG301 2.2 38.3 1.0 F63 A:QNG301 2.2 51.8 1.0 C18 A:QNG301 2.4 30.0 1.0 OE1 D:GLU79 2.6 48.9 1.0 NE D:ARG82 2.7 49.6 1.0 CZ D:ARG82 3.2 48.5 1.0 NH2 D:ARG82 3.4 48.6 1.0 CD D:ARG82 3.4 51.0 1.0 CD D:GLU79 3.5 53.8 1.0 N14 A:QNG301 3.6 32.8 1.0 OE2 D:GLU79 3.7 53.6 1.0 C04 A:QNG301 4.0 26.8 1.0 NH1 D:ARG82 4.1 46.4 1.0 C03 A:QNG301 4.2 25.8 1.0 C13 A:QNG301 4.3 22.6 1.0 CG B:PRO17 4.4 31.3 1.0 N15 A:QNG301 4.4 40.3 1.0 C08 A:QNG301 4.5 33.1 1.0 C02 A:QNG301 4.6 25.5 1.0 C05 A:QNG301 4.7 19.7 1.0 C07 A:QNG301 4.7 27.2 1.0 CG D:ARG82 4.8 46.7 1.0 N06 A:QNG301 4.8 23.8 1.0 CG D:GLU79 4.9 44.3 1.0 O29 A:QNG301 5.0 34.1 1.0 CD B:PRO17 5.0 30.5 1.0

Fluorine binding site 9 out of 180 in the Gag Ca-SP1 Immature Lattice Bound with Lenacapavir From Enveloped Virus Like Particles


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 9 of Gag Ca-SP1 Immature Lattice Bound with Lenacapavir From Enveloped Virus Like Particles within 5.0Å range: probe atom residue distance (Å) B Occ A:F301 b:51.8 occ:1.00 F63 A:QNG301 0.0 51.8 1.0 C60 A:QNG301 1.4 37.9 1.0 F61 A:QNG301 2.2 38.3 1.0 F62 A:QNG301 2.2 46.8 1.0 C18 A:QNG301 2.4 30.0 1.0 N14 A:QNG301 3.1 32.8 1.0 CD D:ARG82 3.2 51.0 1.0 N15 A:QNG301 3.3 40.3 1.0 NE D:ARG82 3.5 49.6 1.0 OE1 D:GLU79 4.2 48.9 1.0 C08 A:QNG301 4.3 33.1 1.0 CZ D:ARG82 4.4 48.5 1.0 C16 A:QNG301 4.4 37.2 1.0 CG D:ARG82 4.5 46.7 1.0 CB D:ARG82 4.8 44.8 1.0 CB A:THR107 4.9 37.1 1.0 C09 A:QNG301 4.9 34.9 1.0

Fluorine binding site 10 out of 180 in the Gag Ca-SP1 Immature Lattice Bound with Lenacapavir From Enveloped Virus Like Particles


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 10 of Gag Ca-SP1 Immature Lattice Bound with Lenacapavir From Enveloped Virus Like Particles within 5.0Å range: probe atom residue distance (Å) B Occ A:F301 b:50.0 occ:1.00 F64 A:QNG301 0.0 50.0 1.0 C40 A:QNG301 1.4 37.5 1.0 F53 A:QNG301 2.2 39.2 1.0 F52 A:QNG301 2.2 44.3 1.0 C35 A:QNG301 2.4 32.7 1.0 OE1 A:GLN67 2.7 54.5 1.0 N34 A:QNG301 2.9 37.5 1.0 NZ A:LYS70 3.6 32.3 1.0 C31 A:QNG301 3.6 30.1 1.0 CE A:LYS70 3.7 32.2 1.0 CD A:GLN67 3.7 52.1 1.0 NH2 B:ARG18 3.9 39.1 1.0 CD A:LYS70 3.9 38.6 1.0 N33 A:QNG301 4.2 30.8 1.0 NE2 A:GLN67 4.3 50.9 1.0 CA A:GLN67 4.5 30.0 1.0 C32 A:QNG301 4.5 31.9 1.0 NE2 A:GLN63 4.6 52.6 1.0 C36 A:QNG301 4.7 34.2 1.0 CB A:GLN67 4.7 33.4 1.0 CG A:GLN67 4.8 45.3 1.0 N A:GLN67 4.8 28.5 1.0 CB A:LYS70 4.9 29.7 1.0 CZ B:ARG18 5.0 44.6 1.0 O A:MET66 5.0 30.6 0.9

C.Wu, M.E.Meuser, J.S.Rey, H.Meshkin, R.Yang, S.C.Devarkar, C.Freniere, J.Shi, C.Aiken, J.R.Perilla, Y.Xiong. Structural Insights Into Inhibitor Mechanisms on Immature Hiv-1 Gag Lattice Revealed By High-Resolution in Situ Single-Particle Cryo-Em. Biorxiv 2024.
ISSN: ISSN 2692-8205
PubMed: 39416065
DOI: 10.1101/2024.10.09.617473