Chlorine 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:

Fluorine

(F)

180 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 18;

Binding sites:

The binding sites of Chlorine 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 Chlorine atom.
In total 18 binding sites of Chlorine where determined in the Gag Ca-SP1 Immature Lattice Bound with Lenacapavir From Enveloped Virus Like Particles, PDB code: 9d6d:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Chlorine binding site 1 out of 18 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 Chlorine with other atoms in the Cl 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:Cl301 b:54.9 occ:1.00 CL47 A:QNG301 0.0 54.9 1.0 C10 A:QNG301 1.8 33.4 1.0 C11 A:QNG301 2.5 27.9 1.0 C09 A:QNG301 3.0 34.9 1.0 CG2 A:ILE73 3.3 17.9 1.0 N17 A:QNG301 3.4 44.0 1.0 OD1 A:ASN74 3.4 37.4 1.0 C16 A:QNG301 3.6 37.2 1.0 C12 A:QNG301 3.9 26.7 1.0 CB A:ILE73 3.9 23.8 1.0 CG A:ASN74 4.0 35.6 1.0 C08 A:QNG301 4.1 33.1 1.0 CB A:ALA105 4.2 25.6 1.0 CG A:LYS70 4.3 35.2 1.0 ND2 A:ASN74 4.3 36.3 1.0 O A:LYS70 4.3 33.2 1.0 CG2 A:THR107 4.4 33.5 1.0 N A:ASN74 4.5 29.0 1.0 C07 A:QNG301 4.5 27.2 1.0 C A:ILE73 4.6 27.3 1.0 CD1 A:ILE73 4.8 18.4 1.0 CA A:ASN74 4.9 30.8 1.0 N15 A:QNG301 4.9 40.3 1.0 CA A:ILE73 4.9 27.2 1.0 S48 A:QNG301 5.0 49.2 1.0 CG1 A:ILE73 5.0 25.2 1.0 CD A:LYS70 5.0 38.6 1.0

Chlorine binding site 2 out of 18 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 Chlorine with other atoms in the Cl 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 B:Cl301 b:56.1 occ:1.00 CL47 B:QNG301 0.0 56.1 1.0 C10 B:QNG301 1.8 35.3 1.0 C11 B:QNG301 2.5 26.8 1.0 C09 B:QNG301 2.9 35.3 1.0 CG2 B:ILE73 3.3 21.6 1.0 N17 B:QNG301 3.4 48.2 1.0 ND2 B:ASN74 3.6 42.2 1.0 C16 B:QNG301 3.6 35.6 1.0 C12 B:QNG301 3.9 30.0 1.0 CB B:ILE73 3.9 25.8 1.0 CG B:ASN74 4.0 42.3 1.0 OD1 B:ASN74 4.1 42.7 1.0 C08 B:QNG301 4.1 36.9 1.0 CB B:ALA105 4.2 26.5 1.0 CG B:LYS70 4.3 35.4 1.0 CG2 B:THR107 4.3 34.0 1.0 O B:LYS70 4.3 36.8 1.0 N B:ASN74 4.5 35.9 1.0 C07 B:QNG301 4.5 30.4 1.0 C B:ILE73 4.7 35.0 1.0 CD1 B:ILE73 4.8 17.7 1.0 N15 B:QNG301 4.9 40.3 1.0 CA B:ASN74 4.9 34.1 1.0 CA B:ILE73 5.0 30.1 1.0 S48 B:QNG301 5.0 57.2 1.0 CG1 B:ILE73 5.0 26.1 1.0

Chlorine binding site 3 out of 18 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 Chlorine with other atoms in the Cl 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 C:Cl302 b:64.4 occ:1.00 CL47 C:QNG302 0.0 64.4 1.0 C10 C:QNG302 1.8 52.7 1.0 C11 C:QNG302 2.5 44.6 1.0 C09 C:QNG302 3.0 49.1 1.0 CG2 C:ILE73 3.4 29.9 1.0 N17 C:QNG302 3.4 60.0 1.0 OD1 C:ASN74 3.4 49.4 1.0 C16 C:QNG302 3.6 51.7 1.0 C12 C:QNG302 3.9 38.4 1.0 CB C:ILE73 3.9 35.4 1.0 CG C:ASN74 3.9 49.4 1.0 ND2 C:ASN74 4.1 46.3 1.0 C08 C:QNG302 4.1 47.7 1.0 CG C:LYS70 4.2 47.7 1.0 O C:LYS70 4.3 39.3 1.0 CB C:ALA105 4.3 35.7 1.0 CG2 C:THR107 4.4 43.5 1.0 N C:ASN74 4.4 38.9 1.0 C07 C:QNG302 4.5 42.7 1.0 C C:ILE73 4.7 38.5 1.0 CD1 C:ILE73 4.8 28.6 1.0 CA C:ASN74 4.9 37.5 1.0 N15 C:QNG302 4.9 54.7 1.0 CA C:ILE73 4.9 38.9 1.0 CD C:LYS70 4.9 53.2 1.0 CA C:LYS70 5.0 39.7 1.0 S48 C:QNG302 5.0 67.0 1.0 CG1 C:ILE73 5.0 35.0 1.0

Chlorine binding site 4 out of 18 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 Chlorine with other atoms in the Cl 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 D:Cl402 b:53.9 occ:1.00 CL47 D:QNG402 0.0 53.9 1.0 C10 D:QNG402 1.8 33.9 1.0 C11 D:QNG402 2.5 25.6 1.0 C09 D:QNG402 2.9 33.0 1.0 CG2 D:ILE73 3.4 17.1 1.0 N17 D:QNG402 3.4 42.6 1.0 ND2 D:ASN74 3.5 35.5 1.0 C16 D:QNG402 3.6 37.2 1.0 C12 D:QNG402 3.9 25.9 1.0 CB D:ILE73 4.0 24.0 1.0 CG D:ASN74 4.0 35.9 1.0 OD1 D:ASN74 4.1 37.9 1.0 C08 D:QNG402 4.1 33.1 1.0 CG D:LYS70 4.2 33.6 1.0 CB D:ALA105 4.2 23.8 1.0 CG2 D:THR107 4.3 33.3 1.0 O D:LYS70 4.4 34.5 1.0 N D:ASN74 4.5 30.4 1.0 C07 D:QNG402 4.5 27.2 1.0 C D:ILE73 4.7 28.7 1.0 CD1 D:ILE73 4.9 18.0 1.0 CA D:ASN74 4.9 31.2 1.0 N15 D:QNG402 4.9 40.8 1.0 CD D:LYS70 4.9 39.1 1.0 S48 D:QNG402 5.0 51.3 1.0 CA D:ILE73 5.0 27.3 1.0

Chlorine binding site 5 out of 18 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 Chlorine with other atoms in the Cl 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 E:Cl301 b:59.2 occ:1.00 CL47 E:QNG301 0.0 59.2 1.0 C10 E:QNG301 1.8 35.1 1.0 C11 E:QNG301 2.5 29.3 1.0 C09 E:QNG301 3.0 36.9 1.0 CG2 E:ILE73 3.4 21.5 1.0 N17 E:QNG301 3.4 49.6 1.0 ND2 E:ASN74 3.6 42.5 1.0 C16 E:QNG301 3.6 39.0 1.0 C12 E:QNG301 3.9 30.6 1.0 CB E:ILE73 4.0 26.6 1.0 CG E:ASN74 4.0 43.0 1.0 OD1 E:ASN74 4.1 46.3 1.0 C08 E:QNG301 4.1 38.3 1.0 CB E:ALA105 4.2 28.5 1.0 CG E:LYS70 4.3 36.8 1.0 CG2 E:THR107 4.3 36.3 1.0 O E:LYS70 4.4 37.1 1.0 C07 E:QNG301 4.5 31.6 1.0 N E:ASN74 4.5 34.1 1.0 C E:ILE73 4.7 33.8 1.0 CD1 E:ILE73 4.8 18.6 1.0 N15 E:QNG301 4.9 42.4 1.0 CA E:ASN74 4.9 34.6 1.0 CA E:ILE73 5.0 30.8 1.0 S48 E:QNG301 5.0 57.0 1.0

Chlorine binding site 6 out of 18 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 Chlorine with other atoms in the Cl 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 F:Cl301 b:61.9 occ:1.00 CL47 F:QNG301 0.0 61.9 1.0 C10 F:QNG301 1.8 49.3 1.0 C11 F:QNG301 2.5 43.4 1.0 C09 F:QNG301 2.9 48.2 1.0 N17 F:QNG301 3.4 58.4 1.0 CG2 F:ILE73 3.4 27.9 1.0 OD1 F:ASN74 3.5 48.7 1.0 C16 F:QNG301 3.6 51.9 1.0 C12 F:QNG301 3.9 37.7 1.0 CB F:ILE73 3.9 34.7 1.0 CG F:ASN74 4.0 50.0 1.0 C08 F:QNG301 4.1 47.6 1.0 ND2 F:ASN74 4.2 49.5 1.0 CG F:LYS70 4.2 45.8 1.0 O F:LYS70 4.3 40.3 1.0 CB F:ALA105 4.3 37.0 1.0 CG2 F:THR107 4.4 43.0 1.0 N F:ASN74 4.5 38.9 1.0 C07 F:QNG301 4.5 42.7 1.0 C F:ILE73 4.7 38.0 1.0 CD1 F:ILE73 4.8 26.4 1.0 CA F:ASN74 4.9 37.7 1.0 N15 F:QNG301 4.9 55.9 1.0 CA F:ILE73 4.9 37.9 1.0 CA F:LYS70 5.0 38.9 1.0 S48 F:QNG301 5.0 63.2 1.0 CD F:LYS70 5.0 51.9 1.0

Chlorine binding site 7 out of 18 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 Chlorine with other atoms in the Cl 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 G:Cl301 b:54.7 occ:1.00 CL47 G:QNG301 0.0 54.7 1.0 C10 G:QNG301 1.8 33.3 1.0 C11 G:QNG301 2.5 27.0 1.0 C09 G:QNG301 2.9 33.2 1.0 CG2 G:ILE73 3.4 17.8 1.0 N17 G:QNG301 3.4 42.8 1.0 C16 G:QNG301 3.6 37.6 1.0 ND2 G:ASN74 3.7 35.2 1.0 C12 G:QNG301 3.9 25.5 1.0 CB G:ILE73 4.0 23.3 1.0 CG G:LYS70 4.1 34.0 1.0 CG G:ASN74 4.1 36.1 1.0 C08 G:QNG301 4.1 34.0 1.0 OD1 G:ASN74 4.2 39.1 1.0 CB G:ALA105 4.2 25.7 1.0 O G:LYS70 4.3 33.9 1.0 CG2 G:THR107 4.4 35.4 1.0 C07 G:QNG301 4.5 26.2 1.0 N G:ASN74 4.5 28.9 1.0 C G:ILE73 4.7 27.9 1.0 CD1 G:ILE73 4.8 18.8 1.0 CD G:LYS70 4.8 37.7 1.0 N15 G:QNG301 4.9 41.2 1.0 CA G:ASN74 4.9 31.2 1.0 CA G:ILE73 5.0 26.9 1.0 S48 G:QNG301 5.0 50.9 1.0

Chlorine binding site 8 out of 18 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 Chlorine with other atoms in the Cl 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 H:Cl301 b:57.0 occ:1.00 CL47 H:QNG301 0.0 57.0 1.0 C10 H:QNG301 1.8 35.2 1.0 C11 H:QNG301 2.5 27.3 1.0 C09 H:QNG301 3.0 35.5 1.0 CG2 H:ILE73 3.4 21.9 1.0 N17 H:QNG301 3.4 47.7 1.0 ND2 H:ASN74 3.5 41.7 1.0 C16 H:QNG301 3.6 36.5 1.0 C12 H:QNG301 3.9 28.7 1.0 CB H:ILE73 3.9 27.0 1.0 CG H:ASN74 4.0 41.8 1.0 OD1 H:ASN74 4.0 45.5 1.0 C08 H:QNG301 4.1 35.4 1.0 CG H:LYS70 4.3 34.3 1.0 CB H:ALA105 4.3 28.4 1.0 O H:LYS70 4.3 37.1 1.0 CG2 H:THR107 4.4 36.0 1.0 N H:ASN74 4.5 36.0 1.0 C07 H:QNG301 4.5 30.1 1.0 C H:ILE73 4.7 34.5 1.0 CD1 H:ILE73 4.8 18.7 1.0 CA H:ASN74 4.9 36.2 1.0 N15 H:QNG301 4.9 38.8 1.0 CA H:ILE73 4.9 31.2 1.0 S48 H:QNG301 5.0 57.6 1.0 CG1 H:ILE73 5.0 26.9 1.0

Chlorine binding site 9 out of 18 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 Chlorine with other atoms in the Cl 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 I:Cl402 b:67.2 occ:1.00 CL47 I:QNG402 0.0 67.2 1.0 C10 I:QNG402 1.8 53.2 1.0 C11 I:QNG402 2.5 45.6 1.0 C09 I:QNG402 3.0 52.7 1.0 CG2 I:ILE73 3.4 30.8 1.0 N17 I:QNG402 3.4 61.6 1.0 ND2 I:ASN74 3.6 44.7 1.0 C16 I:QNG402 3.6 54.0 1.0 C12 I:QNG402 3.9 40.2 1.0 CB I:ILE73 3.9 35.4 1.0 CG I:ASN74 4.0 48.1 1.0 OD1 I:ASN74 4.1 53.0 1.0 C08 I:QNG402 4.1 51.4 1.0 CG I:LYS70 4.2 46.2 1.0 CB I:ALA105 4.2 36.1 1.0 O I:LYS70 4.3 41.8 1.0 CG2 I:THR107 4.4 46.8 1.0 N I:ASN74 4.5 40.2 1.0 C07 I:QNG402 4.5 45.7 1.0 C I:ILE73 4.7 39.9 1.0 CD1 I:ILE73 4.8 28.2 1.0 N15 I:QNG402 4.9 55.9 1.0 CA I:ILE73 4.9 39.1 1.0 CA I:ASN74 4.9 40.4 1.0 CG1 I:ILE73 4.9 37.8 1.0 CA I:LYS70 5.0 40.2 1.0 CD I:LYS70 5.0 53.7 1.0 S48 I:QNG402 5.0 70.0 1.0

Chlorine binding site 10 out of 18 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 Chlorine with other atoms in the Cl 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 J:Cl301 b:54.8 occ:1.00 CL47 J:QNG301 0.0 54.8 1.0 C10 J:QNG301 1.8 33.8 1.0 C11 J:QNG301 2.5 27.9 1.0 C09 J:QNG301 2.9 35.0 1.0 CG2 J:ILE73 3.3 18.0 1.0 N17 J:QNG301 3.4 43.4 1.0 ND2 J:ASN74 3.4 35.1 1.0 C16 J:QNG301 3.6 37.4 1.0 C12 J:QNG301 3.9 26.6 1.0 CB J:ILE73 3.9 23.2 1.0 CG J:ASN74 4.0 37.2 1.0 C08 J:QNG301 4.1 32.9 1.0 CG J:LYS70 4.1 34.6 1.0 OD1 J:ASN74 4.2 39.9 1.0 CB J:ALA105 4.2 26.4 1.0 O J:LYS70 4.3 34.0 1.0 CG2 J:THR107 4.4 33.4 1.0 N J:ASN74 4.5 29.6 1.0 C07 J:QNG301 4.5 26.4 1.0 C J:ILE73 4.6 28.1 1.0 CA J:ASN74 4.9 31.1 1.0 CD1 J:ILE73 4.9 18.6 1.0 N15 J:QNG301 4.9 40.4 1.0 CD J:LYS70 4.9 38.0 1.0 CA J:ILE73 4.9 27.4 1.0 S48 J:QNG301 5.0 48.3 1.0

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