Fluorine in PDB 7rj4: Co-Crystal Structure of Lenacapavir Bound to N74D Mutant of Disulfide Stabilized Hiv-1 Ca Hexamer

The structure of Co-Crystal Structure of Lenacapavir Bound to N74D Mutant of Disulfide Stabilized Hiv-1 Ca Hexamer, PDB code: 7rj4 was solved by S.M.Bester, M.Kvaratskhelia, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.32 / 3.32
Space group	P 6
Cell size a, b, c (Å), α, β, γ (°)	159.089, 159.089, 56.984, 90, 90, 120
R / Rfree (%)	27.8 / 33.1

The structure of Co-Crystal Structure of Lenacapavir Bound to N74D Mutant of Disulfide Stabilized Hiv-1 Ca Hexamer also contains other interesting chemical elements:

Chlorine	(Cl)	21 atoms
Iodine	(I)	3 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30;

Binding sites:

The binding sites of Fluorine atom in the Co-Crystal Structure of Lenacapavir Bound to N74D Mutant of Disulfide Stabilized Hiv-1 Ca Hexamer (pdb code 7rj4). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 30 binding sites of Fluorine where determined in the Co-Crystal Structure of Lenacapavir Bound to N74D Mutant of Disulfide Stabilized Hiv-1 Ca Hexamer, PDB code: 7rj4:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 30 in the Co-Crystal Structure of Lenacapavir Bound to N74D Mutant of Disulfide Stabilized Hiv-1 Ca Hexamer


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Co-Crystal Structure of Lenacapavir Bound to N74D Mutant of Disulfide Stabilized Hiv-1 Ca Hexamer within 5.0Å range: probe atom residue distance (Å) B Occ A:F301 b:77.4 occ:1.00 F26 A:QNG301 0.0 77.4 1.0 C24 A:QNG301 1.4 65.6 1.0 C23 A:QNG301 2.4 65.6 1.0 C25 A:QNG301 2.4 64.0 1.0 O A:MET66 2.8 82.2 1.0 N A:LYS70 2.9 82.3 1.0 CB A:LEU69 3.0 84.9 1.0 CG A:LYS70 3.1 82.6 1.0 C A:LEU69 3.3 87.9 1.0 CG A:LEU69 3.4 86.0 1.0 CA A:LYS70 3.4 86.3 1.0 C20 A:QNG301 3.7 70.8 1.0 CA A:LEU69 3.7 88.3 1.0 C22 A:QNG301 3.7 69.6 1.0 CB A:LYS70 3.7 86.6 1.0 CD2 A:LEU69 3.9 83.3 1.0 C A:MET66 3.9 80.9 1.0 O A:LEU69 4.0 91.8 1.0 C21 A:QNG301 4.2 71.0 1.0 CD1 A:ILE73 4.2 71.2 1.0 F42 A:QNG301 4.3 77.0 1.0 N A:LEU69 4.4 91.8 1.0 CD A:LYS70 4.4 83.9 1.0 CA A:MET66 4.5 81.5 1.0 F27 A:QNG301 4.8 64.0 1.0 CD1 A:LEU69 4.9 85.8 1.0 CB A:MET66 4.9 75.9 1.0 CD1 A:LEU56 4.9 62.0 1.0 C A:LYS70 4.9 86.5 1.0 C19 A:QNG301 4.9 72.7 1.0

Fluorine binding site 2 out of 30 in the Co-Crystal Structure of Lenacapavir Bound to N74D Mutant of Disulfide Stabilized Hiv-1 Ca Hexamer


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Co-Crystal Structure of Lenacapavir Bound to N74D Mutant of Disulfide Stabilized Hiv-1 Ca Hexamer within 5.0Å range: probe atom residue distance (Å) B Occ A:F301 b:64.0 occ:1.00 F27 A:QNG301 0.0 64.0 1.0 C22 A:QNG301 1.4 69.6 1.0 C21 A:QNG301 2.4 71.0 1.0 C23 A:QNG301 2.4 65.6 1.0 F41 A:QNG301 2.8 67.3 1.0 O A:LEU56 2.9 69.5 1.0 CE A:MET66 3.1 62.4 1.0 CG A:MET66 3.4 76.0 1.0 CB A:MET66 3.4 75.9 1.0 C A:LEU56 3.5 64.3 1.0 C20 A:QNG301 3.7 70.8 1.0 C24 A:QNG301 3.7 65.6 1.0 SD A:MET66 4.0 58.1 1.0 C38 A:QNG301 4.0 74.5 1.0 CB A:LEU56 4.0 65.5 1.0 F42 A:QNG301 4.1 77.0 1.0 C25 A:QNG301 4.2 64.0 1.0 N A:ASN57 4.2 63.0 1.0 OD1 A:ASN57 4.3 66.0 1.0 CA A:ASN57 4.3 62.6 1.0 CA A:LEU56 4.3 57.8 1.0 CA A:MET66 4.6 81.5 1.0 F26 A:QNG301 4.8 77.4 1.0 C37 A:QNG301 4.8 81.0 1.0 C19 A:QNG301 5.0 72.7 1.0 N43 A:QNG301 5.0 71.1 1.0 NE2 A:GLN63 5.0 86.5 1.0 O A:MET66 5.0 82.2 1.0

Fluorine binding site 3 out of 30 in the Co-Crystal Structure of Lenacapavir Bound to N74D Mutant of Disulfide Stabilized Hiv-1 Ca Hexamer


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Co-Crystal Structure of Lenacapavir Bound to N74D Mutant of Disulfide Stabilized Hiv-1 Ca Hexamer within 5.0Å range: probe atom residue distance (Å) B Occ A:F301 b:67.3 occ:1.00 F41 A:QNG301 0.0 67.3 1.0 C38 A:QNG301 1.4 74.5 1.0 F42 A:QNG301 2.3 77.0 1.0 C37 A:QNG301 2.4 81.0 1.0 C32 A:QNG301 2.4 75.1 1.0 F27 A:QNG301 2.8 64.0 1.0 C22 A:QNG301 3.0 69.6 1.0 N33 A:QNG301 3.2 78.7 1.0 C31 A:QNG301 3.4 79.0 1.0 C39 A:QNG301 3.4 81.1 1.0 C30 A:QNG301 3.5 73.8 1.0 C36 A:QNG301 3.5 83.3 1.0 C21 A:QNG301 3.5 71.0 1.0 C23 A:QNG301 3.6 65.6 1.0 OE1 A:GLN63 3.6 85.2 1.0 C28 A:QNG301 3.8 73.9 1.0 CB A:MET66 3.9 75.9 1.0 O29 A:QNG301 4.2 72.9 1.0 N43 A:QNG301 4.4 71.1 1.0 C20 A:QNG301 4.4 70.8 1.0 N34 A:QNG301 4.4 88.0 1.0 C24 A:QNG301 4.5 65.6 1.0 C35 A:QNG301 4.5 85.0 1.0 CD A:GLN63 4.5 86.8 1.0 OD1 A:ASN57 4.5 66.0 1.0 CG A:MET66 4.6 76.0 1.0 NE2 A:GLN63 4.8 86.5 1.0 C25 A:QNG301 4.8 64.0 1.0 O A:MET66 4.9 82.2 1.0 C A:MET66 4.9 80.9 1.0

Fluorine binding site 4 out of 30 in the Co-Crystal Structure of Lenacapavir Bound to N74D Mutant of Disulfide Stabilized Hiv-1 Ca Hexamer


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Co-Crystal Structure of Lenacapavir Bound to N74D Mutant of Disulfide Stabilized Hiv-1 Ca Hexamer within 5.0Å range: probe atom residue distance (Å) B Occ A:F301 b:77.0 occ:1.00 F42 A:QNG301 0.0 77.0 1.0 C38 A:QNG301 1.4 74.5 1.0 F41 A:QNG301 2.3 67.3 1.0 C32 A:QNG301 2.4 75.1 1.0 C37 A:QNG301 2.4 81.0 1.0 O29 A:QNG301 3.0 72.9 1.0 CE A:LYS70 3.2 91.7 1.0 CD A:LYS70 3.2 83.9 1.0 C28 A:QNG301 3.2 73.9 1.0 C36 A:QNG301 3.3 83.3 1.0 C31 A:QNG301 3.3 79.0 1.0 N33 A:QNG301 3.3 78.7 1.0 NZ A:LYS70 3.4 95.8 1.0 CG A:LYS70 3.4 82.6 1.0 C23 A:QNG301 3.5 65.6 1.0 C22 A:QNG301 3.5 69.6 1.0 C24 A:QNG301 3.6 65.6 1.0 C21 A:QNG301 3.7 71.0 1.0 C30 A:QNG301 3.7 73.8 1.0 C25 A:QNG301 3.8 64.0 1.0 C20 A:QNG301 3.8 70.8 1.0 C39 A:QNG301 3.9 81.1 1.0 N43 A:QNG301 3.9 71.1 1.0 F27 A:QNG301 4.1 64.0 1.0 O A:MET66 4.2 82.2 1.0 F26 A:QNG301 4.3 77.4 1.0 C01 A:QNG301 4.4 74.0 1.0 C35 A:QNG301 4.4 85.0 1.0 N34 A:QNG301 4.4 88.0 1.0 C A:MET66 4.7 80.9 1.0 CB A:LYS70 4.7 86.6 1.0 C19 A:QNG301 4.7 72.7 1.0 CB A:MET66 4.8 75.9 1.0 OE1 A:GLN67 4.8 96.0 1.0

Fluorine binding site 5 out of 30 in the Co-Crystal Structure of Lenacapavir Bound to N74D Mutant of Disulfide Stabilized Hiv-1 Ca Hexamer


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Co-Crystal Structure of Lenacapavir Bound to N74D Mutant of Disulfide Stabilized Hiv-1 Ca Hexamer within 5.0Å range: probe atom residue distance (Å) B Occ A:F301 b:79.4 occ:1.00 F52 A:QNG301 0.0 79.4 1.0 C40 A:QNG301 1.4 88.4 1.0 F53 A:QNG301 2.2 94.2 1.0 F64 A:QNG301 2.2 91.0 1.0 C35 A:QNG301 2.4 85.0 1.0 C31 A:QNG301 3.0 79.0 1.0 C36 A:QNG301 3.4 83.3 1.0 N34 A:QNG301 3.6 88.0 1.0 NZ A:LYS70 4.2 95.8 1.0 C32 A:QNG301 4.3 75.1 1.0 N33 A:QNG301 4.5 78.7 1.0 C39 A:QNG301 4.6 81.1 1.0 OE1 A:GLN67 4.9 96.0 1.0 C37 A:QNG301 4.9 81.0 1.0

Fluorine binding site 6 out of 30 in the Co-Crystal Structure of Lenacapavir Bound to N74D Mutant of Disulfide Stabilized Hiv-1 Ca Hexamer


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Co-Crystal Structure of Lenacapavir Bound to N74D Mutant of Disulfide Stabilized Hiv-1 Ca Hexamer within 5.0Å range: probe atom residue distance (Å) B Occ A:F301 b:94.2 occ:1.00 F53 A:QNG301 0.0 94.2 1.0 C40 A:QNG301 1.4 88.4 1.0 F52 A:QNG301 2.2 79.4 1.0 F64 A:QNG301 2.2 91.0 1.0 C35 A:QNG301 2.4 85.0 1.0 C31 A:QNG301 3.2 79.0 1.0 N34 A:QNG301 3.4 88.0 1.0 C36 A:QNG301 3.8 83.3 1.0 C32 A:QNG301 4.3 75.1 1.0 N33 A:QNG301 4.4 78.7 1.0 C39 A:QNG301 4.5 81.1 1.0

Fluorine binding site 7 out of 30 in the Co-Crystal Structure of Lenacapavir Bound to N74D Mutant of Disulfide Stabilized Hiv-1 Ca Hexamer


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Co-Crystal Structure of Lenacapavir Bound to N74D Mutant of Disulfide Stabilized Hiv-1 Ca Hexamer within 5.0Å range: probe atom residue distance (Å) B Occ A:F301 b:69.7 occ:1.00 F61 A:QNG301 0.0 69.7 1.0 C60 A:QNG301 1.4 64.1 1.0 F62 A:QNG301 2.2 63.5 1.0 F63 A:QNG301 2.2 63.0 1.0 C18 A:QNG301 2.4 71.7 1.0 CL A:CL304 3.1 47.0 1.0 N14 A:QNG301 3.7 75.1 1.0 C04 A:QNG301 4.4 72.2 1.0 C03 A:QNG301 4.5 70.0 1.0 N15 A:QNG301 4.5 74.2 1.0 C13 A:QNG301 4.5 70.8 1.0 C02 A:QNG301 4.7 73.3 1.0 C08 A:QNG301 4.7 76.5 1.0 C05 A:QNG301 4.7 72.2 1.0 N06 A:QNG301 4.8 75.2 1.0 O29 A:QNG301 4.9 72.9 1.0

Fluorine binding site 8 out of 30 in the Co-Crystal Structure of Lenacapavir Bound to N74D Mutant of Disulfide Stabilized Hiv-1 Ca Hexamer


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Co-Crystal Structure of Lenacapavir Bound to N74D Mutant of Disulfide Stabilized Hiv-1 Ca Hexamer within 5.0Å range: probe atom residue distance (Å) B Occ A:F301 b:63.5 occ:1.00 F62 A:QNG301 0.0 63.5 1.0 C60 A:QNG301 1.4 64.1 1.0 F61 A:QNG301 2.2 69.7 1.0 F63 A:QNG301 2.2 63.0 1.0 C18 A:QNG301 2.4 71.7 1.0 N14 A:QNG301 2.9 75.1 1.0 N15 A:QNG301 3.0 74.2 1.0 C08 A:QNG301 4.1 76.5 1.0 O51 A:QNG301 4.2 94.7 1.0 C16 A:QNG301 4.2 76.0 1.0 C09 A:QNG301 4.8 79.0 1.0 CL A:CL304 5.0 47.0 1.0

Fluorine binding site 9 out of 30 in the Co-Crystal Structure of Lenacapavir Bound to N74D Mutant of Disulfide Stabilized Hiv-1 Ca Hexamer


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 9 of Co-Crystal Structure of Lenacapavir Bound to N74D Mutant of Disulfide Stabilized Hiv-1 Ca Hexamer within 5.0Å range: probe atom residue distance (Å) B Occ A:F301 b:63.0 occ:1.00 F63 A:QNG301 0.0 63.0 1.0 C60 A:QNG301 1.4 64.1 1.0 F61 A:QNG301 2.2 69.7 1.0 F62 A:QNG301 2.2 63.5 1.0 C18 A:QNG301 2.4 71.7 1.0 N14 A:QNG301 2.9 75.1 1.0 C04 A:QNG301 3.4 72.2 1.0 C08 A:QNG301 3.4 76.5 1.0 N15 A:QNG301 3.7 74.2 1.0 C13 A:QNG301 3.7 70.8 1.0 C07 A:QNG301 3.9 75.0 1.0 C03 A:QNG301 4.0 70.0 1.0 CB A:THR107 4.3 89.6 1.0 CG2 A:THR107 4.3 88.7 1.0 C09 A:QNG301 4.4 79.0 1.0 C16 A:QNG301 4.5 76.0 1.0 C05 A:QNG301 4.5 72.2 1.0 CA A:THR107 4.6 88.5 1.0 C02 A:QNG301 4.8 73.3 1.0 CL A:CL304 4.9 47.0 1.0 N06 A:QNG301 5.0 75.2 1.0

Fluorine binding site 10 out of 30 in the Co-Crystal Structure of Lenacapavir Bound to N74D Mutant of Disulfide Stabilized Hiv-1 Ca Hexamer


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 10 of Co-Crystal Structure of Lenacapavir Bound to N74D Mutant of Disulfide Stabilized Hiv-1 Ca Hexamer within 5.0Å range: probe atom residue distance (Å) B Occ A:F301 b:91.0 occ:1.00 F64 A:QNG301 0.0 91.0 1.0 C40 A:QNG301 1.4 88.4 1.0 F52 A:QNG301 2.2 79.4 1.0 F53 A:QNG301 2.2 94.2 1.0 C35 A:QNG301 2.4 85.0 1.0 N34 A:QNG301 2.9 88.0 1.0 C31 A:QNG301 3.7 79.0 1.0 N33 A:QNG301 4.2 78.7 1.0 C32 A:QNG301 4.6 75.1 1.0 C36 A:QNG301 4.9 83.3 1.0

S.M.Bester, D.Adu-Ampratwum, A.S.Annamalai, G.Wei, L.Briganti, B.C.Murphy, R.Haney, J.R.Fuchs, M.Kvaratskhelia. Structural and Mechanistic Bases of Viral Resistance to Hiv-1 Capsid Inhibitor Lenacapavir. Mbio V. 13 80422 2022.
ISSN: ESSN 2150-7511
PubMed: 36190128
DOI: 10.1128/MBIO.01804-22