Chlorine in PDB 7rj2: Co-Crystal Structure of Lenacapavir Bound to Q67H/N74D Mutant of Disulfide Stabilized Hiv-1 Ca Hexamer

The structure of Co-Crystal Structure of Lenacapavir Bound to Q67H/N74D Mutant of Disulfide Stabilized Hiv-1 Ca Hexamer, PDB code: 7rj2 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)	39.92 / 2.32
Space group	P 6
Cell size a, b, c (Å), α, β, γ (°)	92.183, 92.183, 57.965, 90, 90, 120
R / Rfree (%)	19.9 / 24.6

The structure of Co-Crystal Structure of Lenacapavir Bound to Q67H/N74D Mutant of Disulfide Stabilized Hiv-1 Ca Hexamer also contains other interesting chemical elements:

Iodine	(I)	1 atom
Fluorine	(F)	20 atoms

The binding sites of Chlorine atom in the Co-Crystal Structure of Lenacapavir Bound to Q67H/N74D Mutant of Disulfide Stabilized Hiv-1 Ca Hexamer (pdb code 7rj2). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 6 binding sites of Chlorine where determined in the Co-Crystal Structure of Lenacapavir Bound to Q67H/N74D Mutant of Disulfide Stabilized Hiv-1 Ca Hexamer, PDB code: 7rj2:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6;

Chlorine binding site 1 out of 6 in the Co-Crystal Structure of Lenacapavir Bound to Q67H/N74D Mutant of Disulfide Stabilized Hiv-1 Ca Hexamer


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Co-Crystal Structure of Lenacapavir Bound to Q67H/N74D Mutant of Disulfide Stabilized Hiv-1 Ca Hexamer within 5.0Å range: probe atom residue distance (Å) B Occ C:Cl301 b:46.7 occ:0.64 CL47 C:QNG301 0.0 46.7 0.6 CL47 C:QNG301 0.1 46.6 0.4 C10 C:QNG301 1.8 43.6 0.6 C10 C:QNG301 1.9 43.6 0.4 C09 C:QNG301 2.7 48.0 0.6 C09 C:QNG301 2.8 48.1 0.4 C11 C:QNG301 2.8 38.2 0.6 C11 C:QNG301 2.9 38.2 0.4 N17 C:QNG301 2.9 57.5 0.6 N17 C:QNG301 3.0 57.3 0.4 C16 C:QNG301 3.2 51.0 0.6 C16 C:QNG301 3.2 50.9 0.4 OD1 C:ASP74 3.3 58.6 1.0 CG2 C:ILE73 3.6 21.0 1.0 O C:LYS70 3.6 28.7 1.0 CB C:ILE73 3.8 28.8 1.0 CG C:ASP74 3.9 51.5 1.0 CB C:LYS70 4.0 32.7 1.0 CA C:LYS70 4.0 34.2 1.0 C08 C:QNG301 4.0 46.9 0.6 C08 C:QNG301 4.1 46.8 0.4 C12 C:QNG301 4.1 40.8 0.6 OD2 C:ASP74 4.2 61.1 1.0 O C:HOH479 4.2 38.8 1.0 C12 C:QNG301 4.2 40.8 0.4 C C:LYS70 4.2 22.4 1.0 N C:ASP74 4.4 25.1 1.0 CG C:LYS70 4.4 26.1 1.0 CD1 C:ILE73 4.4 18.4 1.0 N15 C:QNG301 4.5 50.3 0.6 S48 C:QNG301 4.5 69.9 0.6 S48 C:QNG301 4.5 69.9 0.4 N15 C:QNG301 4.6 50.4 0.4 C07 C:QNG301 4.6 40.9 0.6 C07 C:QNG301 4.7 41.0 0.4 CG1 C:ILE73 4.7 26.1 1.0 C C:ILE73 4.8 28.2 1.0 CA C:ILE73 4.9 27.1 1.0 N14 C:QNG301 4.9 47.9 0.6 CE C:LYS70 4.9 56.6 1.0 N14 C:QNG301 5.0 47.9 0.4 C49 C:QNG301 5.0 58.0 0.4

Chlorine binding site 2 out of 6 in the Co-Crystal Structure of Lenacapavir Bound to Q67H/N74D Mutant of Disulfide Stabilized Hiv-1 Ca Hexamer


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Co-Crystal Structure of Lenacapavir Bound to Q67H/N74D Mutant of Disulfide Stabilized Hiv-1 Ca Hexamer within 5.0Å range: probe atom residue distance (Å) B Occ C:Cl301 b:46.6 occ:0.36 CL47 C:QNG301 0.0 46.6 0.4 CL47 C:QNG301 0.1 46.7 0.6 C10 C:QNG301 1.7 43.6 0.6 C10 C:QNG301 1.8 43.6 0.4 C09 C:QNG301 2.7 48.0 0.6 C11 C:QNG301 2.7 38.2 0.6 C09 C:QNG301 2.7 48.1 0.4 C11 C:QNG301 2.8 38.2 0.4 N17 C:QNG301 3.0 57.5 0.6 N17 C:QNG301 3.0 57.3 0.4 C16 C:QNG301 3.2 51.0 0.6 C16 C:QNG301 3.3 50.9 0.4 OD1 C:ASP74 3.3 58.6 1.0 CG2 C:ILE73 3.5 21.0 1.0 O C:LYS70 3.7 28.7 1.0 CB C:ILE73 3.8 28.8 1.0 C08 C:QNG301 4.0 46.9 0.6 C12 C:QNG301 4.0 40.8 0.6 CG C:ASP74 4.0 51.5 1.0 C08 C:QNG301 4.1 46.8 0.4 CA C:LYS70 4.1 34.2 1.0 CB C:LYS70 4.1 32.7 1.0 C12 C:QNG301 4.1 40.8 0.4 O C:HOH479 4.1 38.8 1.0 OD2 C:ASP74 4.3 61.1 1.0 C C:LYS70 4.3 22.4 1.0 CD1 C:ILE73 4.4 18.4 1.0 N C:ASP74 4.5 25.1 1.0 CG C:LYS70 4.5 26.1 1.0 N15 C:QNG301 4.5 50.3 0.6 C07 C:QNG301 4.5 40.9 0.6 N15 C:QNG301 4.6 50.4 0.4 S48 C:QNG301 4.6 69.9 0.6 C07 C:QNG301 4.6 41.0 0.4 S48 C:QNG301 4.6 69.9 0.4 CG1 C:ILE73 4.7 26.1 1.0 C C:ILE73 4.8 28.2 1.0 N14 C:QNG301 4.9 47.9 0.6 CA C:ILE73 4.9 27.1 1.0 N14 C:QNG301 4.9 47.9 0.4 CE C:LYS70 5.0 56.6 1.0

Chlorine binding site 3 out of 6 in the Co-Crystal Structure of Lenacapavir Bound to Q67H/N74D Mutant of Disulfide Stabilized Hiv-1 Ca Hexamer


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Co-Crystal Structure of Lenacapavir Bound to Q67H/N74D Mutant of Disulfide Stabilized Hiv-1 Ca Hexamer within 5.0Å range: probe atom residue distance (Å) B Occ C:Cl302 b:24.5 occ:1.00 OE1 C:GLN219 3.2 90.2 1.0 NH1 C:ARG162 3.3 55.5 1.0 CD C:ARG162 3.5 49.4 1.0 CE C:MET215 3.8 41.9 1.0 CD C:GLN219 4.1 88.3 1.0 CZ C:ARG162 4.1 55.4 1.0 NE C:ARG162 4.2 57.3 1.0 CB C:ARG162 4.3 31.0 1.0 CG C:ARG162 4.4 41.2 1.0 CB C:GLN219 4.4 70.4 1.0 O C:HOH473 4.4 18.2 1.0 CB C:MET215 4.5 28.4 1.0 O C:MET215 4.6 33.0 1.0 CG C:GLN219 4.8 81.2 1.0 C C:MET215 4.9 40.4 1.0 NE2 C:GLN219 5.0 81.3 1.0

Chlorine binding site 4 out of 6 in the Co-Crystal Structure of Lenacapavir Bound to Q67H/N74D Mutant of Disulfide Stabilized Hiv-1 Ca Hexamer


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Co-Crystal Structure of Lenacapavir Bound to Q67H/N74D Mutant of Disulfide Stabilized Hiv-1 Ca Hexamer within 5.0Å range: probe atom residue distance (Å) B Occ C:Cl303 b:24.0 occ:1.00 O C:GLY106 3.1 38.6 1.0 CA C:GLN50 3.6 17.4 1.0 CB C:GLN50 3.8 20.8 1.0 ND2 C:ASN53 3.8 21.8 1.0 CG C:GLN50 3.8 28.5 1.0 C C:GLY106 3.9 32.8 1.0 CA C:GLY106 4.0 26.9 1.0 NE2 C:GLN114 4.1 19.3 1.0 N C:GLN50 4.2 18.9 1.0 C03 C:QNG301 4.2 40.6 0.4 C03 C:QNG301 4.3 40.7 0.6 O C:PRO49 4.7 23.2 1.0 C C:PRO49 4.7 20.2 1.0 O C:SER109 4.7 31.1 1.0 C58 C:QNG301 4.7 30.1 0.6 CB C:ASN53 4.7 22.9 1.0 CG C:ASN53 4.8 26.9 1.0 C04 C:QNG301 4.8 39.9 0.4 C C:GLN50 4.8 21.4 1.0 C04 C:QNG301 4.8 39.9 0.6 O C:GLN50 4.9 17.5 1.0 OE1 C:GLN114 5.0 24.6 1.0 CD C:GLN114 5.0 21.2 1.0

Chlorine binding site 5 out of 6 in the Co-Crystal Structure of Lenacapavir Bound to Q67H/N74D Mutant of Disulfide Stabilized Hiv-1 Ca Hexamer


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Co-Crystal Structure of Lenacapavir Bound to Q67H/N74D Mutant of Disulfide Stabilized Hiv-1 Ca Hexamer within 5.0Å range: probe atom residue distance (Å) B Occ C:Cl304 b:30.6 occ:1.00 O C:HOH522 3.5 51.8 1.0 CG C:ARG18 4.1 48.2 1.0 O C:HOH421 4.2 28.0 1.0 CB C:ARG18 4.4 35.2 1.0 CD C:ARG18 4.4 51.0 1.0 NE C:ARG18 4.6 41.0 1.0

Chlorine binding site 6 out of 6 in the Co-Crystal Structure of Lenacapavir Bound to Q67H/N74D Mutant of Disulfide Stabilized Hiv-1 Ca Hexamer


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Co-Crystal Structure of Lenacapavir Bound to Q67H/N74D Mutant of Disulfide Stabilized Hiv-1 Ca Hexamer within 5.0Å range: probe atom residue distance (Å) B Occ C:Cl305 b:18.6 occ:1.00 N C:GLY61 3.8 32.9 1.0 CD C:GLN63 4.0 30.9 1.0 CG C:GLN63 4.0 23.2 1.0 CA C:GLY60 4.2 31.4 1.0 NE2 C:GLN63 4.3 22.7 1.0 OE1 C:GLN63 4.3 33.8 1.0 C C:GLY60 4.5 39.1 1.0 CA C:GLY61 4.8 26.8 1.0 O C:VAL59 4.8 27.8 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