Chlorine 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:

Fluorine	(F)	30 atoms
Iodine	(I)	3 atoms

Pages:

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

Binding sites:

The binding sites of Chlorine 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 Chlorine atom.
In total 21 binding sites of Chlorine 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 Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Chlorine binding site 1 out of 21 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 Chlorine with other atoms in the Cl 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:Cl301 b:81.4 occ:1.00 CL47 A:QNG301 0.0 81.4 1.0 C10 A:QNG301 1.8 75.1 1.0 C11 A:QNG301 2.8 74.5 1.0 C09 A:QNG301 2.8 79.0 1.0 OD1 A:ASP74 2.9 89.6 1.0 O A:HOH411 3.1 57.2 1.0 N17 A:QNG301 3.2 73.4 1.0 C16 A:QNG301 3.3 76.0 1.0 CG2 A:ILE73 3.9 81.7 1.0 CG A:ASP74 3.9 89.5 1.0 C12 A:QNG301 4.1 79.2 1.0 C08 A:QNG301 4.1 76.5 1.0 O A:LYS70 4.3 89.6 1.0 OD2 A:ASP74 4.4 101.7 1.0 CB A:ILE73 4.4 77.1 1.0 CG2 A:THR107 4.5 88.7 1.0 C07 A:QNG301 4.6 75.0 1.0 N15 A:QNG301 4.6 74.2 1.0 CB A:ALA105 4.7 71.8 1.0 N A:ASP74 4.7 77.4 1.0 CB A:LYS70 4.8 86.6 1.0 S48 A:QNG301 4.8 90.2 1.0 CD A:LYS70 4.9 83.9 1.0 CG A:LYS70 4.9 82.6 1.0 CA A:LYS70 4.9 86.3 1.0 N14 A:QNG301 5.0 75.1 1.0 C A:LYS70 5.0 86.5 1.0 CA A:ASP74 5.0 77.3 1.0

Chlorine binding site 2 out of 21 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 Chlorine with other atoms in the Cl 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:Cl302 b:48.5 occ:1.00 N A:ARG18 3.9 70.9 1.0 CA A:ARG18 3.9 72.8 1.0 C A:PRO17 3.9 68.7 1.0 O A:PRO17 4.0 68.5 1.0 CB A:PRO17 4.1 67.1 1.0 CB A:ARG18 4.5 68.4 1.0 CB A:ASN21 4.6 86.5 1.0 CA A:PRO17 4.7 70.6 1.0

Chlorine binding site 3 out of 21 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 Chlorine with other atoms in the Cl 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:Cl303 b:61.6 occ:1.00 N A:GLY61 3.6 81.1 1.0 NE2 A:GLN63 3.8 86.5 1.0 CD A:GLN63 3.8 86.8 1.0 CG A:GLN63 3.9 84.0 1.0 CA A:GLY60 4.2 93.5 1.0 OE1 A:GLN63 4.4 85.2 1.0 C A:GLY60 4.5 86.3 1.0 CA A:GLY61 4.5 85.3 1.0 O A:VAL59 4.6 78.9 1.0

Chlorine binding site 4 out of 21 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 Chlorine with other atoms in the Cl 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:Cl304 b:47.0 occ:1.00 O A:HOH422 2.8 47.6 1.0 F61 A:QNG301 3.1 69.7 1.0 N06 A:QNG301 3.7 75.2 1.0 C30 A:QNG301 3.7 73.8 1.0 C28 A:QNG301 3.7 73.9 1.0 C18 A:QNG301 3.9 71.7 1.0 C02 A:QNG301 3.9 73.3 1.0 N43 A:QNG301 4.0 71.1 1.0 C60 A:QNG301 4.1 64.1 1.0 C44 A:QNG301 4.1 73.7 1.0 O29 A:QNG301 4.2 72.9 1.0 C05 A:QNG301 4.3 72.2 1.0 C45 A:QNG301 4.5 72.9 1.0 C03 A:QNG301 4.7 70.0 1.0 N33 A:QNG301 4.7 78.7 1.0 ND2 A:ASN57 4.7 68.6 1.0 C01 A:QNG301 4.7 74.0 1.0 OD1 A:ASN57 4.8 66.0 1.0 N34 A:QNG301 4.9 88.0 1.0 F63 A:QNG301 4.9 63.0 1.0 C13 A:QNG301 5.0 70.8 1.0 F62 A:QNG301 5.0 63.5 1.0

Chlorine binding site 5 out of 21 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 Chlorine with other atoms in the Cl 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:Cl305 b:56.0 occ:1.00 CB A:ARG18 3.6 68.4 1.0 N A:ARG18 3.9 70.9 1.0 CB A:SER16 4.0 70.4 1.0 CD A:PRO17 4.2 70.4 1.0 OG A:SER16 4.4 65.4 1.0 CA A:ARG18 4.4 72.8 1.0 N A:PRO17 4.6 69.7 1.0 CG A:PRO17 4.8 68.6 1.0 CB A:PRO17 4.9 67.1 1.0 CA A:SER16 5.0 68.8 1.0 C A:PRO17 5.0 68.7 1.0

Chlorine binding site 6 out of 21 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 Chlorine with other atoms in the Cl 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:Cl306 b:63.0 occ:1.00 O A:GLY106 3.4 85.3 1.0 CG A:GLN50 3.5 69.8 1.0 CA A:GLN50 3.6 69.1 1.0 CB A:GLN50 3.7 65.8 1.0 ND2 A:ASN53 3.9 73.1 1.0 NE2 A:GLN114 3.9 68.5 1.0 N A:GLN50 4.1 69.3 1.0 C A:GLY106 4.2 82.9 1.0 CA A:GLY106 4.3 82.0 1.0 C03 A:QNG301 4.5 70.0 1.0 C58 A:QNG301 4.5 80.2 1.0 O A:SER109 4.6 83.9 1.0 C A:PRO49 4.7 72.2 1.0 CD A:GLN50 4.7 75.0 1.0 O A:PRO49 4.8 76.8 1.0 NE2 A:GLN50 4.8 78.0 1.0 C A:GLN50 4.8 65.0 1.0 CG A:ASN53 4.9 71.0 1.0 CB A:ASN53 4.9 69.2 1.0 CD A:GLN114 4.9 68.9 1.0 OE1 A:GLN114 4.9 72.4 1.0 O A:GLN50 5.0 65.0 1.0

Chlorine binding site 7 out of 21 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 Chlorine with other atoms in the Cl 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:Cl307 b:60.8 occ:1.00 O A:GLY60 2.8 78.9 1.0 CG A:GLU28 3.8 106.1 1.0 C A:GLY60 3.8 86.3 1.0 NE2 A:HIS62 3.9 83.8 1.0 CD2 A:HIS62 4.0 82.4 1.0 CA A:GLU28 4.2 97.5 1.0 CB A:GLU28 4.5 102.3 1.0 CA A:GLY60 4.6 93.5 1.0 N A:GLY61 4.7 81.1 1.0 N A:GLU28 4.7 98.4 1.0 N A:GLY60 4.8 89.1 1.0 CA A:GLY61 4.8 85.3 1.0 O A:VAL27 4.9 108.2 1.0 CD A:GLU28 4.9 108.8 1.0

Chlorine binding site 8 out of 21 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 Chlorine with other atoms in the Cl 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 B:Cl301 b:88.5 occ:1.00 CL47 B:QNG301 0.0 88.5 1.0 C10 B:QNG301 1.8 68.3 1.0 C09 B:QNG301 2.8 72.0 1.0 C11 B:QNG301 2.8 66.8 1.0 O B:HOH405 2.8 60.7 1.0 OD1 B:ASP74 3.0 95.2 1.0 N17 B:QNG301 3.1 77.4 1.0 C16 B:QNG301 3.3 75.8 1.0 CG2 B:ILE73 3.4 73.7 1.0 O B:LYS70 3.5 76.8 1.0 CB B:ILE73 3.7 65.2 1.0 CG B:ASP74 3.9 89.6 1.0 C08 B:QNG301 4.1 68.3 1.0 C12 B:QNG301 4.1 69.3 1.0 CA B:LYS70 4.2 75.2 1.0 C B:LYS70 4.3 76.0 1.0 N B:ASP74 4.3 74.4 1.0 OD2 B:ASP74 4.4 93.9 1.0 CD1 B:ILE73 4.5 71.4 1.0 C B:ILE73 4.6 84.2 1.0 N15 B:QNG301 4.6 73.2 1.0 C07 B:QNG301 4.6 71.0 1.0 CB B:LYS70 4.6 84.3 1.0 S48 B:QNG301 4.7 88.0 1.0 CG1 B:ILE73 4.7 70.1 1.0 CA B:ILE73 4.7 73.2 1.0 CE B:LYS70 4.8 75.8 1.0 CA B:ASP74 4.8 77.2 1.0 CG B:LYS70 4.9 78.7 1.0 CB B:ASP74 4.9 82.8 1.0 N14 B:QNG301 5.0 69.1 1.0 CB B:ALA105 5.0 83.9 1.0

Chlorine binding site 9 out of 21 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 Chlorine with other atoms in the Cl 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 B:Cl302 b:43.5 occ:1.00 CD B:PRO17 3.9 71.2 1.0 CB B:SER16 4.0 70.8 1.0 N B:ARG18 4.4 71.7 1.0 CB B:ARG18 4.5 64.5 1.0 N B:PRO17 4.5 64.8 1.0 CG B:PRO17 4.5 82.1 1.0 OG B:SER16 4.6 68.5 1.0 CA B:SER16 4.8 66.1 1.0 CB B:PRO17 4.9 75.0 1.0

Chlorine binding site 10 out of 21 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 Chlorine with other atoms in the Cl 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 B:Cl303 b:44.1 occ:1.00 N B:GLY61 3.7 56.5 1.0 NE2 B:GLN63 3.9 64.0 1.0 CD B:GLN63 3.9 61.6 1.0 CG B:GLN63 4.0 63.9 1.0 OE1 B:GLN63 4.4 66.3 1.0 CA B:GLY60 4.4 69.7 1.0 CA B:GLY61 4.5 62.4 1.0 C B:GLY60 4.6 60.4 1.0 O B:VAL59 4.8 66.7 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