Chlorine in PDB 6dj2: Hiv-1 Protease with Single Mutation L76V in Complex with Lopinavir

The structure of Hiv-1 Protease with Single Mutation L76V in Complex with Lopinavir, PDB code: 6dj2 was solved by Y.-F.Wang, A.E.Wong-Sam, Y.Zhang, I.T.Weber, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.00 / 1.36
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	60.011, 85.377, 46.430, 90.00, 90.00, 90.00
R / Rfree (%)	14.8 / 19.6

The structure of Hiv-1 Protease with Single Mutation L76V in Complex with Lopinavir also contains other interesting chemical elements:

Sodium

(Na)

1 atom

The binding sites of Chlorine atom in the Hiv-1 Protease with Single Mutation L76V in Complex with Lopinavir (pdb code 6dj2). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 3 binding sites of Chlorine where determined in the Hiv-1 Protease with Single Mutation L76V in Complex with Lopinavir, PDB code: 6dj2:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in the Hiv-1 Protease with Single Mutation L76V in Complex with Lopinavir


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Hiv-1 Protease with Single Mutation L76V in Complex with Lopinavir within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl502 b:16.0 occ:1.00 O A:HOH715 2.9 37.0 1.0 O A:HOH709 3.0 19.4 0.4 N A:THR74 3.2 12.4 1.0 ND2 A:ASN88 3.3 10.2 1.0 CB A:ASN88 3.8 11.6 1.0 CA A:GLY73 3.8 13.6 1.0 CB A:THR74 3.9 12.8 1.0 OG1 A:THR74 3.9 17.1 1.0 C A:GLY73 4.0 11.7 1.0 CG A:ASN88 4.0 10.3 1.0 CA A:THR74 4.2 12.6 1.0 O A:HOH655 4.5 21.8 1.0 O A:HOH619 4.5 21.5 0.6 O A:ASN88 4.6 13.0 1.0 O A:THR74 4.7 14.9 1.0 CA A:ASN88 4.8 10.3 1.0 C A:THR74 5.0 11.6 1.0 C A:ASN88 5.0 11.5 1.0

Chlorine binding site 2 out of 3 in the Hiv-1 Protease with Single Mutation L76V in Complex with Lopinavir


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Hiv-1 Protease with Single Mutation L76V in Complex with Lopinavir within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl202 b:12.8 occ:0.75 O B:HOH420 3.1 32.1 1.0 O A:HOH639 3.2 14.9 1.0 NE1 B:TRP6 3.3 13.6 1.0 CZ2 B:TRP6 3.9 13.4 1.0 CE2 B:TRP6 4.0 13.5 1.0 CG2 B:THR4 4.1 17.7 1.0 CD1 B:TRP6 4.5 13.8 1.0 CB B:THR4 4.8 13.0 1.0 O B:HOH321 4.8 25.4 0.5

Chlorine binding site 3 out of 3 in the Hiv-1 Protease with Single Mutation L76V in Complex with Lopinavir


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Hiv-1 Protease with Single Mutation L76V in Complex with Lopinavir within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl203 b:16.6 occ:1.00 O B:HOH374 3.0 18.8 1.0 O B:HOH424 3.0 30.4 0.5 O B:HOH416 3.1 37.0 1.0 N B:THR74 3.2 10.6 1.0 ND2 B:ASN88 3.2 11.9 1.0 CA B:GLY73 3.8 11.3 1.0 CB B:ASN88 3.9 10.5 1.0 OG1 B:THR74 3.9 13.9 1.0 CB B:THR74 3.9 10.2 1.0 C B:GLY73 4.0 11.0 1.0 CG B:ASN88 4.0 10.4 1.0 CA B:THR74 4.1 9.6 1.0 O B:HOH344 4.3 18.1 1.0 CD2 B:LEU89 4.4 15.5 1.0 O B:THR74 4.7 12.2 1.0 O B:HOH332 4.7 27.9 1.0 O B:ASN88 4.7 13.5 1.0 C B:ASN88 4.8 10.4 1.0 CA B:ASN88 4.9 10.6 1.0 O B:HOH436 4.9 24.1 0.5 O B:HOH314 4.9 35.2 1.0 NE2 B:GLN92 5.0 15.4 1.0 C B:THR74 5.0 8.7 1.0

A.Wong-Sam, Y.F.Wang, Y.Zhang, A.K.Ghosh, R.W.Harrison, I.T.Weber. Drug Resistance Mutation L76V Alters Nonpolar Interactions at the Flap-Core Interface of Hiv-1 Protease. Acs Omega V. 3 12132 2018.
ISSN: ESSN 2470-1343
PubMed: 30288468
DOI: 10.1021/ACSOMEGA.8B01683