Chlorine in PDB 6dj1: Wild-Type Hiv-1 Protease in Complex with Lopinavir

The structure of Wild-Type Hiv-1 Protease in Complex with Lopinavir, PDB code: 6dj1 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)	34.00 / 1.26
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	59.726, 85.199, 46.266, 90.00, 90.00, 90.00
R / Rfree (%)	17.1 / 20.8

The structure of Wild-Type Hiv-1 Protease in Complex with Lopinavir also contains other interesting chemical elements:

Sodium

(Na)

1 atom

The binding sites of Chlorine atom in the Wild-Type Hiv-1 Protease in Complex with Lopinavir (pdb code 6dj1). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 3 binding sites of Chlorine where determined in the Wild-Type Hiv-1 Protease in Complex with Lopinavir, PDB code: 6dj1:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in the Wild-Type Hiv-1 Protease 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 Wild-Type Hiv-1 Protease in Complex with Lopinavir within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl502 b:16.9 occ:1.00 O A:HOH681 3.2 29.8 1.0 N A:THR74 3.2 13.1 1.0 ND2 A:ASN88 3.2 12.1 1.0 CA A:GLY73 3.8 12.6 1.0 CB A:ASN88 3.8 12.2 1.0 CB A:THR74 3.9 13.3 1.0 OG1 A:THR74 3.9 17.3 1.0 C A:GLY73 4.0 11.8 1.0 CG A:ASN88 4.0 12.4 1.0 CA A:THR74 4.2 12.8 1.0 O A:HOH639 4.4 19.9 1.0 O A:ASN88 4.6 13.9 1.0 O A:THR74 4.8 14.3 1.0 CA A:ASN88 4.8 11.1 1.0 C A:ASN88 5.0 11.1 1.0

Chlorine binding site 2 out of 3 in the Wild-Type Hiv-1 Protease 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 Wild-Type Hiv-1 Protease in Complex with Lopinavir within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl202 b:18.6 occ:1.00 O A:HOH637 3.2 15.0 1.0 NE1 B:TRP6 3.3 14.2 1.0 CZ2 B:TRP6 3.8 13.4 1.0 CE2 B:TRP6 3.9 13.8 1.0 CG2 B:THR4 4.2 18.5 1.0 CD1 B:TRP6 4.5 14.2 1.0 CB B:THR4 4.8 16.0 1.0

Chlorine binding site 3 out of 3 in the Wild-Type Hiv-1 Protease 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 Wild-Type Hiv-1 Protease in Complex with Lopinavir within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl203 b:20.2 occ:1.00 O B:HOH361 3.0 30.2 1.0 N B:THR74 3.1 12.7 1.0 ND2 B:ASN88 3.1 14.0 1.0 O B:HOH402 3.5 31.0 0.5 CA B:GLY73 3.7 14.0 1.0 OG1 B:THR74 3.8 15.6 1.0 CB B:ASN88 3.9 12.2 1.0 CB B:THR74 3.9 12.4 1.0 C B:GLY73 3.9 12.2 1.0 CG B:ASN88 4.0 13.6 1.0 CA B:THR74 4.1 12.2 1.0 O B:HOH335 4.2 18.3 1.0 CD2 B:LEU89 4.4 18.6 1.0 O B:ASN88 4.6 17.7 1.0 O B:THR74 4.7 13.9 1.0 C B:ASN88 4.7 12.6 1.0 CA B:ASN88 4.8 12.0 1.0 NE2 B:GLN92 4.9 22.0 1.0 C B:THR74 5.0 11.7 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