Chlorine in PDB 6dif: Wild-Type Hiv-1 Protease in Complex with Tipranavir

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

Resolution Low / High (Å)	25.00 / 1.20
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	58.300, 86.259, 46.005, 90.00, 90.00, 90.00
R / Rfree (%)	15.4 / 18.7

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

Fluorine	(F)	6 atoms
Sodium	(Na)	1 atom

The binding sites of Chlorine atom in the Wild-Type Hiv-1 Protease in Complex with Tipranavir (pdb code 6dif). 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 Tipranavir, PDB code: 6dif:
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 Tipranavir


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 Tipranavir within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl502 b:13.2 occ:1.00 O A:HOH695 3.1 29.8 1.0 N A:THR74 3.2 9.9 1.0 ND2 A:ASN88 3.3 9.9 1.0 CA A:GLY73 3.8 10.5 1.0 CB A:ASN88 3.8 9.0 1.0 OG1 A:THR74 3.8 12.9 1.0 CB A:THR74 3.8 10.6 1.0 C A:GLY73 4.0 10.0 1.0 CG A:ASN88 4.1 9.3 1.0 CA A:THR74 4.1 9.7 1.0 O A:HOH647 4.4 16.1 1.0 O A:HOH618 4.5 30.5 0.5 O A:HOH643 4.5 34.4 1.0 O A:ASN88 4.7 10.4 1.0 O A:THR74 4.7 10.5 1.0 CA A:ASN88 4.9 8.4 1.0 C A:THR74 5.0 9.1 1.0

Chlorine binding site 2 out of 3 in the Wild-Type Hiv-1 Protease in Complex with Tipranavir


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 Tipranavir within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl503 b:24.7 occ:1.00 O A:HOH688 2.9 26.4 1.0 OE1 A:GLN18 3.3 24.9 1.0 N A:SER37 3.3 14.3 1.0 OG A:SER37 3.5 20.2 0.3 CA A:MET36 3.7 11.5 1.0 CB A:MET36 3.7 12.7 1.0 CB A:SER37 3.9 15.9 0.3 C A:MET36 4.0 12.5 1.0 CA A:SER37 4.3 14.6 0.3 CB A:SER37 4.3 15.9 0.3 CD A:GLN18 4.3 22.8 1.0 CA A:SER37 4.4 14.6 0.3 O A:HOH639 4.4 26.9 0.5 CA A:SER37 4.4 14.1 0.3 CB A:SER37 4.5 15.9 0.3 OG A:SER37 4.5 16.7 0.3 NE2 A:GLN18 4.6 25.9 1.0 O A:SER37 4.7 15.3 1.0

Chlorine binding site 3 out of 3 in the Wild-Type Hiv-1 Protease in Complex with Tipranavir


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 Tipranavir within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl202 b:13.2 occ:0.75 O B:HOH333 2.9 14.7 1.0 O B:HOH397 3.0 23.8 0.5 N B:THR74 3.1 9.0 1.0 ND2 B:ASN88 3.2 9.4 1.0 OG1 B:THR74 3.7 12.5 1.0 CB B:THR74 3.7 10.2 1.0 CA B:GLY73 3.8 9.8 1.0 CB B:ASN88 3.9 9.1 1.0 C B:GLY73 4.0 8.8 1.0 CG B:ASN88 4.0 9.0 1.0 CA B:THR74 4.0 8.9 1.0 O B:HOH344 4.1 14.7 1.0 NE2 B:GLN92 4.4 9.9 1.0 CD2 B:LEU89 4.5 11.6 1.0 O B:ASN88 4.5 10.8 1.0 O B:THR74 4.7 9.3 1.0 O B:HOH301 4.7 20.0 0.5 C B:ASN88 4.8 8.7 1.0 CA B:ASN88 4.9 8.8 1.0 C B:THR74 4.9 8.7 1.0 O B:HOH328 4.9 30.3 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