Chlorine in PDB 3dk1: Wild Type Hiv-1 Protease with Potent Antiviral Inhibitor Grl-0105A

All present enzymatic activity of Wild Type Hiv-1 Protease with Potent Antiviral Inhibitor Grl-0105A:
3.4.23.16;

The structure of Wild Type Hiv-1 Protease with Potent Antiviral Inhibitor Grl-0105A, PDB code: 3dk1 was solved by 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)	10.00 / 1.07
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	58.003, 86.338, 45.833, 90.00, 90.00, 90.00
R / Rfree (%)	15.1 / 17.7

The structure of Wild Type Hiv-1 Protease with Potent Antiviral Inhibitor Grl-0105A also contains other interesting chemical elements:

Sodium

(Na)

1 atom

The binding sites of Chlorine atom in the Wild Type Hiv-1 Protease with Potent Antiviral Inhibitor Grl-0105A (pdb code 3dk1). 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 with Potent Antiviral Inhibitor Grl-0105A, PDB code: 3dk1:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in the Wild Type Hiv-1 Protease with Potent Antiviral Inhibitor Grl-0105A


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 with Potent Antiviral Inhibitor Grl-0105A within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl501 b:13.6 occ:1.00 O A:HOH1176 3.0 20.1 0.2 N A:THR74 3.3 10.4 1.0 ND2 A:ASN88 3.3 10.5 1.0 CB A:ASN88 3.8 9.9 1.0 CA A:GLY73 3.8 11.2 1.0 CB A:THR74 3.9 11.5 1.0 OG1 A:THR74 3.9 13.7 1.0 CG A:ASN88 4.0 10.8 1.0 C A:GLY73 4.0 10.2 1.0 CA A:THR74 4.2 10.1 1.0 O A:HOH1027 4.4 17.2 1.0 O A:ASN88 4.7 10.5 1.0 O A:THR74 4.7 10.4 1.0 CA A:ASN88 4.9 9.0 1.0 C A:THR74 5.0 10.0 1.0

Chlorine binding site 2 out of 3 in the Wild Type Hiv-1 Protease with Potent Antiviral Inhibitor Grl-0105A


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 with Potent Antiviral Inhibitor Grl-0105A within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl502 b:15.8 occ:1.00 O B:HOH1056 3.1 27.3 1.0 O A:HOH1012 3.3 13.5 1.0 NE1 B:TRP106 3.3 11.6 1.0 CZ2 B:TRP106 3.8 11.5 1.0 CE2 B:TRP106 3.9 10.6 1.0 CG2 B:THR104 4.2 16.8 1.0 CD1 B:TRP106 4.4 11.3 1.0 O B:HOH1152 4.8 23.1 0.5 CB B:THR104 4.8 13.0 1.0

Chlorine binding site 3 out of 3 in the Wild Type Hiv-1 Protease with Potent Antiviral Inhibitor Grl-0105A


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 with Potent Antiviral Inhibitor Grl-0105A within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl503 b:18.1 occ:1.00 O B:HOH1007 2.9 16.9 1.0 ND2 B:ASN188 3.2 11.4 1.0 N B:THR174 3.2 9.6 1.0 OG1 B:THR174 3.7 13.8 1.0 CB B:THR174 3.8 11.0 1.0 CA B:GLY173 3.8 10.6 1.0 CB B:ASN188 3.8 10.0 1.0 C B:GLY173 4.0 9.7 1.0 CG B:ASN188 4.0 10.1 1.0 CA B:THR174 4.1 10.2 1.0 O B:HOH1018 4.1 14.9 1.0 NE2 B:GLN192 4.4 11.6 1.0 O B:ASN188 4.4 11.9 1.0 CD2 B:LEU189 4.6 14.2 1.0 O B:THR174 4.7 10.2 1.0 C B:ASN188 4.8 9.6 1.0 CA B:ASN188 4.8 9.3 1.0 C B:THR174 4.9 9.5 1.0

A.K.Ghosh, S.Gemma, J.Takayama, A.Baldridge, S.Leshchenko-Yashchuk, H.B.Miller, Y.F.Wang, A.Y.Kovalevsky, Y.Koh, I.T.Weber, H.Mitsuya. Potent Hiv-1 Protease Inhibitors Incorporating Meso-Bicyclic Urethanes As P2-Ligands: Structure-Based Design, Synthesis, Biological Evaluation and Protein-Ligand X-Ray Studies Org.Biomol.Chem. V. 6 3703 2008.
ISSN: ISSN 1477-0520
PubMed: 18843400
DOI: 10.1039/B809178A