Chlorine in PDB 4i53: Crystal Structure of Clade C1086 Hiv-1 GP120 Core in Complex with Dmj- II-121

The structure of Crystal Structure of Clade C1086 Hiv-1 GP120 Core in Complex with Dmj- II-121, PDB code: 4i53 was solved by M.Le-Khac, W.A.Hendrickson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.82 / 2.50
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	67.450, 127.670, 192.900, 90.00, 90.00, 90.00
R / Rfree (%)	25.4 / 27.3

The structure of Crystal Structure of Clade C1086 Hiv-1 GP120 Core in Complex with Dmj- II-121 also contains other interesting chemical elements:

Fluorine

(F)

2 atoms

The binding sites of Chlorine atom in the Crystal Structure of Clade C1086 Hiv-1 GP120 Core in Complex with Dmj- II-121 (pdb code 4i53). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 2 binding sites of Chlorine where determined in the Crystal Structure of Clade C1086 Hiv-1 GP120 Core in Complex with Dmj- II-121, PDB code: 4i53:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in the Crystal Structure of Clade C1086 Hiv-1 GP120 Core in Complex with Dmj- II-121


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of Clade C1086 Hiv-1 GP120 Core in Complex with Dmj- II-121 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl501 b:53.2 occ:1.00 CL1 A:1C1501 0.0 53.2 1.0 C24 A:1C1501 1.7 53.2 1.0 C22 A:1C1501 2.7 53.2 1.0 C26 A:1C1501 2.7 53.2 1.0 F23 A:1C1501 2.9 53.2 1.0 C A:PHE376 3.4 21.2 1.0 CA A:PHE376 3.5 21.5 1.0 N A:PHE376 3.6 23.0 1.0 O A:PHE376 3.7 21.3 1.0 CD2 A:PHE382 3.8 8.4 1.0 N A:ASN377 3.8 7.8 1.0 C21 A:1C1501 3.9 53.2 1.0 C27 A:1C1501 4.0 53.2 1.0 CG1 A:VAL255 4.0 4.9 1.0 O A:VAL255 4.1 3.9 1.0 CE2 A:PHE382 4.2 8.1 1.0 C A:SER375 4.2 8.8 1.0 CH2 A:TRP112 4.4 12.8 1.0 C20 A:1C1501 4.4 53.2 1.0 OG A:SER375 4.5 8.9 1.0 O A:SER375 4.5 10.0 1.0 CB A:ASN377 4.5 7.2 1.0 CA A:ASN377 4.6 8.4 1.0 CB A:SER375 4.6 9.0 1.0 C A:VAL255 4.8 4.5 1.0 CB A:VAL255 4.8 4.8 1.0 CG A:PHE382 4.9 8.5 1.0 CB A:PHE376 4.9 22.8 1.0

Chlorine binding site 2 out of 2 in the Crystal Structure of Clade C1086 Hiv-1 GP120 Core in Complex with Dmj- II-121


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of Clade C1086 Hiv-1 GP120 Core in Complex with Dmj- II-121 within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl501 b:53.2 occ:1.00 CL1 B:1C1501 0.0 53.2 1.0 C24 B:1C1501 1.7 53.2 1.0 C22 B:1C1501 2.7 53.2 1.0 C26 B:1C1501 2.7 53.2 1.0 F23 B:1C1501 2.9 53.2 1.0 C B:PHE376 3.5 13.7 1.0 CA B:PHE376 3.6 14.1 1.0 CD2 B:PHE382 3.8 13.2 1.0 N B:ASN377 3.8 21.3 1.0 N B:PHE376 3.9 14.2 1.0 O B:PHE376 3.9 13.5 1.0 C21 B:1C1501 3.9 53.2 1.0 CG1 B:VAL255 4.0 22.5 1.0 C27 B:1C1501 4.0 53.2 1.0 O B:VAL255 4.1 17.1 1.0 CE2 B:PHE382 4.1 12.8 1.0 CH2 B:TRP112 4.2 20.2 1.0 C20 B:1C1501 4.4 53.2 1.0 C B:SER375 4.4 14.5 1.0 CB B:ASN377 4.5 20.3 1.0 CA B:ASN377 4.6 20.9 1.0 CB B:VAL255 4.6 21.0 1.0 O B:SER375 4.7 14.7 1.0 C B:VAL255 4.7 23.1 1.0 OG B:SER375 4.7 13.4 1.0 CB B:SER375 4.8 13.8 1.0 CG B:PHE382 5.0 13.3 1.0 CZ3 B:TRP112 5.0 19.9 1.0

J.M.Lalonde, M.Le-Khac, D.M.Jones, J.R.Courter, J.Park, A.Schon, A.M.Princiotto, X.Wu, J.R.Mascola, E.Freire, J.Sodroski, N.Madani, W.A.Hendrickson, A.B.Smith. Structure-Based Design and Synthesis of An Hiv-1 Entry Inhibitor Exploiting X-Ray and Thermodynamic Characterization. Acs Med Chem Lett V. 4 338 2013.
PubMed: 23667716
DOI: 10.1021/ML300407Y