Chlorine in PDB 4dko: Crystal Structure of Clade A/E 93TH057 Hiv-1 GP120 Core in Complex with Ts-II-224

The structure of Crystal Structure of Clade A/E 93TH057 Hiv-1 GP120 Core in Complex with Ts-II-224, PDB code: 4dko was solved by Y.D.Kwon, J.M.Lalonde, D.M.Jones, A.W.Sun, J.R.Courter, T.Soeta, T.Kobayashi, A.M.Princiotto, X.Wu, J.Mascola, A.Schon, E.Freire, J.Sodroski, N.Madani, A.B.Smith Iii, P.D.Kwong, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.94 / 1.98
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	64.723, 68.902, 94.515, 90.00, 91.23, 90.00
R / Rfree (%)	20.3 / 23.9

The structure of Crystal Structure of Clade A/E 93TH057 Hiv-1 GP120 Core in Complex with Ts-II-224 also contains other interesting chemical elements:

Fluorine

(F)

2 atoms

The binding sites of Chlorine atom in the Crystal Structure of Clade A/E 93TH057 Hiv-1 GP120 Core in Complex with Ts-II-224 (pdb code 4dko). 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 A/E 93TH057 Hiv-1 GP120 Core in Complex with Ts-II-224, PDB code: 4dko:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in the Crystal Structure of Clade A/E 93TH057 Hiv-1 GP120 Core in Complex with Ts-II-224


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 A/E 93TH057 Hiv-1 GP120 Core in Complex with Ts-II-224 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl513 b:64.6 occ:1.00 CL A:0LM513 0.0 64.6 1.0 C02 A:0LM513 1.7 50.2 1.0 C03 A:0LM513 2.7 53.0 1.0 C01 A:0LM513 2.7 47.8 1.0 F25 A:0LM513 2.9 46.7 1.0 CD2 A:PHE382 3.7 22.7 1.0 C A:PHE376 3.8 21.1 1.0 CA A:PHE376 3.9 16.8 1.0 CE2 A:PHE382 3.9 27.4 1.0 O A:VAL255 3.9 22.6 1.0 C04 A:0LM513 4.0 53.3 1.0 C06 A:0LM513 4.0 62.2 1.0 CG1 A:VAL255 4.0 18.0 1.0 N A:ASN377 4.1 20.5 1.0 N A:PHE376 4.1 15.9 1.0 O A:PHE376 4.1 23.1 1.0 OG A:SER375 4.4 30.2 1.0 C A:SER375 4.5 24.1 1.0 CB A:ASN377 4.5 17.4 1.0 CH2 A:TRP112 4.5 21.5 1.0 C05 A:0LM513 4.5 64.5 1.0 C A:VAL255 4.6 24.3 1.0 O A:SER375 4.6 22.1 1.0 CB A:VAL255 4.7 15.5 1.0 CA A:ASN377 4.7 22.6 1.0 CB A:SER375 4.8 19.2 1.0 CG A:PHE382 4.9 20.7 1.0

Chlorine binding site 2 out of 2 in the Crystal Structure of Clade A/E 93TH057 Hiv-1 GP120 Core in Complex with Ts-II-224


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 A/E 93TH057 Hiv-1 GP120 Core in Complex with Ts-II-224 within 5.0Å range: probe atom residue distance (Å) B Occ C:Cl513 b:62.6 occ:1.00 CL C:0LM513 0.0 62.6 1.0 C02 C:0LM513 1.7 49.7 1.0 C03 C:0LM513 2.7 51.9 1.0 C01 C:0LM513 2.7 55.8 1.0 F25 C:0LM513 2.9 59.5 1.0 O C:VAL255 3.6 34.0 1.0 C C:PHE376 3.7 31.3 1.0 CA C:PHE376 3.7 35.9 1.0 O C:HOH702 3.8 42.0 1.0 N C:ASN377 3.9 28.4 1.0 C06 C:0LM513 4.0 72.5 1.0 C04 C:0LM513 4.0 54.3 1.0 N C:PHE376 4.1 26.6 1.0 CD2 C:PHE382 4.1 30.7 1.0 CG1 C:VAL255 4.1 20.4 1.0 O C:PHE376 4.1 28.6 1.0 CH2 C:TRP112 4.2 24.2 1.0 CE2 C:PHE382 4.3 39.8 1.0 C C:VAL255 4.4 31.8 1.0 C C:SER375 4.4 30.9 1.0 CB C:ASN377 4.4 19.8 1.0 O C:SER375 4.5 26.6 1.0 CB C:VAL255 4.5 21.0 1.0 C05 C:0LM513 4.5 72.6 1.0 CA C:ASN377 4.7 18.2 1.0 OG C:SER375 4.7 37.1 1.0 CZ3 C:TRP112 4.8 25.3 1.0 CB C:SER375 5.0 33.7 1.0

J.M.Lalonde, Y.D.Kwon, D.M.Jones, A.W.Sun, J.R.Courter, T.Soeta, T.Kobayashi, A.M.Princiotto, X.Wu, A.Schon, E.Freire, P.D.Kwong, J.R.Mascola, J.Sodroski, N.Madani, A.B.Smith. Structure-Based Design, Synthesis, and Characterization of Dual Hotspot Small-Molecule Hiv-1 Entry Inhibitors. J.Med.Chem. V. 55 4382 2012.
ISSN: ISSN 0022-2623
PubMed: 22497421
DOI: 10.1021/JM300265J