Chlorine in PDB 4dkv: Crystal Structure of Clade A/E 93TH057 Hiv-1 GP120 Core in Complex with Nbd-10007

The structure of Crystal Structure of Clade A/E 93TH057 Hiv-1 GP120 Core in Complex with Nbd-10007, PDB code: 4dkv was solved by Y.D.Kwon, A.K.Debnath, P.D.Kwong, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	27.60 / 2.18
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	64.333, 68.773, 93.848, 90.00, 91.74, 90.00
R / Rfree (%)	20 / 23.5

The binding sites of Chlorine atom in the Crystal Structure of Clade A/E 93TH057 Hiv-1 GP120 Core in Complex with Nbd-10007 (pdb code 4dkv). 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 Nbd-10007, PDB code: 4dkv:
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 Nbd-10007


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 Nbd-10007 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl513 b:62.8 occ:1.00 CL1 A:0KW513 0.0 62.8 1.0 C01 A:0KW513 1.7 59.8 1.0 C06 A:0KW513 2.6 51.6 1.0 C02 A:0KW513 2.7 61.4 1.0 H4 A:0KW513 2.7 61.9 1.0 H1 A:0KW513 2.8 73.7 1.0 CA A:PHE376 3.5 25.0 1.0 C A:PHE376 3.6 32.1 1.0 N A:PHE376 3.7 33.4 1.0 O A:VAL255 3.8 33.8 1.0 C05 A:0KW513 3.9 51.9 1.0 C03 A:0KW513 3.9 60.6 1.0 CD2 A:PHE382 3.9 43.2 1.0 N A:ASN377 3.9 37.5 1.0 O A:PHE376 4.0 30.7 1.0 C A:SER375 4.0 33.4 1.0 CG1 A:VAL255 4.0 28.2 1.0 O A:SER375 4.2 34.0 1.0 CE2 A:PHE382 4.2 35.4 1.0 OG A:SER375 4.3 49.4 1.0 C04 A:0KW513 4.4 60.3 1.0 C A:VAL255 4.5 36.6 1.0 CB A:SER375 4.5 33.4 1.0 H3 A:0KW513 4.6 62.2 1.0 CB A:ASN377 4.6 41.9 1.0 H2 A:0KW513 4.7 72.7 1.0 CA A:ASN377 4.7 39.0 1.0 CB A:VAL255 4.8 27.9 1.0 CA A:SER256 4.8 26.0 1.0 CA A:SER375 4.9 34.0 1.0 CB A:PHE376 4.9 27.8 1.0 CH2 A:TRP112 4.9 42.6 1.0 N A:SER256 4.9 30.4 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 Nbd-10007


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 Nbd-10007 within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl511 b:91.0 occ:1.00 CL1 B:0KW511 0.0 91.0 1.0 C01 B:0KW511 1.7 0.6 1.0 C06 B:0KW511 2.6 0.3 1.0 C02 B:0KW511 2.7 97.3 1.0 H4 B:0KW511 2.7 0.6 1.0 H1 B:0KW511 2.8 0.8 1.0 CA B:PHE376 3.7 46.5 1.0 C B:PHE376 3.7 45.3 1.0 C05 B:0KW511 3.9 0.6 1.0 N B:PHE376 3.9 43.5 1.0 C03 B:0KW511 3.9 0.8 1.0 O B:VAL255 4.0 40.0 1.0 CD2 B:PHE382 4.0 53.5 1.0 N B:ASN377 4.0 40.1 1.0 O B:PHE376 4.1 41.1 1.0 C B:SER375 4.2 42.9 1.0 OG B:SER375 4.3 53.6 1.0 CE2 B:PHE382 4.4 48.5 1.0 C04 B:0KW511 4.4 0.1 1.0 CH2 B:TRP112 4.4 35.0 1.0 CG1 B:VAL255 4.4 37.4 1.0 O B:SER375 4.4 38.7 1.0 CB B:SER375 4.5 50.6 1.0 H3 B:0KW511 4.6 0.7 1.0 CB B:ASN377 4.6 34.5 1.0 H2 B:0KW511 4.7 0.4 1.0 C B:VAL255 4.7 43.6 1.0 CA B:ASN377 4.8 39.6 1.0 CB B:VAL255 4.9 42.6 1.0 CZ3 B:TRP112 5.0 40.8 1.0 CA B:SER375 5.0 41.9 1.0

F.Curreli, Y.D.Kwon, H.Zhang, Y.Yang, D.Scacalossi, P.D.Kwong, A.K.Debnath. Binding Mode Characterization of Nbd Series CD4-Mimetic Hiv-1 Entry Inhibitors By X-Ray Structure and Resistance Study. Antimicrob. Agents V. 58 5478 2014CHEMOTHER..
ISSN: ESSN 1098-6596
PubMed: 25001301
DOI: 10.1128/AAC.03339-14