Chlorine in PDB 8dcq: Crystal Structure of Hiv-1 Lm/Ht Clade A/E CRF01 GP120 Core in Complex with Yir-821

The structure of Crystal Structure of Hiv-1 Lm/Ht Clade A/E CRF01 GP120 Core in Complex with Yir-821, PDB code: 8dcq was solved by W.D.Tolbert, M.Pazgier, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.69 / 3.20
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	65.66, 67.28, 87.38, 90, 90, 90
R / Rfree (%)	21.8 / 27.3

The binding sites of Chlorine atom in the Crystal Structure of Hiv-1 Lm/Ht Clade A/E CRF01 GP120 Core in Complex with Yir-821 (pdb code 8dcq). 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 Hiv-1 Lm/Ht Clade A/E CRF01 GP120 Core in Complex with Yir-821, PDB code: 8dcq:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in the Crystal Structure of Hiv-1 Lm/Ht Clade A/E CRF01 GP120 Core in Complex with Yir-821


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 Hiv-1 Lm/Ht Clade A/E CRF01 GP120 Core in Complex with Yir-821 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl511 b:46.7 occ:0.58 CL20 A:R5K511 0.0 46.7 0.6 CL20 A:R5K511 0.2 46.1 0.4 C19 A:R5K511 1.8 32.8 0.4 C19 A:R5K511 1.8 31.6 0.6 C21 A:R5K511 2.7 31.4 0.4 C21 A:R5K511 2.7 30.8 0.6 C18 A:R5K511 2.8 33.9 0.6 C18 A:R5K511 2.9 34.3 0.4 C A:PHE376 3.0 26.1 1.0 O A:VAL255 3.0 31.3 1.0 N A:ASN377 3.1 34.0 1.0 CB A:ASN377 3.3 27.4 1.0 O A:PHE376 3.4 25.6 1.0 CA A:PHE376 3.5 19.7 1.0 CA A:ASN377 3.6 24.9 1.0 CD2 A:PHE382 3.9 34.7 1.0 C17 A:R5K511 4.1 43.0 0.6 N A:PHE376 4.1 23.1 1.0 C17 A:R5K511 4.1 35.9 0.4 CE2 A:PHE382 4.1 38.6 1.0 C22 A:R5K511 4.1 30.2 0.4 C22 A:R5K511 4.1 29.9 0.6 CH2 A:TRP112 4.2 31.0 1.0 C A:VAL255 4.2 32.2 1.0 ND2 A:ASN377 4.3 28.1 1.0 CG1 A:VAL255 4.3 35.5 1.0 O A:THR375 4.3 33.9 1.0 CG A:ASN377 4.3 30.3 1.0 C A:THR375 4.4 22.9 1.0 CG2 A:THR375 4.5 30.0 1.0 C16 A:R5K511 4.6 30.1 0.6 C16 A:R5K511 4.6 30.4 0.4 CZ3 A:TRP112 4.7 28.2 1.0 CB A:VAL255 4.8 28.2 1.0 CB A:PHE376 4.8 32.8 1.0

Chlorine binding site 2 out of 2 in the Crystal Structure of Hiv-1 Lm/Ht Clade A/E CRF01 GP120 Core in Complex with Yir-821


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 Hiv-1 Lm/Ht Clade A/E CRF01 GP120 Core in Complex with Yir-821 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl511 b:46.1 occ:0.42 CL20 A:R5K511 0.0 46.1 0.4 CL20 A:R5K511 0.2 46.7 0.6 C19 A:R5K511 1.8 32.8 0.4 C19 A:R5K511 1.8 31.6 0.6 C21 A:R5K511 2.7 31.4 0.4 C21 A:R5K511 2.7 30.8 0.6 C18 A:R5K511 2.9 33.9 0.6 C18 A:R5K511 2.9 34.3 0.4 O A:VAL255 2.9 31.3 1.0 N A:ASN377 3.2 34.0 1.0 C A:PHE376 3.2 26.1 1.0 CB A:ASN377 3.3 27.4 1.0 O A:PHE376 3.6 25.6 1.0 CA A:PHE376 3.6 19.7 1.0 CA A:ASN377 3.7 24.9 1.0 CH2 A:TRP112 4.0 31.0 1.0 CD2 A:PHE382 4.0 34.7 1.0 C17 A:R5K511 4.1 35.9 0.4 C17 A:R5K511 4.1 43.0 0.6 CE2 A:PHE382 4.1 38.6 1.0 C A:VAL255 4.1 32.2 1.0 C22 A:R5K511 4.1 30.2 0.4 C22 A:R5K511 4.2 29.9 0.6 CG1 A:VAL255 4.2 35.5 1.0 N A:PHE376 4.2 23.1 1.0 ND2 A:ASN377 4.3 28.1 1.0 CG A:ASN377 4.3 30.3 1.0 O A:THR375 4.4 33.9 1.0 CZ3 A:TRP112 4.5 28.2 1.0 C A:THR375 4.5 22.9 1.0 CB A:VAL255 4.6 28.2 1.0 C16 A:R5K511 4.6 30.4 0.4 C16 A:R5K511 4.6 30.1 0.6 CG2 A:THR375 4.7 30.0 1.0 CB A:PHE376 4.9 32.8 1.0 CA A:VAL255 4.9 32.7 1.0 CZ2 A:TRP112 5.0 31.4 1.0

K.Matsumoto, T.Kuwata, W.D.Tolbert, J.Richard, S.Ding, J.Prevost, S.Takahama, G.P.Judicate, T.Ueno, H.Nakata, T.Kobayakawa, K.Tsuji, H.Tamamura, A.B.Smith 3Rd, M.Pazgier, A.Finzi, S.Matsushita. Characterization of A Novel CD4 Mimetic Compound Yir-821 Against Hiv-1 Clinical Isolates. J.Virol. 63822 2022.
ISSN: ESSN 1098-5514
PubMed: 36511698
DOI: 10.1128/JVI.01638-22