Bromine in PDB 4dvs: Crystal Structure of Clade A/E 93TH057 Hiv-1 GP120 Core in Complex with Nbd-557

The structure of Crystal Structure of Clade A/E 93TH057 Hiv-1 GP120 Core in Complex with Nbd-557, PDB code: 4dvs was solved by Y.D.Kwon, P.D.Kwong, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.07 / 2.10
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	64.644, 68.223, 94.021, 90.00, 91.48, 90.00
R / Rfree (%)	19.3 / 23.2

The binding sites of Bromine atom in the Crystal Structure of Clade A/E 93TH057 Hiv-1 GP120 Core in Complex with Nbd-557 (pdb code 4dvs). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 2 binding sites of Bromine where determined in the Crystal Structure of Clade A/E 93TH057 Hiv-1 GP120 Core in Complex with Nbd-557, PDB code: 4dvs:
Jump to Bromine binding site number: 1; 2;

Bromine binding site 1 out of 2 in the Crystal Structure of Clade A/E 93TH057 Hiv-1 GP120 Core in Complex with Nbd-557


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 1 of Crystal Structure of Clade A/E 93TH057 Hiv-1 GP120 Core in Complex with Nbd-557 within 5.0Å range: probe atom residue distance (Å) B Occ A:Br512 b:41.7 occ:1.00 BR A:0LY512 0.0 41.7 1.0 C2 A:0LY512 1.9 38.1 1.0 C3 A:0LY512 2.9 33.4 1.0 C7 A:0LY512 2.9 37.5 1.0 H1 A:0LY512 2.9 45.0 1.0 H25 A:0LY512 3.0 40.0 1.0 C A:PHE376 3.5 31.4 1.0 CA A:PHE376 3.5 30.4 1.0 N A:ASN377 3.7 35.8 1.0 O A:VAL255 3.7 30.2 1.0 CD2 A:PHE382 3.8 37.1 1.0 N A:PHE376 3.8 31.5 1.0 O A:PHE376 4.0 32.7 1.0 CE2 A:PHE382 4.0 32.6 1.0 CG1 A:VAL255 4.1 26.7 1.0 C6 A:0LY512 4.2 39.5 1.0 C4 A:0LY512 4.2 32.7 1.0 C A:SER375 4.2 34.7 1.0 CB A:ASN377 4.3 32.8 1.0 CH2 A:TRP112 4.3 24.6 1.0 C A:VAL255 4.4 33.9 1.0 O A:SER375 4.5 34.1 1.0 CA A:ASN377 4.5 34.6 1.0 CB A:VAL255 4.6 28.7 1.0 C5 A:0LY512 4.7 38.0 1.0 CB A:SER375 4.7 34.7 1.0 CB A:PHE376 5.0 33.7 1.0 CG A:PHE382 5.0 38.6 1.0 CA A:SER256 5.0 21.8 1.0 H2 A:0LY512 5.0 47.4 1.0 H24 A:0LY512 5.0 39.3 1.0 O A:HOH674 5.0 45.4 1.0

Bromine binding site 2 out of 2 in the Crystal Structure of Clade A/E 93TH057 Hiv-1 GP120 Core in Complex with Nbd-557


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 2 of Crystal Structure of Clade A/E 93TH057 Hiv-1 GP120 Core in Complex with Nbd-557 within 5.0Å range: probe atom residue distance (Å) B Occ B:Br512 b:53.5 occ:1.00 BR B:0LY512 0.0 53.5 1.0 C2 B:0LY512 1.9 51.2 1.0 C3 B:0LY512 2.9 50.0 1.0 C7 B:0LY512 2.9 50.8 1.0 H1 B:0LY512 3.0 60.9 1.0 H25 B:0LY512 3.0 60.0 1.0 CA B:PHE376 3.5 40.6 1.0 C B:PHE376 3.6 42.7 1.0 O B:VAL255 3.7 45.9 1.0 N B:ASN377 3.8 44.9 1.0 N B:PHE376 3.8 40.5 1.0 O B:PHE376 4.0 42.3 1.0 CD1 B:PHE382 4.1 42.6 1.0 C4 B:0LY512 4.2 54.8 1.0 C6 B:0LY512 4.2 59.4 1.0 C B:SER375 4.2 42.2 1.0 CG1 B:VAL255 4.2 34.9 1.0 CH2 B:TRP112 4.3 32.2 1.0 CE1 B:PHE382 4.4 38.9 1.0 O B:SER375 4.4 40.1 1.0 C B:VAL255 4.4 41.7 1.0 CB B:ASN377 4.5 32.9 1.0 CA B:ASN377 4.6 38.3 1.0 CB B:VAL255 4.6 33.4 1.0 C5 B:0LY512 4.7 62.7 1.0 OG B:SER375 4.7 49.0 1.0 CB B:SER375 4.7 50.7 1.0 O B:HOH623 4.9 38.8 1.0 CB B:PHE376 4.9 39.0 1.0 CZ3 B:TRP112 4.9 36.6 1.0 H24 B:0LY512 5.0 65.8 1.0 CA B:SER256 5.0 39.9 1.0 H2 B:0LY512 5.0 71.2 1.0

Y.D.Kwon, J.M.Lalonde, Y.Yang, M.A.Elban, A.Sugawara, J.R.Courter, D.M.Jones, A.B.Smith, A.K.Debnath, P.D.Kwong. Crystal Structures of Hiv-1 GP120 Envelope Glycoprotein in Complex with Nbd Analogues That Target the CD4-Binding Site. Plos One V. 9 85940 2014.
ISSN: ESSN 1932-6203
PubMed: 24489681
DOI: 10.1371/JOURNAL.PONE.0085940