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

Protein crystallography data

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

Bromine Binding Sites:

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 4dvs

Go back to Bromine Binding Sites List in 4dvs
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 4dvs

Go back to Bromine Binding Sites List in 4dvs
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

Reference:

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
Page generated: Sat Dec 12 02:19:04 2020

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